Mercurial > repos > iuc > lineagespot
annotate test-data/SampleC_freebayes_ann.vcf @ 0:5e8505f27681 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
| author | iuc |
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| date | Tue, 08 Aug 2023 15:11:47 +0000 |
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| rev | line source |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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1 ##fileformat=VCFv4.2 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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2 ##fileDate=20210722 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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3 ##source=freeBayes v1.3.2-dirty |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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4 ##reference=NC_045512.fasta |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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5 ##contig=<ID=NC_045512.2,length=29903> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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6 ##phasing=none |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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7 ##commandline="freebayes -f NC_045512.fasta -F 0.01 -C 1 --pooled-continuous L23MM_S3_sorted_uniq.bam" |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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8 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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10 ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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11 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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12 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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13 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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14 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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15 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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16 ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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17 ##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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18 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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19 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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20 ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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21 ##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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22 ##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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23 ##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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24 ##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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25 ##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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26 ##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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27 ##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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28 ##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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29 ##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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30 ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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31 ##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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32 ##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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33 ##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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34 ##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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35 ##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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36 ##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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37 ##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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38 ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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39 ##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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40 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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41 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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42 ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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43 ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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44 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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45 ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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46 ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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47 ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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48 ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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49 ##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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50 ##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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51 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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52 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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53 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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54 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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55 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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56 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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57 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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58 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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59 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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60 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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61 ##SnpEffVersion="5.0 (build 2020-08-09 21:23), by Pablo Cingolani" |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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62 ##SnpEffCmd="SnpEff NC_045512.2 L23MM_S3_freebayes.vcf " |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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63 ##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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64 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
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changeset
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65 NC_045512.2 32 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=564;DPB=564;DPRA=0;EPP=3.0103;EPPR=12.7391;GTI=0;LEN=1;MEANALT=1;MQM=39;MQMR=15.4892;NS=1;NUMALT=1;ODDS=729.572;PAIRED=1;PAIREDR=0.362007;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=18462;RO=558;RPL=0;RPP=16.0391;RPPR=1214.69;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=304;SRP=12.7391;SRR=254;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-234C>A|||||234| GT:DP:AD:RO:QR:AO:QA:GL 0/0:564:558,6:558:18462:6:204:0,-155.891,-622.102 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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66 NC_045512.2 64 . CTC TTT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=99;CIGAR=1X1M1X;DP=1151;DPB=1156;DPRA=0;EPP=4.08507;EPPR=7.37801;GTI=0;LEN=3;MEANALT=1;MQM=41.4444;MQMR=15.4496;NS=1;NUMALT=1;ODDS=740.69;PAIRED=1;PAIREDR=0.415399;PAO=15;PQA=262;PQR=0;PRO=0;QA=3503;QR=37047;RO=1052;RPL=6;RPP=169.029;RPPR=1164.09;RPR=93;RUN=1;SAF=53;SAP=4.08507;SAR=46;SRF=566;SRP=16.2208;SRR=486;TYPE=complex;ANN=TTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-202_-200delCTCinsTTT|||||202| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1151:1052,99:1052:37047:99:3503:0,-95.224,-953.379 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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67 NC_045512.2 92 . C T 3142.56 . AB=0.43932;ABP=16.1867;AC=1;AF=0.5;AN=2;AO=181;CIGAR=1X;DP=412;DPB=412;DPRA=0;EPP=3.11827;EPPR=3.47092;GTI=0;LEN=1;MEANALT=1;MQM=43.0718;MQMR=51.9048;NS=1;NUMALT=1;ODDS=723.602;PAIRED=0.933702;PAIREDR=0.982684;PAO=0;PQA=0;PQR=0;PRO=0;QA=6095;QR=8033;RO=231;RPL=38;RPP=135.278;RPPR=91.4578;RPR=143;RUN=1;SAF=92;SAP=3.11827;SAR=89;SRF=120;SRP=3.77173;SRR=111;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-174C>T|||||174| GT:DP:AD:RO:QR:AO:QA:GL 0/1:412:231,181:231:8033:181:6095:-336.686,0,-565.664 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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68 NC_045512.2 100 . C T 3907.17 . AB=0.441501;ABP=16.4753;AC=1;AF=0.5;AN=2;AO=200;CIGAR=1X;DP=453;DPB=453;DPRA=0;EPP=3.05373;EPPR=3.14817;GTI=0;LEN=1;MEANALT=2;MQM=45.335;MQMR=52.9603;NS=1;NUMALT=1;ODDS=899.659;PAIRED=0.935;PAIREDR=0.984127;PAO=0;PQA=0;PQR=0;PRO=0;QA=6978;QR=8772;RO=252;RPL=49;RPP=115.97;RPPR=69.74;RPR=151;RUN=1;SAF=102;SAP=3.18402;SAR=98;SRF=130;SRP=3.56179;SRR=122;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-166C>T|||||166| GT:DP:AD:RO:QR:AO:QA:GL 0/1:453:252,200:252:8772:200:6978:-410.991,0,-630.697 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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69 NC_045512.2 124 . G A 1.09393E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=8;CIGAR=1X;DP=585;DPB=585;DPRA=0;EPP=4.09604;EPPR=6.62691;GTI=0;LEN=1;MEANALT=1;MQM=39.5;MQMR=50.1023;NS=1;NUMALT=1;ODDS=735.632;PAIRED=1;PAIREDR=0.968804;PAO=0;PQA=0;PQR=0;PRO=0;QA=266;QR=19810;RO=577;RPL=5;RPP=4.09604;RPPR=24.1793;RPR=3;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=296;SRP=3.85706;SRR=281;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-142G>A|||||142| GT:DP:AD:RO:QR:AO:QA:GL 0/0:585:577,8:577:19810:8:266:0,-157.006,-1656.16 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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70 NC_045512.2 164 . C T 6382.88 . AB=0.480127;ABP=5.16796;AC=1;AF=0.5;AN=2;AO=302;CIGAR=1X;DP=629;DPB=629;DPRA=0;EPP=3.0103;EPPR=3.96948;GTI=0;LEN=1;MEANALT=2;MQM=45.1656;MQMR=52.0337;NS=1;NUMALT=1;ODDS=1469.71;PAIRED=0.960265;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10610;QR=11356;RO=326;RPL=162;RPP=6.49041;RPPR=5.67468;RPR=140;RUN=1;SAF=153;SAP=3.12534;SAR=149;SRF=166;SRP=3.25009;SRR=160;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-102C>T|||||102| GT:DP:AD:RO:QR:AO:QA:GL 0/1:629:326,302:326:11356:302:10610:-646.358,0,-794.471 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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71 NC_045512.2 210 . G T 14518.1 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=536;CIGAR=1X;DP=537;DPB=537;DPRA=0;EPP=3.0265;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=43.8228;MQMR=52;NS=1;NUMALT=1;ODDS=741.615;PAIRED=0.996269;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18923;QR=14;RO=1;RPL=318;RPP=43.5228;RPPR=5.18177;RPR=218;RUN=1;SAF=265;SAP=3.15615;SAR=271;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-56G>T|||||56| GT:DP:AD:RO:QR:AO:QA:GL 1/1:537:1,536:1:14:536:18923:-1459.38,-160.253,0 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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72 NC_045512.2 241 . C T 12516.3 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=461;CIGAR=1X;DP=461;DPB=461;DPRA=0;EPP=3.12806;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=43.4707;MQMR=0;NS=1;NUMALT=1;ODDS=643.687;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=16150;QR=0;RO=0;RPL=224;RPP=3.80635;RPPR=0;RPR=237;RUN=1;SAF=232;SAP=3.05269;SAR=229;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-25C>T|||||25| GT:DP:AD:RO:QR:AO:QA:GL 1/1:461:0,461:0:0:461:16150:-1256.02,-138.775,0 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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73 NC_045512.2 280 . CC TT 3525.62 . AB=0.387879;ABP=57.0602;AC=1;AF=0.5;AN=2;AO=192;CIGAR=2X;DP=495;DPB=497;DPRA=0;EPP=3.0103;EPPR=3.03906;GTI=0;LEN=2;MEANALT=2;MQM=42.0052;MQMR=49.4834;NS=1;NUMALT=1;ODDS=811.803;PAIRED=1;PAIREDR=0.993377;PAO=4;PQA=140;PQR=0;PRO=0;QA=6736;QR=10479;RO=302;RPL=98;RPP=3.19126;RPPR=3.72933;RPR=94;RUN=1;SAF=94;SAP=3.19126;SAR=98;SRF=148;SRP=3.26915;SRR=154;TYPE=mnp;ANN=TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.15_16delCCinsTT|p.Pro6Ser|15/21291|15/21291|5/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:495:302,192:302:10479:192:6736:-365.116,0,-736.846 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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74 NC_045512.2 335 . CGC TGT 1775.99 . AB=0.217114;ABP=547.262;AC=1;AF=0.5;AN=2;AO=170;CIGAR=1X1M1X;DP=783;DPB=785.333;DPRA=0;EPP=3.21467;EPPR=8.43363;GTI=0;LEN=3;MEANALT=4;MQM=46.1059;MQMR=51.1593;NS=1;NUMALT=1;ODDS=408.938;PAIRED=0.976471;PAIREDR=0.985222;PAO=7;PQA=223;PQR=0;PRO=0;QA=5931;QR=21070;RO=609;RPL=92;RPP=5.51388;RPPR=296.708;RPR=78;RUN=1;SAF=83;SAP=3.21467;SAR=87;SRF=319;SRP=6.009;SRR=290;TYPE=complex;ANN=TGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.70_72delCGCinsTGT|p.Arg24Cys|70/21291|70/21291|24/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:783:609,170:609:21070:170:5931:-241.995,0,-1561.83 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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75 NC_045512.2 346 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=10;CIGAR=1X;DP=914;DPB=914;DPRA=0;EPP=3.0103;EPPR=5.17216;GTI=0;LEN=1;MEANALT=1;MQM=47.6;MQMR=47.8728;NS=1;NUMALT=1;ODDS=1156.65;PAIRED=1;PAIREDR=0.915929;PAO=0;PQA=0;PQR=0;PRO=0;QA=347;QR=31647;RO=904;RPL=6;RPP=3.87889;RPPR=520.167;RPR=4;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=461;SRP=3.78857;SRR=443;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.81C>T|p.Leu27Leu|81/21291|81/21291|27/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:914:904,10:904:31647:10:347:0,-246.309,-2560.77 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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76 NC_045512.2 396 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=19;CIGAR=1X;DP=1364;DPB=1364;DPRA=0;EPP=3.12459;EPPR=4.1025;GTI=0;LEN=1;MEANALT=2;MQM=42.2632;MQMR=49.3222;NS=1;NUMALT=1;ODDS=1698.24;PAIRED=0.894737;PAIREDR=0.959821;PAO=0;PQA=0;PQR=0;PRO=0;QA=666;QR=46617;RO=1344;RPL=2;RPP=28.7251;RPPR=62.5707;RPR=17;RUN=1;SAF=10;SAP=3.12459;SAR=9;SRF=677;SRP=3.17187;SRR=667;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.131A>G|p.Gln44Arg|131/21291|131/21291|44/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1364:1344,19:1344:46617:19:666:0,-362.653,-3817.07 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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77 NC_045512.2 613 . G A 29424.0 . AB=0.828234;ABP=1348.68;AC=1;AF=0.5;AN=2;AO=1191;CIGAR=1X;DP=1438;DPB=1438;DPRA=0;EPP=6.07516;EPPR=4.98836;GTI=0;LEN=1;MEANALT=1;MQM=50.6507;MQMR=52.753;NS=1;NUMALT=1;ODDS=354.736;PAIRED=0.991604;PAIREDR=0.991903;PAO=0;PQA=0;PQR=0;PRO=0;QA=41710;QR=8642;RO=247;RPL=553;RPP=16.1832;RPPR=4.07406;RPR=638;RUN=1;SAF=578;SAP=5.24376;SAR=613;SRF=120;SRP=3.44108;SRR=127;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.348G>A|p.Val116Val|348/21291|348/21291|116/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1438:247,1191:247:8642:1191:41710:-3099.14,0,-308.276 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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78 NC_045512.2 682 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=79;CIGAR=1X;DP=1852;DPB=1852;DPRA=0;EPP=3.03779;EPPR=17.0482;GTI=0;LEN=1;MEANALT=3;MQM=38.1519;MQMR=50.3139;NS=1;NUMALT=1;ODDS=1840.13;PAIRED=0.949367;PAIREDR=0.967815;PAO=0;PQA=0;PQR=0;PRO=0;QA=2754;QR=59839;RO=1771;RPL=4;RPP=141.572;RPPR=68.4377;RPR=75;RUN=1;SAF=39;SAP=3.03779;SAR=40;SRF=896;SRP=3.55102;SRR=875;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.417T>C|p.Asp139Asp|417/21291|417/21291|139/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1852:1771,79:1771:59839:79:2754:0,-360.966,-4800.3 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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79 NC_045512.2 823 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=22;CIGAR=1X;DP=1547;DPB=1547;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=41.9545;MQMR=52.4665;NS=1;NUMALT=1;ODDS=1927.38;PAIRED=0.909091;PAIREDR=0.985564;PAO=0;PQA=0;PQR=0;PRO=0;QA=775;QR=52847;RO=1524;RPL=0;RPP=50.7827;RPPR=3.28957;RPR=22;RUN=1;SAF=11;SAP=3.0103;SAR=11;SRF=753;SRP=3.47195;SRR=771;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.558C>T|p.Val186Val|558/21291|558/21291|186/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1547:1524,22:1524:52847:22:775:0,-410.536,-4495.54 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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80 NC_045512.2 895 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=89;CIGAR=1X;DP=1742;DPB=1742;DPRA=0;EPP=3.0347;EPPR=3.70522;GTI=0;LEN=1;MEANALT=1;MQM=47.8876;MQMR=51.1881;NS=1;NUMALT=1;ODDS=1489.29;PAIRED=0.977528;PAIREDR=0.989716;PAO=0;PQA=0;PQR=0;PRO=0;QA=3176;QR=58126;RO=1653;RPL=47;RPP=3.62026;RPPR=3.11671;RPR=42;RUN=1;SAF=43;SAP=3.22989;SAR=46;SRF=800;SRP=6.70036;SRR=853;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.630A>T|p.Lys210Asn|630/21291|630/21291|210/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1742:1653,89:1653:58126:89:3176:0,-268.331,-4688.37 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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81 NC_045512.2 913 . C T 353.303 . AB=0.150661;ABP=1846.36;AC=1;AF=0.5;AN=2;AO=262;CIGAR=1X;DP=1739;DPB=1739;DPRA=0;EPP=3.04345;EPPR=3.93292;GTI=0;LEN=1;MEANALT=2;MQM=49.5611;MQMR=51.2447;NS=1;NUMALT=1;ODDS=81.351;PAIRED=1;PAIREDR=0.991842;PAO=0;PQA=0;PQR=0;PRO=0;QA=9234;QR=50659;RO=1471;RPL=143;RPP=7.78422;RPPR=8.5032;RPR=119;RUN=1;SAF=129;SAP=3.14291;SAR=133;SRF=719;SRP=4.61787;SRR=752;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.648C>T|p.Ser216Ser|648/21291|648/21291|216/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1739:1471,262:1471:50659:262:9234:-245.319,0,-3801.26 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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82 NC_045512.2 1048 . G T 55959.4 . AB=0.711473;ABP=1265.83;AC=1;AF=0.5;AN=2;AO=2313;CIGAR=1X;DP=3251;DPB=3251;DPRA=0;EPP=5.26439;EPPR=3.46404;GTI=0;LEN=1;MEANALT=1;MQM=49.3562;MQMR=51.451;NS=1;NUMALT=1;ODDS=3880.56;PAIRED=0.996541;PAIREDR=0.984009;PAO=0;PQA=0;PQR=0;PRO=0;QA=81232;QR=33087;RO=938;RPL=1050;RPP=45.6033;RPPR=91.9434;RPR=1263;RUN=1;SAF=1190;SAP=7.22463;SAR=1123;SRF=477;SRP=3.60294;SRR=461;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.783G>T|p.Lys261Asn|783/21291|783/21291|261/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3251:938,2313:938:33087:2313:81232:-5740.35,0,-1833.27 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
83 NC_045512.2 1259 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=194;CIGAR=1X;DP=2654;DPB=2654;DPRA=0;EPP=3.05507;EPPR=3.26551;GTI=0;LEN=1;MEANALT=2;MQM=51.634;MQMR=51.1745;NS=1;NUMALT=1;ODDS=1663.73;PAIRED=1;PAIREDR=0.9939;PAO=0;PQA=0;PQR=0;PRO=0;QA=6829;QR=85866;RO=2459;RPL=120;RPP=26.695;RPPR=136.638;RPR=74;RUN=1;SAF=94;SAP=3.41325;SAR=100;SRF=1211;SRP=4.21922;SRR=1248;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.994C>T|p.Gln332*|994/21291|994/21291|332/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2654:2459,194:2459:85866:194:6829:0,-215.703,-6715.49 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
84 NC_045512.2 1441 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=18;CIGAR=1X;DP=1222;DPB=1222;DPRA=0;EPP=3.0103;EPPR=3.02655;GTI=0;LEN=1;MEANALT=2;MQM=53.5;MQMR=52.1155;NS=1;NUMALT=1;ODDS=1481.16;PAIRED=1;PAIREDR=0.978387;PAO=0;PQA=0;PQR=0;PRO=0;QA=644;QR=41870;RO=1203;RPL=12;RPP=7.35324;RPPR=9.29367;RPR=6;RUN=1;SAF=9;SAP=3.0103;SAR=9;SRF=601;SRP=3.01211;SRR=602;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1176C>T|p.Gly392Gly|1176/21291|1176/21291|392/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1222:1203,18:1203:41870:18:644:0,-310.787,-3538.8 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
85 NC_045512.2 1469 . C T 1.64659E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=109;CIGAR=1X;DP=1145;DPB=1145;DPRA=0;EPP=3.03022;EPPR=3.04384;GTI=0;LEN=1;MEANALT=1;MQM=44.6606;MQMR=52.5444;NS=1;NUMALT=1;ODDS=585.618;PAIRED=1;PAIREDR=0.985521;PAO=0;PQA=0;PQR=0;PRO=0;QA=3677;QR=36019;RO=1036;RPL=64;RPP=10.2021;RPPR=3.31213;RPR=45;RUN=1;SAF=54;SAP=3.03022;SAR=55;SRF=510;SRP=3.54688;SRR=526;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1204C>T|p.Arg402Cys|1204/21291|1204/21291|402/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1145:1036,109:1036:36019:109:3677:0,-58.5213,-2826.07 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
86 NC_045512.2 1485 . GAG GG 1184.03 . AB=0.19145;ABP=892.781;AC=1;AF=0.5;AN=2;AO=206;CIGAR=1M1D1M;DP=1076;DPB=1009.33;DPRA=0;EPP=3.38978;EPPR=3.07291;GTI=0;LEN=1;MEANALT=4;MQM=47.3544;MQMR=51.9769;NS=1;NUMALT=1;ODDS=272.632;PAIRED=0.985437;PAIREDR=0.988466;PAO=3;PQA=102;PQR=102;PRO=3;QA=6730;QR=30243;RO=867;RPL=112;RPP=6.42563;RPPR=3.91445;RPR=94;RUN=1;SAF=100;SAP=3.38978;SAR=106;SRF=421;SRP=4.57566;SRR=446;TYPE=del;ANN=GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1221delA|p.Gly408fs|1221/21291|1221/21291|407/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1076:867,206:867:30243:206:6730:-221.186,0,-2270.15 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
87 NC_045512.2 1644 . ACAT CCAA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=1X2M1X;DP=3724;DPB=3727;DPRA=0;EPP=3.0608;EPPR=4.80063;GTI=0;LEN=4;MEANALT=7;MQM=30.7209;MQMR=51.8566;NS=1;NUMALT=1;ODDS=4720.41;PAIRED=0.953488;PAIREDR=0.990461;PAO=12;PQA=304;PQR=0;PRO=0;QA=1484;QR=129421;RO=3669;RPL=20;RPP=3.46479;RPPR=579.566;RPR=23;RUN=1;SAF=23;SAP=3.46479;SAR=20;SRF=1875;SRP=6.89338;SRR=1794;TYPE=complex;ANN=CCAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1379_1382delACATinsCCAA|p.AsnIle460ThrAsn|1379/21291|1379/21291|460/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3724:3669,43:3669:129421:43:1484:0,-1028.38,-11045.6 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
88 NC_045512.2 1656 . TTGG ATGT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=61;CIGAR=1X2M1X;DP=3885;DPB=3898;DPRA=0;EPP=3.0459;EPPR=10.286;GTI=0;LEN=4;MEANALT=8;MQM=32.3279;MQMR=51.9625;NS=1;NUMALT=1;ODDS=4763.18;PAIRED=0.934426;PAIREDR=0.988454;PAO=2;PQA=64;PQR=0;PRO=0;QA=2084;QR=133325;RO=3811;RPL=26;RPP=5.89373;RPPR=94.6332;RPR=35;RUN=1;SAF=32;SAP=3.33068;SAR=29;SRF=1958;SRP=9.29224;SRR=1853;TYPE=complex;ANN=ATGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1391_1394delTTGGinsATGT|p.ValGly464AspVal|1391/21291|1391/21291|464/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3885:3811,61:3811:133325:61:2084:0,-1032.69,-11349.3 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
89 NC_045512.2 1700 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=66;CIGAR=1X;DP=4549;DPB=4549;DPRA=0;EPP=3.53672;EPPR=3.26665;GTI=0;LEN=1;MEANALT=3;MQM=50.2121;MQMR=52.9005;NS=1;NUMALT=1;ODDS=5535.53;PAIRED=0.939394;PAIREDR=0.996653;PAO=0;PQA=0;PQR=0;PRO=0;QA=2243;QR=155182;RO=4481;RPL=36;RPP=4.19474;RPPR=3.01466;RPR=30;RUN=1;SAF=33;SAP=3.0103;SAR=33;SRF=2333;SRP=19.5956;SRR=2148;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1435T>C|p.Ser479Pro|1435/21291|1435/21291|479/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4549:4481,66:4481:155182:66:2243:0,-1178.54,-13249.9 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
90 NC_045512.2 1820 . G A 1.28256E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=225;CIGAR=1X;DP=4790;DPB=4790;DPRA=0;EPP=3.25157;EPPR=5.0218;GTI=0;LEN=1;MEANALT=3;MQM=53.3333;MQMR=52.6884;NS=1;NUMALT=1;ODDS=4172.54;PAIRED=0.982222;PAIREDR=0.992326;PAO=0;PQA=0;PQR=0;PRO=0;QA=7870;QR=158733;RO=4561;RPL=134;RPP=20.855;RPPR=145.462;RPR=91;RUN=1;SAF=110;SAP=3.25157;SAR=115;SRF=2212;SRP=11.9461;SRR=2349;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1555G>A|p.Gly519Ser|1555/21291|1555/21291|519/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4790:4561,225:4561:158733:225:7870:0,-756.291,-13041.7 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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91 NC_045512.2 2095 . G A 1.24765E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1292;DPB=1292;DPRA=0;EPP=3.0103;EPPR=3.50327;GTI=0;LEN=1;MEANALT=2;MQM=50;MQMR=50.7745;NS=1;NUMALT=1;ODDS=1604.84;PAIRED=1;PAIREDR=0.990573;PAO=0;PQA=0;PQR=0;PRO=0;QA=546;QR=43930;RO=1273;RPL=8;RPP=3.0103;RPPR=3.2167;RPR=8;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=636;SRP=3.01201;SRR=637;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1830G>A|p.Ser610Ser|1830/21291|1830/21291|610/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1292:1273,16:1273:43930:16:546:0,-341.229,-3662.66 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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92 NC_045512.2 2155 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1466;DPB=1466;DPRA=0;EPP=3.44459;EPPR=4.10732;GTI=0;LEN=1;MEANALT=3;MQM=42.65;MQMR=52.0596;NS=1;NUMALT=1;ODDS=1811.26;PAIRED=0.9;PAIREDR=0.991684;PAO=0;PQA=0;PQR=0;PRO=0;QA=708;QR=50315;RO=1443;RPL=11;RPP=3.44459;RPPR=55.6328;RPR=9;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=710;SRP=3.80636;SRR=733;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1890G>A|p.Trp630*|1890/21291|1890/21291|630/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1466:1443,20:1443:50315:20:708:0,-386.729,-4291.72 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
93 NC_045512.2 2763 . TGC TC 2885.41 . AB=0.180095;ABP=2628.85;AC=1;AF=0.5;AN=2;AO=532;CIGAR=1M1D1M;DP=2954;DPB=2776.67;DPRA=0;EPP=3.15724;EPPR=4.17803;GTI=0;LEN=1;MEANALT=5;MQM=48.9643;MQMR=52.4178;NS=1;NUMALT=1;ODDS=664.391;PAIRED=0.99812;PAIREDR=0.992946;PAO=0;PQA=0;PQR=0;PRO=0;QA=17759;QR=83546;RO=2410;RPL=244;RPP=10.9125;RPPR=20.6704;RPR=288;RUN=1;SAF=261;SAP=3.41847;SAR=271;SRF=1192;SRP=3.61939;SRR=1218;TYPE=del;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2499delG|p.Gln834fs|2499/21291|2499/21291|833/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2954:2410,532:2410:83546:532:17759:-579.218,0,-6324.54 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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94 NC_045512.2 3037 . CTAC TTAT,TTAC 50614.4 . AB=0.158792,0.840721;ABP=2079.08,2073.16;AC=1,1;AF=0.5,0.5;AN=2;AO=326,1726;CIGAR=1X2M1X,1X3M;DP=2053;DPB=2097.75;DPRA=0,0;EPP=3.0103,3.03043;EPPR=0;GTI=0;LEN=4,1;MEANALT=3,3;MQM=46.1135,50.1877;MQMR=0;NS=1;NUMALT=2;ODDS=76.3459;PAIRED=1,0.998841;PAIREDR=0;PAO=96,83;PQA=2101.5,1661.5;PQR=0;PRO=0;QA=11160,56774;QR=0;RO=0;RPL=162,808;RPP=3.03694,18.2333;RPPR=0;RPR=164,918;RUN=1,1;SAF=165,869;SAP=3.11688,3.19147;SAR=161,857;SRF=0;SRP=0;SRR=0;TYPE=complex,snp;ANN=TTAC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2772C>T|p.Phe924Phe|2772/21291|2772/21291|924/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/2:2053:0,326,1726:0:0:326,1726:11160,56774:-5303.39,-4514.98,-4416.84,-787.998,0,-268.42 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
95 NC_045512.2 3244 . C T 6.49718E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=1X;DP=3062;DPB=3062;DPRA=0;EPP=3.0608;EPPR=6.84328;GTI=0;LEN=1;MEANALT=1;MQM=45.3721;MQMR=48.8029;NS=1;NUMALT=1;ODDS=3757.35;PAIRED=1;PAIREDR=0.991388;PAO=0;PQA=0;PQR=0;PRO=0;QA=1492;QR=106008;RO=3019;RPL=16;RPP=9.12072;RPPR=199.751;RPR=27;RUN=1;SAF=23;SAP=3.46479;SAR=20;SRF=1547;SRP=7.05619;SRR=1472;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2979C>T|p.Gly993Gly|2979/21291|2979/21291|993/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3062:3019,43:3019:106008:43:1492:0,-801.627,-8549.01 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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96 NC_045512.2 3267 . C T 66510.3 . AB=0.84347;ABP=3439.83;AC=1;AF=0.5;AN=2;AO=2829;CIGAR=1X;DP=3354;DPB=3354;DPRA=0;EPP=5.00677;EPPR=3.82253;GTI=0;LEN=1;MEANALT=2;MQM=48.4143;MQMR=52.4637;NS=1;NUMALT=1;ODDS=445.319;PAIRED=0.994344;PAIREDR=0.984733;PAO=0;PQA=0;PQR=0;PRO=0;QA=99448;QR=18506;RO=524;RPL=1337;RPP=21.4513;RPPR=8.99428;RPR=1492;RUN=1;SAF=1456;SAP=8.29813;SAR=1373;SRF=272;SRP=4.66791;SRR=252;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3002C>T|p.Thr1001Ile|3002/21291|3002/21291|1001/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3354:524,2829:524:18506:2829:99448:-7040.97,0,-580.514 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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97 NC_045512.2 3290 . C G 2.34573E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=92;CIGAR=1X;DP=3816;DPB=3816;DPRA=0;EPP=3.0103;EPPR=5.63136;GTI=0;LEN=1;MEANALT=3;MQM=39.1957;MQMR=50.4792;NS=1;NUMALT=1;ODDS=4359.88;PAIRED=0.978261;PAIREDR=0.986287;PAO=0;PQA=0;PQR=0;PRO=0;QA=3202;QR=130715;RO=3719;RPL=46;RPP=3.0103;RPPR=63.9266;RPR=46;RUN=1;SAF=46;SAP=3.0103;SAR=46;SRF=1908;SRP=8.50408;SRR=1811;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3025C>G|p.Gln1009Glu|3025/21291|3025/21291|1009/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3816:3719,92:3719:130715:92:3202:0,-927.881,-10728.8 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
98 NC_045512.2 3327 . AGA AA 0.0 . AB=0.133491;ABP=4451.89;AC=1;AF=0.5;AN=2;AO=509;CIGAR=1M1D1M;DP=3813;DPB=3645.33;DPRA=0;EPP=3.21934;EPPR=4.22957;GTI=0;LEN=1;MEANALT=5;MQM=51.2692;MQMR=52.2961;NS=1;NUMALT=1;ODDS=425.428;PAIRED=0.996071;PAIREDR=0.992104;PAO=2;PQA=68;PQR=102;PRO=3;QA=17227;QR=115481;RO=3293;RPL=269;RPP=6.59814;RPPR=7.55305;RPR=240;RUN=1;SAF=256;SAP=3.0487;SAR=253;SRF=1646;SRP=3.01096;SRR=1647;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3063delG|p.Thr1022fs|3063/21291|3063/21291|1021/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3813:3293,509:3293:115481:509:17227:-318.157,0,-8788 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
99 NC_045512.2 3483 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=35;CIGAR=1X;DP=2793;DPB=2793;DPRA=0;EPP=3.07234;EPPR=8.70913;GTI=0;LEN=1;MEANALT=3;MQM=39.1143;MQMR=51.0527;NS=1;NUMALT=1;ODDS=3506.37;PAIRED=0.885714;PAIREDR=0.984381;PAO=0;PQA=0;PQR=0;PRO=0;QA=1145;QR=96319;RO=2753;RPL=7;RPP=30.3709;RPPR=550.326;RPR=28;RUN=1;SAF=16;SAP=3.56868;SAR=19;SRF=1344;SRP=6.34284;SRR=1409;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3218G>T|p.Gly1073Val|3218/21291|3218/21291|1073/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2793:2753,35:2753:96319:35:1145:0,-756.489,-8079.93 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
100 NC_045512.2 3491 . AA TT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=47;CIGAR=2X;DP=2589;DPB=2589;DPRA=0;EPP=3.0565;EPPR=13.3547;GTI=0;LEN=2;MEANALT=3;MQM=40;MQMR=50.6949;NS=1;NUMALT=1;ODDS=3087.91;PAIRED=0.914894;PAIREDR=0.983858;PAO=0;PQA=0;PQR=0;PRO=0;QA=1679;QR=89098;RO=2540;RPL=16;RPP=13.4056;RPPR=539.265;RPR=31;RUN=1;SAF=22;SAP=3.42611;SAR=25;SRF=1223;SRP=10.5643;SRR=1317;TYPE=complex;ANN=TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3226_3227delAAinsTT|p.Asn1076Phe|3226/21291|3226/21291|1076/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2589:2540,47:2540:89098:47:1679:0,-657.215,-7396.86 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
101 NC_045512.2 3500 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=49;CIGAR=1X;DP=2368;DPB=2368;DPRA=0;EPP=3.40914;EPPR=11.1091;GTI=0;LEN=1;MEANALT=1;MQM=47.1429;MQMR=50.5442;NS=1;NUMALT=1;ODDS=2753.48;PAIRED=0.918367;PAIREDR=0.983614;PAO=0;PQA=0;PQR=0;PRO=0;QA=1649;QR=80645;RO=2319;RPL=15;RPP=19.0083;RPPR=387.752;RPR=34;RUN=1;SAF=25;SAP=3.05462;SAR=24;SRF=1130;SRP=6.26985;SRR=1189;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3235A>C|p.Thr1079Pro|3235/21291|3235/21291|1079/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2368:2319,49:2319:80645:49:1649:0,-578.836,-6661.83 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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102 NC_045512.2 3522 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=156;CIGAR=1X;DP=1893;DPB=1893;DPRA=0;EPP=3.51141;EPPR=16.793;GTI=0;LEN=1;MEANALT=1;MQM=49.0577;MQMR=51.5181;NS=1;NUMALT=1;ODDS=1071.28;PAIRED=0.961538;PAIREDR=0.98388;PAO=0;PQA=0;PQR=0;PRO=0;QA=5381;QR=60781;RO=1737;RPL=55;RPP=32.4644;RPPR=275.649;RPR=101;RUN=1;SAF=76;SAP=3.23302;SAR=80;SRF=845;SRP=5.77183;SRR=892;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3257A>T|p.Glu1086Val|3257/21291|3257/21291|1086/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1893:1737,156:1737:60781:156:5381:0,-119.28,-4729.35 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
103 NC_045512.2 3668 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=1674;DPB=1674;DPRA=0;EPP=3.13803;EPPR=3.76559;GTI=0;LEN=1;MEANALT=2;MQM=42.4118;MQMR=52.933;NS=1;NUMALT=1;ODDS=2143.47;PAIRED=0.882353;PAIREDR=0.9843;PAO=0;PQA=0;PQR=0;PRO=0;QA=572;QR=58169;RO=1656;RPL=11;RPP=6.20364;RPPR=3.19912;RPR=6;RUN=1;SAF=10;SAP=4.1599;SAR=7;SRF=834;SRP=3.19912;SRR=822;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3403T>G|p.Tyr1135Asp|3403/21291|3403/21291|1135/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1674:1656,17:1656:58169:17:572:0,-462.9,-5012.95 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
104 NC_045512.2 3961 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=5;CIGAR=1X;DP=455;DPB=455;DPRA=0;EPP=3.44459;EPPR=3.0296;GTI=0;LEN=1;MEANALT=1;MQM=55.2;MQMR=53.5956;NS=1;NUMALT=1;ODDS=575.059;PAIRED=1;PAIREDR=0.991111;PAO=0;PQA=0;PQR=0;PRO=0;QA=180;QR=15627;RO=450;RPL=2;RPP=3.44459;RPPR=3.0103;RPR=3;RUN=1;SAF=3;SAP=3.44459;SAR=2;SRF=227;SRP=3.08751;SRR=223;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3696C>T|p.Ile1232Ile|3696/21291|3696/21291|1232/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:455:450,5:450:15627:5:180:0,-120.462,-1356.23 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
105 NC_045512.2 4038 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=363;DPB=363;DPRA=0;EPP=3.0103;EPPR=3.30835;GTI=0;LEN=1;MEANALT=1;MQM=37.8333;MQMR=54.3165;NS=1;NUMALT=1;ODDS=446.545;PAIRED=1;PAIREDR=0.994398;PAO=0;PQA=0;PQR=0;PRO=0;QA=216;QR=12513;RO=357;RPL=6;RPP=16.0391;RPPR=22.7725;RPR=0;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=176;SRP=3.16236;SRR=181;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3773A>C|p.Asp1258Ala|3773/21291|3773/21291|1258/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:363:357,6:357:12513:6:216:0,-92.3258,-1088.77 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
106 NC_045512.2 4102 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1952;DPB=1952;DPRA=0;EPP=3.0103;EPPR=4.46694;GTI=0;LEN=1;MEANALT=1;MQM=38.85;MQMR=51.4073;NS=1;NUMALT=1;ODDS=2496.52;PAIRED=1;PAIREDR=0.98913;PAO=0;PQA=0;PQR=0;PRO=0;QA=708;QR=67459;RO=1932;RPL=4;RPP=18.6449;RPPR=1095.71;RPR=16;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=983;SRP=4.30959;SRR=949;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3837A>T|p.Leu1279Phe|3837/21291|3837/21291|1279/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1952:1932,20:1932:67459:20:708:0,-538.151,-5712.79 |
|
5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
107 NC_045512.2 4162 . G T 3.59212E-13 . AB=0.123522;ABP=2813.62;AC=1;AF=0.5;AN=2;AO=282;CIGAR=1X;DP=2283;DPB=2283;DPRA=0;EPP=3.0411;EPPR=5.40749;GTI=0;LEN=1;MEANALT=1;MQM=49.4752;MQMR=50.932;NS=1;NUMALT=1;ODDS=430.424;PAIRED=0.98227;PAIREDR=0.996002;PAO=0;PQA=0;PQR=0;PRO=0;QA=9779;QR=69865;RO=2001;RPL=137;RPP=3.50312;RPPR=113.441;RPR=145;RUN=1;SAF=145;SAP=3.50312;SAR=137;SRF=1019;SRP=4.49593;SRR=982;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3897G>T|p.Val1299Val|3897/21291|3897/21291|1299/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2283:2001,282:2001:69865:282:9779:-137.285,0,-5222.59 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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108 NC_045512.2 4181 . G T 28777.7 . AB=0.575386;ABP=111.706;AC=1;AF=0.5;AN=2;AO=1267;CIGAR=1X;DP=2202;DPB=2202;DPRA=0;EPP=4.08147;EPPR=3.24279;GTI=0;LEN=1;MEANALT=2;MQM=48.9811;MQMR=52.2934;NS=1;NUMALT=1;ODDS=4866.93;PAIRED=0.998421;PAIREDR=0.995717;PAO=0;PQA=0;PQR=0;PRO=0;QA=43524;QR=32368;RO=934;RPL=667;RPP=10.7039;RPPR=3.15909;RPR=600;RUN=1;SAF=646;SAP=4.08147;SAR=621;SRF=479;SRP=4.34945;SRR=455;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3916G>T|p.Ala1306Ser|3916/21291|3916/21291|1306/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2202:934,1267:934:32368:1267:43524:-2898.44,0,-2133.35 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
109 NC_045512.2 4268 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=32;CIGAR=1X;DP=2364;DPB=2364;DPRA=0;EPP=3.0103;EPPR=3.01402;GTI=0;LEN=1;MEANALT=1;MQM=37.5312;MQMR=52.0746;NS=1;NUMALT=1;ODDS=2958.12;PAIRED=0.5625;PAIREDR=0.985849;PAO=0;PQA=0;PQR=0;PRO=0;QA=1148;QR=82280;RO=2332;RPL=31;RPP=64.083;RPPR=3.0103;RPR=1;RUN=1;SAF=15;SAP=3.28173;SAR=17;SRF=1169;SRP=3.04382;SRR=1163;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4003A>G|p.Asn1335Asp|4003/21291|4003/21291|1335/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2364:2332,32:2332:82280:32:1148:0,-633.643,-7000.81 |
|
5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
110 NC_045512.2 4435 . T C 3.44749E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=25;CIGAR=1X;DP=1857;DPB=1857;DPRA=0;EPP=3.79203;EPPR=7.42322;GTI=0;LEN=1;MEANALT=2;MQM=57.28;MQMR=53.1436;NS=1;NUMALT=1;ODDS=2286.49;PAIRED=1;PAIREDR=0.995085;PAO=0;PQA=0;PQR=0;PRO=0;QA=807;QR=64472;RO=1831;RPL=10;RPP=5.18177;RPPR=3.63767;RPR=15;RUN=1;SAF=13;SAP=3.09716;SAR=12;SRF=931;SRP=4.15;SRR=900;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4170T>C|p.Pro1390Pro|4170/21291|4170/21291|1390/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1857:1831,25:1831:64472:25:807:0,-486.055,-5542.5 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
111 NC_045512.2 4747 . T C 8.73969E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=644;DPB=644;DPRA=0;EPP=3.55317;EPPR=3.59559;GTI=0;LEN=1;MEANALT=2;MQM=41.0625;MQMR=53.3876;NS=1;NUMALT=1;ODDS=745.803;PAIRED=0.625;PAIREDR=0.985646;PAO=0;PQA=0;PQR=0;PRO=0;QA=576;QR=21917;RO=627;RPL=0;RPP=37.7539;RPPR=23.544;RPR=16;RUN=1;SAF=7;SAP=3.55317;SAR=9;SRF=326;SRP=5.17485;SRR=301;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4482T>C|p.Ser1494Ser|4482/21291|4482/21291|1494/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:644:627,16:627:21917:16:576:0,-153.532,-1879.62 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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112 NC_045512.2 4752 . C T 2.15769E-13 . AB=0.138414;ABP=733.223;AC=1;AF=0.5;AN=2;AO=89;CIGAR=1X;DP=643;DPB=643;DPRA=0;EPP=3.22989;EPPR=3.67391;GTI=0;LEN=1;MEANALT=2;MQM=48.8427;MQMR=53.2984;NS=1;NUMALT=1;ODDS=48.6552;PAIRED=0.977528;PAIREDR=0.976492;PAO=0;PQA=0;PQR=0;PRO=0;QA=3118;QR=19372;RO=553;RPL=48;RPP=4.20583;RPPR=10.9619;RPR=41;RUN=1;SAF=45;SAP=3.0347;SAR=44;SRF=279;SRP=3.10847;SRR=274;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4487C>T|p.Thr1496Ile|4487/21291|4487/21291|1496/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:643:553,89:553:19372:89:3118:-66.622,0,-1499.26 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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113 NC_045512.2 4839 . T C 1.23554E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=596;DPB=596;DPRA=0;EPP=3.0103;EPPR=3.02502;GTI=0;LEN=1;MEANALT=1;MQM=56.5;MQMR=53.1797;NS=1;NUMALT=1;ODDS=758.227;PAIRED=1;PAIREDR=0.99322;PAO=0;PQA=0;PQR=0;PRO=0;QA=212;QR=20811;RO=590;RPL=2;RPP=4.45795;RPPR=5.49829;RPR=4;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=298;SRP=3.1428;SRR=292;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4574T>C|p.Ile1525Thr|4574/21291|4574/21291|1525/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:596:590,6:590:20811:6:212:0,-160.023,-1801.04 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
114 NC_045512.2 4850 . A G 8.74157E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=8;CIGAR=1X;DP=650;DPB=650;DPRA=0;EPP=3.0103;EPPR=3.06442;GTI=0;LEN=1;MEANALT=1;MQM=40.625;MQMR=53.7212;NS=1;NUMALT=1;ODDS=823.193;PAIRED=1;PAIREDR=0.993769;PAO=0;PQA=0;PQR=0;PRO=0;QA=284;QR=22334;RO=642;RPL=0;RPP=20.3821;RPPR=3.0103;RPR=8;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=320;SRP=3.02383;SRR=322;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4585A>G|p.Lys1529Glu|4585/21291|4585/21291|1529/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:650:642,8:642:22334:8:284:0,-174.183,-1944 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
115 NC_045512.2 4955 . GAAGT GAGT,GACGT 2.43493E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=13,48;CIGAR=1M1D3M,2M1X2M;DP=1155;DPB=1152;DPRA=0,0;EPP=3.17734,3.0103;EPPR=4.68418;GTI=0;LEN=1,1;MEANALT=4,4;MQM=43.8462,51.9167;MQMR=50.1815;NS=1;NUMALT=2;ODDS=1052.3;PAIRED=1,1;PAIREDR=0.983501;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=392,1680;QR=38285;RO=1091;RPL=0,32;RPP=31.2394,14.5915;RPPR=594.194;RPR=13,16;RUN=1,1;SAF=7,24;SAP=3.17734,3.0103;SAR=6,24;SRF=549;SRP=3.10783;SRR=542;TYPE=del,snp;ANN=GAGT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4692delA|p.Val1565fs|4692/21291|4692/21291|1564/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1155:1091,13,48:1091:38285:13,48:392,1680:0,-298.202,-3197.09,-193.338,-3065.95,-3081.74 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
116 NC_045512.2 5118 . TTT AAA 7.71464E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=3X;DP=2311;DPB=2311;DPRA=0;EPP=5.48477;EPPR=3.51746;GTI=0;LEN=3;MEANALT=3;MQM=46.9535;MQMR=53.1435;NS=1;NUMALT=1;ODDS=2722.45;PAIRED=1;PAIREDR=0.996026;PAO=0;PQA=0;PQR=0;PRO=0;QA=1544;QR=79153;RO=2265;RPL=16;RPP=9.12072;RPPR=37.9849;RPR=27;RUN=1;SAF=23;SAP=3.46479;SAR=20;SRF=1141;SRP=3.28737;SRR=1124;TYPE=complex;ANN=AAA|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4853_4855delTTTinsAAA|p.PheTyr1618*|4853/21291|4853/21291|1618/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2311:2265,43:2265:79153:43:1544:0,-573.594,-6798.82 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
117 NC_045512.2 5182 . T C 7092.28 . AB=0.252637;ABP=1061.18;AC=1;AF=0.5;AN=2;AO=503;CIGAR=1X;DP=1991;DPB=1991;DPRA=0;EPP=3.53266;EPPR=4.15595;GTI=0;LEN=1;MEANALT=3;MQM=48.9344;MQMR=52.5188;NS=1;NUMALT=1;ODDS=1633.06;PAIRED=0.986083;PAIREDR=0.992598;PAO=0;PQA=0;PQR=0;PRO=0;QA=17356;QR=52385;RO=1486;RPL=246;RPP=3.53266;RPPR=4.50666;RPR=257;RUN=1;SAF=250;SAP=3.04915;SAR=253;SRF=734;SRP=3.48376;SRR=752;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4917T>C|p.Asp1639Asp|4917/21291|4917/21291|1639/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1991:1486,503:1486:52385:503:17356:-827.643,0,-3932.59 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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118 NC_045512.2 5184 . C T 1768.41 . AB=0.166249;ABP=1935.14;AC=1;AF=0.5;AN=2;AO=332;CIGAR=1X;DP=1997;DPB=1997;DPRA=0;EPP=3.03646;EPPR=3.82738;GTI=0;LEN=1;MEANALT=2;MQM=50.6807;MQMR=51.7821;NS=1;NUMALT=1;ODDS=407.191;PAIRED=1;PAIREDR=0.989163;PAO=0;PQA=0;PQR=0;PRO=0;QA=11718;QR=57567;RO=1661;RPL=186;RPP=13.4752;RPPR=3.16849;RPR=146;RUN=1;SAF=167;SAP=3.03646;SAR=165;SRF=823;SRP=3.30445;SRR=838;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4919C>T|p.Pro1640Leu|4919/21291|4919/21291|1640/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1997:1661,332:1661:57567:332:11718:-395.676,0,-4326.74 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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119 NC_045512.2 5239 . C T 8067.02 . AB=0.283776;ABP=721.382;AC=1;AF=0.5;AN=2;AO=502;CIGAR=1X;DP=1769;DPB=1769;DPRA=0;EPP=3.63319;EPPR=4.45394;GTI=0;LEN=1;MEANALT=2;MQM=46.5538;MQMR=52.3399;NS=1;NUMALT=1;ODDS=1857.5;PAIRED=0.998008;PAIREDR=0.993676;PAO=0;PQA=0;PQR=0;PRO=0;QA=17697;QR=44483;RO=1265;RPL=246;RPP=3.44286;RPPR=34.295;RPR=256;RUN=1;SAF=249;SAP=3.07951;SAR=253;SRF=620;SRP=4.08316;SRR=645;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4974C>T|p.Tyr1658Tyr|4974/21291|4974/21291|1658/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1769:1265,502:1265:44483:502:17697:-888.788,0,-3300.25 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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120 NC_045512.2 5283 . AC GT 3.00147E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=2X;DP=1943;DPB=1943;DPRA=0;EPP=3.0103;EPPR=4.93047;GTI=0;LEN=2;MEANALT=5;MQM=27.9167;MQMR=50.6312;NS=1;NUMALT=1;ODDS=2370.54;PAIRED=0.944444;PAIREDR=0.996318;PAO=0;PQA=0;PQR=0;PRO=0;QA=1258;QR=66807;RO=1901;RPL=24;RPP=11.6962;RPPR=22.019;RPR=12;RUN=1;SAF=16;SAP=3.9754;SAR=20;SRF=946;SRP=3.10282;SRR=955;TYPE=complex;ANN=GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5018_5019delACinsGT|p.Asn1673Ser|5018/21291|5018/21291|1673/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1943:1901,36:1901:66807:36:1258:0,-517.448,-5588.85 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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121 NC_045512.2 5388 . C A 15425.8 . AB=0.421856;ABP=89.8904;AC=1;AF=0.5;AN=2;AO=691;CIGAR=1X;DP=1638;DPB=1638;DPRA=0;EPP=4.14475;EPPR=3.12289;GTI=0;LEN=1;MEANALT=2;MQM=50.8871;MQMR=52.8868;NS=1;NUMALT=1;ODDS=3551.93;PAIRED=0.994211;PAIREDR=0.996825;PAO=0;PQA=0;PQR=0;PRO=0;QA=24252;QR=33052;RO=945;RPL=343;RPP=3.08886;RPPR=10.476;RPR=348;RUN=1;SAF=347;SAP=3.03858;SAR=344;SRF=484;SRP=4.22586;SRR=461;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5123C>A|p.Ala1708Asp|5123/21291|5123/21291|1708/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1638:945,691:945:33052:691:24252:-1559.56,0,-2377.37 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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122 NC_045512.2 5584 . A G 4302.11 . AB=0.25588;ABP=729.246;AC=1;AF=0.5;AN=2;AO=359;CIGAR=1X;DP=1403;DPB=1403;DPRA=0;EPP=3.30668;EPPR=3.26222;GTI=0;LEN=1;MEANALT=2;MQM=41.5766;MQMR=50.7507;NS=1;NUMALT=1;ODDS=990.597;PAIRED=1;PAIREDR=0.999041;PAO=0;PQA=0;PQR=0;PRO=0;QA=12643;QR=36358;RO=1043;RPL=241;RPP=94.5206;RPPR=6.51006;RPR=118;RUN=1;SAF=176;SAP=3.30668;SAR=183;SRF=520;SRP=3.02904;SRR=523;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5319A>G|p.Thr1773Thr|5319/21291|5319/21291|1773/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1403:1043,359:1043:36358:359:12643:-522.975,0,-2660.57 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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123 NC_045512.2 5765 . GG AC 2.41084E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=2X;DP=638;DPB=639;DPRA=0;EPP=3.20771;EPPR=3.09772;GTI=0;LEN=2;MEANALT=4;MQM=38;MQMR=53.4525;NS=1;NUMALT=1;ODDS=776.345;PAIRED=1;PAIREDR=0.996779;PAO=2;PQA=64;PQR=0;PRO=0;QA=362;QR=21351;RO=621;RPL=1;RPP=19.0002;RPPR=3.04177;RPR=10;RUN=1;SAF=6;SAP=3.20771;SAR=5;SRF=308;SRP=3.09772;SRR=313;TYPE=complex;ANN=AC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5500_5501delGGinsAC|p.Gly1834Thr|5500/21291|5500/21291|1834/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:638:621,11:621:21351:11:362:0,-164.517,-1844.91 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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124 NC_045512.2 5818 . T C 5838.01 . AB=0.4;ABP=59.4686;AC=1;AF=0.5;AN=2;AO=260;CIGAR=1X;DP=650;DPB=650;DPRA=0;EPP=3.04371;EPPR=3.21074;GTI=0;LEN=1;MEANALT=1;MQM=52.7192;MQMR=53.2333;NS=1;NUMALT=1;ODDS=1344.25;PAIRED=1;PAIREDR=0.984615;PAO=0;PQA=0;PQR=0;PRO=0;QA=9096;QR=13642;RO=390;RPL=135;RPP=3.84548;RPPR=7.37552;RPR=125;RUN=1;SAF=130;SAP=3.0103;SAR=130;SRF=197;SRP=3.09939;SRR=193;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5553T>C|p.Ala1851Ala|5553/21291|5553/21291|1851/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:650:390,260:390:13642:260:9096:-596.985,0,-994.554 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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125 NC_045512.2 5909 . TAT TT 0.0 . AB=0.156273;ABP=1401.75;AC=1;AF=0.5;AN=2;AO=213;CIGAR=1M1D1M;DP=1363;DPB=1294.33;DPRA=0;EPP=5.30411;EPPR=6.83731;GTI=0;LEN=1;MEANALT=2;MQM=35.23;MQMR=50.8407;NS=1;NUMALT=1;ODDS=246.516;PAIRED=1;PAIREDR=0.996519;PAO=3.5;PQA=115.5;PQR=115.5;PRO=3.5;QA=7203;QR=39975;RO=1149;RPL=22;RPP=294.181;RPPR=95.3139;RPR=191;RUN=1;SAF=114;SAP=5.30411;SAR=99;SRF=595;SRP=6.18719;SRR=554;TYPE=del;ANN=TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5645delA|p.Tyr1882fs|5645/21291|5645/21291|1882/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1363:1149,213:1149:39975:213:7203:-87.388,0,-2987.82 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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126 NC_045512.2 5944 . C T 3592.72 . AB=0.230724;ABP=1081.24;AC=1;AF=0.5;AN=2;AO=395;CIGAR=1X;DP=1712;DPB=1712;DPRA=0;EPP=3.93936;EPPR=5.52194;GTI=0;LEN=1;MEANALT=2;MQM=38.6253;MQMR=51.3338;NS=1;NUMALT=1;ODDS=827.255;PAIRED=1;PAIREDR=0.996198;PAO=0;PQA=0;PQR=0;PRO=0;QA=13976;QR=46014;RO=1315;RPL=120;RPP=135.085;RPPR=20.529;RPR=275;RUN=1;SAF=205;SAP=4.24721;SAR=190;SRF=665;SRP=3.38184;SRR=650;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5679C>T|p.Asp1893Asp|5679/21291|5679/21291|1893/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1712:1315,395:1315:46014:395:13976:-494.233,0,-3429.74 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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127 NC_045512.2 5986 . CACAG TACAA,TACAG 13031.4 . AB=0.329331,0.288165;ABP=445.51,684.722;AC=1,0;AF=0.5,0;AN=2;AO=576,504;CIGAR=1X3M1X,1X4M;DP=1749;DPB=1765.2;DPRA=0,0;EPP=3.25157,3.02753;EPPR=3.09318;GTI=0;LEN=5,1;MEANALT=8,8;MQM=48.3976,43.7917;MQMR=52.0015;NS=1;NUMALT=2;ODDS=771.741;PAIRED=0.996528,0.996032;PAIREDR=0.996947;PAO=55,26;PQA=1715.5,887.5;PQR=0;PRO=0;QA=20335,15262;QR=22850;RO=655;RPL=279,257;RPP=4.23175,3.44115;RPPR=8.05276;RPR=297,247;RUN=1,1;SAF=287,256;SAP=3.02538,3.28604;SAR=289,248;SRF=333;SRP=3.41144;SRR=322;TYPE=complex,snp;ANN=TACAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5721_5725delCACAGinsTACAA|p.Glu1909Lys|5721/21291|5721/21291|1907/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1749:655,576,504:655:22850:576,504:20335,15262:-1312.47,0,-1588.23,-332.158,-584.148,-1942.05 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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128 NC_045512.2 6401 . CC GT,CT 41378.4 . AB=0.0133511,0.5751;ABP=6165.94,149.78;AC=0,1;AF=0,0.5;AN=2;AO=40,1723;CIGAR=2X,1M1X;DP=2996;DPB=2997;DPRA=0,0;EPP=3.0103,4.92719;EPPR=4.20567;GTI=0;LEN=2,1;MEANALT=5,5;MQM=50.125,50.3186;MQMR=53.1954;NS=1;NUMALT=2;ODDS=6500.05;PAIRED=1,0.993035;PAIREDR=0.989414;PAO=1.5,0.5;PQA=48,16;PQR=0;PRO=0;QA=1416,60413;QR=42916;RO=1228;RPL=23,837;RPP=4.96463,6.03625;RPPR=51.7376;RPR=17,886;RUN=1,1;SAF=19,845;SAP=3.22745,4.38275;SAR=21,878;SRF=606;SRP=3.46298;SRR=622;TYPE=complex,snp;ANN=CT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6137C>T|p.Pro2046Leu|6137/21291|6137/21291|2046/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/2:2996:1228,40,1723:1228:42916:40,1723:1416,60413:-4165.56,-4430.39,-7791.85,0,-3268.69,-2854.85 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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129 NC_045512.2 6459 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=47;CIGAR=1X;DP=2778;DPB=2778;DPRA=0;EPP=3.42611;EPPR=9.88729;GTI=0;LEN=1;MEANALT=1;MQM=40.6809;MQMR=52.4357;NS=1;NUMALT=1;ODDS=3365.28;PAIRED=0.595745;PAIREDR=0.992677;PAO=0;PQA=0;PQR=0;PRO=0;QA=1642;QR=96439;RO=2731;RPL=0;RPP=105.07;RPPR=159.052;RPR=47;RUN=1;SAF=22;SAP=3.42611;SAR=25;SRF=1324;SRP=8.48788;SRR=1407;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6194A>G|p.Asn2065Ser|6194/21291|6194/21291|2065/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2778:2731,47:2731:96439:47:1642:0,-709.432,-8216.17 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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130 NC_045512.2 6581 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=42;CIGAR=1X;DP=3950;DPB=3950;DPRA=0;EPP=3.0103;EPPR=9.87224;GTI=0;LEN=1;MEANALT=2;MQM=53.7143;MQMR=53.3706;NS=1;NUMALT=1;ODDS=4948;PAIRED=1;PAIREDR=0.99051;PAO=0;PQA=0;PQR=0;PRO=0;QA=1448;QR=137583;RO=3899;RPL=24;RPP=4.87156;RPPR=11.4361;RPR=18;RUN=1;SAF=21;SAP=3.0103;SAR=21;SRF=1980;SRP=5.08264;SRR=1919;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6316A>G|p.Thr2106Ala|6316/21291|6316/21291|2106/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3950:3899,42:3899:137583:42:1448:0,-1057.38,-11906.7 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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131 NC_045512.2 6654 . TTAATAGTGTCCCTTGGGATACTATAGCT TT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=90;CIGAR=1M27D1M;DP=2584;DPB=2502.62;DPRA=0;EPP=3.87889;EPPR=3.33544;GTI=0;LEN=27;MEANALT=41;MQM=49.5111;MQMR=53.8523;NS=1;NUMALT=1;ODDS=2613.21;PAIRED=1;PAIREDR=0.994608;PAO=8;PQA=245;PQR=626;PRO=23;QA=2527;QR=83585;RO=2411;RPL=56;RPP=14.688;RPPR=13.7109;RPR=34;RUN=1;SAF=44;SAP=3.10681;SAR=46;SRF=1215;SRP=3.33544;SRR=1196;TYPE=del;ANN=TT|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6394_6420delAGTGTCCCTTGGGATACTATAGCTAAT|p.Ser2132_Asn2140del|6394/21291|6394/21291|2132/7096||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/0:2584:2411,90:2411:83585:90:2527:0,-542.491,-7120.65 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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132 NC_045512.2 6728 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=131;CIGAR=1X;DP=4495;DPB=4495;DPRA=0;EPP=3.02688;EPPR=3.0347;GTI=0;LEN=1;MEANALT=3;MQM=52.626;MQMR=52.7916;NS=1;NUMALT=1;ODDS=4749.06;PAIRED=0.984733;PAIREDR=0.984637;PAO=0;PQA=0;PQR=0;PRO=0;QA=4607;QR=153668;RO=4361;RPL=65;RPP=3.02688;RPPR=567.775;RPR=66;RUN=1;SAF=63;SAP=3.4247;SAR=68;SRF=2187;SRP=3.09445;SRR=2174;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6463A>G|p.Asn2155Asp|6463/21291|6463/21291|2155/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4495:4361,131:4361:153668:131:4607:0,-960.457,-12910.3 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
133 NC_045512.2 6772 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=72;CIGAR=1X;DP=5961;DPB=5961;DPRA=0;EPP=3.13094;EPPR=4.2522;GTI=0;LEN=1;MEANALT=3;MQM=47.5833;MQMR=51.9471;NS=1;NUMALT=1;ODDS=7432.86;PAIRED=1;PAIREDR=0.991159;PAO=0;PQA=0;PQR=0;PRO=0;QA=2518;QR=206887;RO=5882;RPL=9;RPP=90.9549;RPPR=574.318;RPR=63;RUN=1;SAF=38;SAP=3.49285;SAR=34;SRF=2959;SRP=3.48875;SRR=2923;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6507G>A|p.Met2169Ile|6507/21291|6507/21291|2169/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5961:5882,72:5882:206887:72:2518:0,-1588.67,-17552.3 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
134 NC_045512.2 6954 . T C 78261.2 . AB=0.74609;ABP=2290.15;AC=1;AF=0.5;AN=2;AO=3244;CIGAR=1X;DP=4348;DPB=4348;DPRA=0;EPP=3.39586;EPPR=3.51658;GTI=0;LEN=1;MEANALT=3;MQM=49.9263;MQMR=53.5255;NS=1;NUMALT=1;ODDS=4109.19;PAIRED=0.99476;PAIREDR=0.993625;PAO=0;PQA=0;PQR=0;PRO=0;QA=112718;QR=38145;RO=1098;RPL=1650;RPP=5.10948;RPPR=11.1108;RPR=1594;RUN=1;SAF=1620;SAP=3.02101;SAR=1624;SRF=546;SRP=3.0815;SRR=552;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6689T>C|p.Ile2230Thr|6689/21291|6689/21291|2230/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4348:1098,3244:1098:38145:3244:112718:-8076.53,0,-2034.93 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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135 NC_045512.2 7124 . C T 36735.9 . AB=0.593619;ABP=203.456;AC=1;AF=0.5;AN=2;AO=1563;CIGAR=1X;DP=2633;DPB=2633;DPRA=0;EPP=3.87861;EPPR=6.09993;GTI=0;LEN=1;MEANALT=2;MQM=48.3762;MQMR=52.6707;NS=1;NUMALT=1;ODDS=5513.12;PAIRED=0.997441;PAIREDR=0.992516;PAO=0;PQA=0;PQR=0;PRO=0;QA=55234;QR=37290;RO=1069;RPL=642;RPP=111.155;RPPR=68.0956;RPR=921;RUN=1;SAF=815;SAP=9.24686;SAR=748;SRF=544;SRP=3.7436;SRR=525;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6859C>T|p.Pro2287Ser|6859/21291|6859/21291|2287/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2633:1069,1563:1069:37290:1563:55234:-3714.31,0,-2430.12 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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136 NC_045512.2 7262 . C A 7.353E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=1X;DP=2907;DPB=2907;DPRA=0;EPP=32.2045;EPPR=8.10485;GTI=0;LEN=1;MEANALT=2;MQM=54.75;MQMR=52.6598;NS=1;NUMALT=1;ODDS=3772.74;PAIRED=1;PAIREDR=0.995813;PAO=0;PQA=0;PQR=0;PRO=0;QA=526;QR=95172;RO=2866;RPL=29;RPP=32.2045;RPPR=29.2225;RPR=7;RUN=1;SAF=36;SAP=81.1833;SAR=0;SRF=1432;SRP=3.01333;SRR=1434;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6997C>A|p.Leu2333Ile|6997/21291|6997/21291|2333/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2907:2866,36:2866:95172:36:526:0,-827.217,-8169.18 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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137 NC_045512.2 7363 . G C 2.6519E-13 . AB=0.121355;ABP=3974.32;AC=1;AF=0.5;AN=2;AO=387;CIGAR=1X;DP=3189;DPB=3189;DPRA=0;EPP=3.46479;EPPR=5.99569;GTI=0;LEN=1;MEANALT=3;MQM=45.4703;MQMR=50.912;NS=1;NUMALT=1;ODDS=883.768;PAIRED=0.994832;PAIREDR=0.995351;PAO=0;PQA=0;PQR=0;PRO=0;QA=13459;QR=98261;RO=2796;RPL=311;RPP=312.88;RPPR=63.0318;RPR=76;RUN=1;SAF=189;SAP=3.46479;SAR=198;SRF=1396;SRP=3.02273;SRR=1400;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7098G>C|p.Trp2366Cys|7098/21291|7098/21291|2366/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3189:2796,387:2796:98261:387:13459:-103.873,0,-7409.47 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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138 NC_045512.2 7429 . A G 17852.7 . AB=0.408913;ABP=150.168;AC=1;AF=0.5;AN=2;AO=835;CIGAR=1X;DP=2042;DPB=2042;DPRA=0;EPP=4.15715;EPPR=4.42428;GTI=0;LEN=1;MEANALT=2;MQM=50.1353;MQMR=52.887;NS=1;NUMALT=1;ODDS=4110.74;PAIRED=0.99521;PAIREDR=0.994186;PAO=0;PQA=0;PQR=0;PRO=0;QA=28871;QR=42302;RO=1204;RPL=398;RPP=6.96576;RPPR=4.2295;RPR=437;RUN=1;SAF=423;SAP=3.32497;SAR=412;SRF=613;SRP=3.88322;SRR=591;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7164A>G|p.Ala2388Ala|7164/21291|7164/21291|2388/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2042:1204,835:1204:42302:835:28871:-1808.82,0,-3057.19 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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139 NC_045512.2 8172 . C T 7.05188E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=841;DPB=841;DPRA=0;EPP=3.13803;EPPR=3.02084;GTI=0;LEN=1;MEANALT=1;MQM=50.0588;MQMR=52.818;NS=1;NUMALT=1;ODDS=984.169;PAIRED=1;PAIREDR=0.970874;PAO=0;PQA=0;PQR=0;PRO=0;QA=577;QR=28651;RO=824;RPL=11;RPP=6.20364;RPPR=7.22675;RPR=6;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=419;SRP=3.52682;SRR=405;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7907C>T|p.Ala2636Val|7907/21291|7907/21291|2636/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:841:824,17:824:28651:17:577:0,-204.864,-2432.99 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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140 NC_045512.2 8364 . A G 8004.45 . AB=0.408027;ABP=68.917;AC=1;AF=0.5;AN=2;AO=366;CIGAR=1X;DP=897;DPB=897;DPRA=0;EPP=3.0103;EPPR=3.27252;GTI=0;LEN=1;MEANALT=2;MQM=50.4071;MQMR=53.6094;NS=1;NUMALT=1;ODDS=1843.09;PAIRED=1;PAIREDR=0.992453;PAO=0;PQA=0;PQR=0;PRO=0;QA=12874;QR=18616;RO=530;RPL=173;RPP=5.38349;RPPR=9.56569;RPR=193;RUN=1;SAF=184;SAP=3.03403;SAR=182;SRF=268;SRP=3.1578;SRR=262;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8099A>G|p.Asn2700Ser|8099/21291|8099/21291|2700/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:897:530,366:530:18616:366:12874:-814.947,0,-1355.26 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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141 NC_045512.2 8557 . A G 7207.18 . AB=0.361084;ABP=176.158;AC=1;AF=0.5;AN=2;AO=373;CIGAR=1X;DP=1033;DPB=1033;DPRA=0;EPP=3.29556;EPPR=4.60271;GTI=0;LEN=1;MEANALT=1;MQM=46.622;MQMR=52.8197;NS=1;NUMALT=1;ODDS=1659.51;PAIRED=0.991957;PAIREDR=0.993939;PAO=0;PQA=0;PQR=0;PRO=0;QA=13232;QR=23292;RO=660;RPL=194;RPP=4.32017;RPPR=3.85257;RPR=179;RUN=1;SAF=178;SAP=4.69275;SAR=195;SRF=321;SRP=4.0763;SRR=339;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8292A>G|p.Lys2764Lys|8292/21291|8292/21291|2764/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1033:660,373:660:23292:373:13232:-746.33,0,-1718.1 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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142 NC_045512.2 8565 . ATAA GTAG 5776.02 . AB=0.3433;ABP=195.603;AC=1;AF=0.5;AN=2;AO=310;CIGAR=1X2M1X;DP=903;DPB=910;DPRA=0;EPP=3.0103;EPPR=5.48989;GTI=0;LEN=4;MEANALT=2;MQM=46.2516;MQMR=53.3649;NS=1;NUMALT=1;ODDS=1329.98;PAIRED=0.987097;PAIREDR=0.996622;PAO=26;PQA=880;PQR=0;PRO=2;QA=11017;QR=20793;RO=592;RPL=153;RPP=3.12238;RPPR=17.1102;RPR=157;RUN=1;SAF=152;SAP=3.26247;SAR=158;SRF=288;SRP=3.94932;SRR=304;TYPE=complex;ANN=GTAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8300_8303delATAAinsGTAG|p.AsnAsn2767SerSer|8300/21291|8300/21291|2767/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:903:592,310:592:20793:310:11017:-604.693,0,-1551.51 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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143 NC_045512.2 8634 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=71;CIGAR=1X;DP=694;DPB=694;DPRA=0;EPP=3.7749;EPPR=6.1523;GTI=0;LEN=1;MEANALT=2;MQM=47.1831;MQMR=51.8006;NS=1;NUMALT=1;ODDS=331.413;PAIRED=0.971831;PAIREDR=0.96463;PAO=0;PQA=0;PQR=0;PRO=0;QA=2483;QR=21417;RO=622;RPL=71;RPP=157.185;RPPR=178.18;RPR=0;RUN=1;SAF=33;SAP=3.7749;SAR=38;SRF=307;SRP=3.23373;SRR=315;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8369T>C|p.Ile2790Thr|8369/21291|8369/21291|2790/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:694:622,71:622:21417:71:2483:0,-7.8921,-1639.83 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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144 NC_045512.2 8716 . TC GA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=5;CIGAR=2X;DP=265;DPB=265;DPRA=0;EPP=3.44459;EPPR=3.84548;GTI=0;LEN=2;MEANALT=1;MQM=46.6;MQMR=54.0346;NS=1;NUMALT=1;ODDS=322.356;PAIRED=0.8;PAIREDR=0.965385;PAO=0;PQA=0;PQR=0;PRO=0;QA=178;QR=9081;RO=260;RPL=0;RPP=13.8677;RPPR=3.54482;RPR=5;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=131;SRP=3.04371;SRR=129;TYPE=complex;ANN=GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8451_8452delTCinsGA|p.Arg2818Ser|8451/21291|8451/21291|2817/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:265:260,5:260:9081:5:178:0,-65.7297,-782.204 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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145 NC_045512.2 8782 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=295;DPB=295;DPRA=0;EPP=3.0103;EPPR=3.07746;GTI=0;LEN=1;MEANALT=1;MQM=56.5;MQMR=53.7766;NS=1;NUMALT=1;ODDS=368.964;PAIRED=1;PAIREDR=0.979381;PAO=0;PQA=0;PQR=0;PRO=0;QA=140;QR=10001;RO=291;RPL=0;RPP=11.6962;RPPR=3.37594;RPR=4;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=140;SRP=3.91321;SRR=151;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8517C>A|p.Ser2839Arg|8517/21291|8517/21291|2839/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:295:291,4:291:10001:4:140:0,-75.8695,-867.135 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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146 NC_045512.2 8844 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=330;DPB=330;DPRA=0;EPP=3.0103;EPPR=3.03761;GTI=0;LEN=1;MEANALT=1;MQM=44.6667;MQMR=51.5503;NS=1;NUMALT=1;ODDS=343.81;PAIRED=0.666667;PAIREDR=0.943396;PAO=0;PQA=0;PQR=0;PRO=0;QA=432;QR=11050;RO=318;RPL=0;RPP=29.068;RPPR=3.44733;RPR=12;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=151;SRP=4.7584;SRR=167;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8579G>A|p.Arg2860Lys|8579/21291|8579/21291|2860/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:330:318,12:318:11050:12:432:0,-64.5233,-902.184 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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147 NC_045512.2 8873 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=293;DPB=293;DPRA=0;EPP=3.73412;EPPR=3.61891;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=52.3633;NS=1;NUMALT=1;ODDS=376.316;PAIRED=0.333333;PAIREDR=0.955017;PAO=0;PQA=0;PQR=0;PRO=0;QA=104;QR=9921;RO=289;RPL=3;RPP=9.52472;RPPR=3.01781;RPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=139;SRP=3.91946;SRR=150;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8608C>T|p.Pro2870Ser|8608/21291|8608/21291|2870/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:293:289,3:289:9921:3:104:0,-78.3896,-844.462 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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148 NC_045512.2 8986 . C T 19981.1 . AB=0.873913;ABP=1120.24;AC=1;AF=0.5;AN=2;AO=804;CIGAR=1X;DP=920;DPB=920;DPRA=0;EPP=3.53966;EPPR=3.0103;GTI=0;LEN=1;MEANALT=3;MQM=49.1704;MQMR=53.2895;NS=1;NUMALT=1;ODDS=139.322;PAIRED=0.992537;PAIREDR=0.991228;PAO=0;PQA=0;PQR=0;PRO=0;QA=28119;QR=3988;RO=114;RPL=329;RPP=60.5813;RPPR=3.0103;RPR=475;RUN=1;SAF=414;SAP=4.56598;SAR=390;SRF=60;SRP=3.69603;SRR=54;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8721C>T|p.Asp2907Asp|8721/21291|8721/21291|2907/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:920:114,804:114:3988:804:28119:-2078.41,0,-73.1119 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
149 NC_045512.2 9026 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=71;CIGAR=1X;DP=1113;DPB=1113;DPRA=0;EPP=3.04088;EPPR=4.01893;GTI=0;LEN=1;MEANALT=1;MQM=41.831;MQMR=49.8301;NS=1;NUMALT=1;ODDS=885.288;PAIRED=1;PAIREDR=0.997121;PAO=0;PQA=0;PQR=0;PRO=0;QA=2421;QR=36529;RO=1042;RPL=33;RPP=3.7749;RPPR=21.4241;RPR=38;RUN=1;SAF=36;SAP=3.04088;SAR=35;SRF=532;SRP=4.01893;SRR=510;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8761A>T|p.Ile2921Phe|8761/21291|8761/21291|2921/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1113:1042,71:1042:36529:71:2421:0,-157.653,-2908.65 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
150 NC_045512.2 9053 . G T 22309.4 . AB=0.843808;ABP=1113.91;AC=1;AF=0.5;AN=2;AO=913;CIGAR=1X;DP=1082;DPB=1082;DPRA=0;EPP=3.06976;EPPR=3.12594;GTI=0;LEN=1;MEANALT=1;MQM=49.3527;MQMR=52.2071;NS=1;NUMALT=1;ODDS=124.118;PAIRED=0.996714;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32053;QR=5942;RO=169;RPL=427;RPP=11.2895;RPPR=17.0028;RPR=486;RUN=1;SAF=458;SAP=3.03171;SAR=455;SRF=84;SRP=3.02315;SRR=85;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8788G>T|p.Val2930Leu|8788/21291|8788/21291|2930/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1082:169,913:169:5942:913:32053:-2362.09,0,-184.534 |
|
5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
151 NC_045512.2 9241 . A T 1.11862E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=60;CIGAR=1X;DP=1557;DPB=1557;DPRA=0;EPP=4.31318;EPPR=9.9256;GTI=0;LEN=1;MEANALT=2;MQM=47.4833;MQMR=49.9773;NS=1;NUMALT=1;ODDS=1548.51;PAIRED=0.966667;PAIREDR=0.968562;PAO=0;PQA=0;PQR=0;PRO=0;QA=2105;QR=52635;RO=1495;RPL=6;RPP=86.3948;RPPR=275.336;RPR=54;RUN=1;SAF=33;SAP=4.31318;SAR=27;SRF=749;SRP=3.02337;SRR=746;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8976A>T|p.Ser2992Ser|8976/21291|8976/21291|2992/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1557:1495,60:1495:52635:60:2105:0,-298.895,-4239.78 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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152 NC_045512.2 9445 . T C 2.15045E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=91;CIGAR=1X;DP=1927;DPB=1927;DPRA=0;EPP=3.22506;EPPR=3.12857;GTI=0;LEN=1;MEANALT=1;MQM=49.0769;MQMR=50.7925;NS=1;NUMALT=1;ODDS=1726.32;PAIRED=1;PAIREDR=0.961329;PAO=0;PQA=0;PQR=0;PRO=0;QA=3146;QR=64355;RO=1836;RPL=56;RPP=13.5336;RPPR=8.16222;RPR=35;RUN=1;SAF=44;SAP=3.22506;SAR=47;SRF=896;SRP=5.30004;SRR=940;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9180T>C|p.Leu3060Leu|9180/21291|9180/21291|3060/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1927:1836,91:1836:64355:91:3146:0,-321.171,-5169.55 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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153 NC_045512.2 9511 . T C 4.64324E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=220;CIGAR=1X;DP=2576;DPB=2576;DPRA=0;EPP=3.16823;EPPR=19.815;GTI=0;LEN=1;MEANALT=2;MQM=48.6909;MQMR=51.9338;NS=1;NUMALT=1;ODDS=1399.05;PAIRED=0.986364;PAIREDR=0.990658;PAO=0;PQA=0;PQR=0;PRO=0;QA=7616;QR=83328;RO=2355;RPL=124;RPP=10.7486;RPPR=413.229;RPR=96;RUN=1;SAF=108;SAP=3.16823;SAR=112;SRF=1215;SRP=8.19694;SRR=1140;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9246T>C|p.Thr3082Thr|9246/21291|9246/21291|3082/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2576:2355,220:2355:83328:220:7616:0,-150.664,-6510.68 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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154 NC_045512.2 9521 . C T 5.11094E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=56;CIGAR=1X;DP=2683;DPB=2683;DPRA=0;EPP=3.63072;EPPR=12.4812;GTI=0;LEN=1;MEANALT=2;MQM=42.4643;MQMR=51.472;NS=1;NUMALT=1;ODDS=3128.98;PAIRED=0.946429;PAIREDR=0.992762;PAO=0;PQA=0;PQR=0;PRO=0;QA=1974;QR=91769;RO=2625;RPL=11;RPP=47.8357;RPPR=156.677;RPR=45;RUN=1;SAF=29;SAP=3.16541;SAR=27;SRF=1329;SRP=3.91115;SRR=1296;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9256C>T|p.Leu3086Phe|9256/21291|9256/21291|3086/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2683:2625,56:2625:91769:56:1974:0,-659.011,-7674.21 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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155 NC_045512.2 9627 . CTTTTTTAG CTTTTTAG 3.32693E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=30;CIGAR=1M1D7M;DP=2471;DPB=2468.56;DPRA=0;EPP=3.29983;EPPR=8.18457;GTI=0;LEN=1;MEANALT=11;MQM=48.4667;MQMR=52.5949;NS=1;NUMALT=1;ODDS=3061.58;PAIRED=1;PAIREDR=0.987624;PAO=1.5;PQA=40;PQR=40;PRO=1.5;QA=944;QR=85133;RO=2424;RPL=17;RPP=4.16842;RPPR=20.5684;RPR=13;RUN=1;SAF=15;SAP=3.0103;SAR=15;SRF=1234;SRP=4.74461;SRR=1190;TYPE=del;ANN=CTTTTTAG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9368delT|p.Leu3123fs|9368/21291|9368/21291|3123/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2471:2424,30:2424:85133:30:944:0,-655.432,-7265.75 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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156 NC_045512.2 9734 . T C 10284.7 . AB=0.267343;ABP=1161.96;AC=1;AF=0.5;AN=2;AO=659;CIGAR=1X;DP=2465;DPB=2465;DPRA=0;EPP=3.09268;EPPR=4.65908;GTI=0;LEN=1;MEANALT=2;MQM=49.393;MQMR=51.5042;NS=1;NUMALT=1;ODDS=2368.13;PAIRED=1;PAIREDR=0.993344;PAO=0;PQA=0;PQR=0;PRO=0;QA=22831;QR=63717;RO=1803;RPL=324;RPP=3.40901;RPPR=35.0091;RPR=335;RUN=1;SAF=327;SAP=3.09268;SAR=332;SRF=892;SRP=3.44508;SRR=911;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9469T>C|p.Phe3157Leu|9469/21291|9469/21291|3157/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2465:1803,659:1803:63717:659:22831:-1156.78,0,-4685.13 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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157 NC_045512.2 9865 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=1X;DP=945;DPB=945;DPRA=0;EPP=3.20771;EPPR=4.13556;GTI=0;LEN=1;MEANALT=1;MQM=50.3636;MQMR=51.8437;NS=1;NUMALT=1;ODDS=1188.97;PAIRED=0.909091;PAIREDR=0.981799;PAO=0;PQA=0;PQR=0;PRO=0;QA=377;QR=32898;RO=934;RPL=4;RPP=4.78696;RPPR=16.439;RPR=7;RUN=1;SAF=6;SAP=3.20771;SAR=5;SRF=483;SRP=5.39101;SRR=451;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9600T>C|p.Pro3200Pro|9600/21291|9600/21291|3200/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:945:934,11:934:32898:11:377:0,-252.906,-2775.77 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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158 NC_045512.2 9891 . C T 7564.06 . AB=0.350235;ABP=210.495;AC=1;AF=0.5;AN=2;AO=373;CIGAR=1X;DP=1065;DPB=1065;DPRA=0;EPP=3.99416;EPPR=4.97437;GTI=0;LEN=1;MEANALT=2;MQM=50.5684;MQMR=52.7902;NS=1;NUMALT=1;ODDS=1741.69;PAIRED=0.994638;PAIREDR=0.984081;PAO=0;PQA=0;PQR=0;PRO=0;QA=13059;QR=24218;RO=691;RPL=182;RPP=3.48185;RPPR=6.43249;RPR=191;RUN=1;SAF=188;SAP=3.06269;SAR=185;SRF=347;SRP=3.03858;SRR=344;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9626C>T|p.Ala3209Val|9626/21291|9626/21291|3209/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1065:691,373:691:24218:373:13059:-785.258,0,-1781.24 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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159 NC_045512.2 10029 . C T 9917.01 . AB=0.509918;ABP=3.74257;AC=1;AF=0.5;AN=2;AO=437;CIGAR=1X;DP=857;DPB=857;DPRA=0;EPP=4.80412;EPPR=3.01548;GTI=0;LEN=1;MEANALT=2;MQM=48.9451;MQMR=53.5131;NS=1;NUMALT=1;ODDS=2283.48;PAIRED=0.990847;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15164;QR=14518;RO=419;RPL=203;RPP=7.78555;RPPR=4.17637;RPR=234;RUN=1;SAF=216;SAP=3.13453;SAR=221;SRF=209;SRP=3.01548;SRR=210;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9764C>T|p.Thr3255Ile|9764/21291|9764/21291|3255/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:857:419,437:419:14518:437:15164:-1000.27,0,-1019.67 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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160 NC_045512.2 10228 . C T 13986.5 . AB=0.280464;ABP=1267.26;AC=1;AF=0.5;AN=2;AO=847;CIGAR=1X;DP=3020;DPB=3020;DPRA=0;EPP=3.01286;EPPR=3.58669;GTI=0;LEN=1;MEANALT=3;MQM=49.3318;MQMR=52.8512;NS=1;NUMALT=1;ODDS=3220.5;PAIRED=0.995277;PAIREDR=0.99447;PAO=0;PQA=0;PQR=0;PRO=0;QA=29649;QR=76244;RO=2170;RPL=439;RPP=5.47404;RPPR=3.07434;RPR=408;RUN=1;SAF=423;SAP=3.01286;SAR=424;SRF=1084;SRP=3.0143;SRR=1086;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9963C>T|p.Leu3321Leu|9963/21291|9963/21291|3321/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3020:2170,847:2170:76244:847:29649:-1537.73,0,-5713.37 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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161 NC_045512.2 10408 . C T 7069.66 . AB=0.250962;ABP=1263.03;AC=1;AF=0.5;AN=2;AO=587;CIGAR=1X;DP=2339;DPB=2339;DPRA=0;EPP=3.30994;EPPR=4.99565;GTI=0;LEN=1;MEANALT=2;MQM=45.0187;MQMR=51.1657;NS=1;NUMALT=1;ODDS=1627.85;PAIRED=0.945486;PAIREDR=0.993714;PAO=0;PQA=0;PQR=0;PRO=0;QA=20801;QR=61151;RO=1750;RPL=466;RPP=443.316;RPPR=97.5326;RPR=121;RUN=1;SAF=290;SAP=3.19156;SAR=297;SRF=870;SRP=3.13438;SRR=880;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10143C>T|p.Tyr3381Tyr|10143/21291|10143/21291|3381/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2339:1750,587:1750:61151:587:20801:-893.549,0,-4490.38 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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162 NC_045512.2 10487 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=60;CIGAR=1X;DP=1268;DPB=1268;DPRA=0;EPP=3.15506;EPPR=4.85102;GTI=0;LEN=1;MEANALT=1;MQM=50.7;MQMR=52.9139;NS=1;NUMALT=1;ODDS=1130.67;PAIRED=1;PAIREDR=0.990066;PAO=0;PQA=0;PQR=0;PRO=0;QA=2080;QR=42478;RO=1208;RPL=27;RPP=4.31318;RPPR=45.6416;RPR=33;RUN=1;SAF=32;SAP=3.58936;SAR=28;SRF=611;SRP=3.36262;SRR=597;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10222T>C|p.Cys3408Arg|10222/21291|10222/21291|3408/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1268:1208,60:1208:42478:60:2080:0,-207.823,-3511.98 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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163 NC_045512.2 11074 . CTTTTTTTTGTATGA CTTTTTTTGTATGA,CTTTTTTTTTGTATGA 4.6288E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=13,12;CIGAR=1M1D13M,1M1I14M;DP=552;DPB=552;DPRA=0,0;EPP=3.17734,3.0103;EPPR=3.07737;GTI=0;LEN=1,1;MEANALT=9,9;MQM=54,48.9167;MQMR=49.0734;NS=1;NUMALT=2;ODDS=598.293;PAIRED=0.923077,0.833333;PAIREDR=0.878378;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=433,386;QR=17910;RO=518;RPL=4,6;RPP=7.18621,3.0103;RPPR=209.61;RPR=9,6;RUN=1,1;SAF=6,6;SAP=3.17734,3.0103;SAR=7,6;SRF=273;SRP=6.29685;SRR=245;TYPE=del,ins;ANN=CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10817delT|p.Leu3606fs|10817/21291|10817/21291|3606/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:552:518,13,12:518:17910:13,12:433,386:0,-121.139,-1418.29,-125.159,-1391.45,-1422.6 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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164 NC_045512.2 11151 . T A 9.76452E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=800;DPB=800;DPRA=0;EPP=3.73412;EPPR=3.40712;GTI=0;LEN=1;MEANALT=1;MQM=42.8333;MQMR=53.0863;NS=1;NUMALT=1;ODDS=993.402;PAIRED=0.5;PAIREDR=0.984772;PAO=0;PQA=0;PQR=0;PRO=0;QA=375;QR=27325;RO=788;RPL=2;RPP=14.5915;RPPR=3.55041;RPR=10;RUN=1;SAF=7;SAP=3.73412;SAR=5;SRF=403;SRP=3.90314;SRR=385;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10886T>A|p.Val3629Asp|10886/21291|10886/21291|3629/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:800:788,12:788:27325:12:375:0,-211.506,-2350.92 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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165 NC_045512.2 11201 . A G 19964.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=744;CIGAR=1X;DP=801;DPB=801;DPRA=0;EPP=8.6608;EPPR=3.16541;GTI=0;LEN=1;MEANALT=2;MQM=52.1452;MQMR=55.5179;NS=1;NUMALT=1;ODDS=516.482;PAIRED=0.978495;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=25349;QR=1957;RO=56;RPL=371;RPP=3.02197;RPPR=4.40625;RPR=373;RUN=1;SAF=363;SAP=3.95594;SAR=381;SRF=28;SRP=3.0103;SRR=28;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10936A>G|p.Thr3646Ala|10936/21291|10936/21291|3646/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:801:56,744:56:1957:744:25349:-1998.63,-65.2713,0 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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166 NC_045512.2 11332 . A G 18029.6 . AB=0.54144;ABP=24.967;AC=1;AF=0.5;AN=2;AO=797;CIGAR=1X;DP=1472;DPB=1472;DPRA=0;EPP=11.2521;EPPR=6.73467;GTI=0;LEN=1;MEANALT=2;MQM=48.9849;MQMR=50.908;NS=1;NUMALT=1;ODDS=3264.3;PAIRED=0.991217;PAIREDR=0.991098;PAO=0;PQA=0;PQR=0;PRO=0;QA=27379;QR=23660;RO=674;RPL=287;RPP=138.5;RPPR=1116.92;RPR=510;RUN=1;SAF=397;SAP=3.03482;SAR=400;SRF=351;SRP=5.53617;SRR=323;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11067A>G|p.Val3689Val|11067/21291|11067/21291|3689/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1472:674,797:674:23660:797:27379:-1828.07,0,-1561.87 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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167 NC_045512.2 11418 . T C 1582.81 . AB=0.162816;ABP=2695.99;AC=1;AF=0.5;AN=2;AO=444;CIGAR=1X;DP=2727;DPB=2727;DPRA=0;EPP=3.08855;EPPR=9.28929;GTI=0;LEN=1;MEANALT=3;MQM=49.1554;MQMR=52.3698;NS=1;NUMALT=1;ODDS=364.456;PAIRED=0.984234;PAIREDR=0.990745;PAO=0;PQA=0;PQR=0;PRO=0;QA=15540;QR=78990;RO=2269;RPL=231;RPP=4.59489;RPPR=4.94826;RPR=213;RUN=1;SAF=227;SAP=3.49937;SAR=217;SRF=1153;SRP=4.32046;SRR=1116;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11153T>C|p.Val3718Ala|11153/21291|11153/21291|3718/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2727:2269,444:2269:78990:444:15540:-458.018,0,-6000.58 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
168 NC_045512.2 11514 . C T 1173.47 . AB=0.159434;ABP=2208.29;AC=1;AF=0.5;AN=2;AO=349;CIGAR=1X;DP=2189;DPB=2189;DPRA=0;EPP=3.01652;EPPR=3.03982;GTI=0;LEN=1;MEANALT=2;MQM=49.7536;MQMR=50.8967;NS=1;NUMALT=1;ODDS=270.201;PAIRED=0.988539;PAIREDR=0.990212;PAO=0;PQA=0;PQR=0;PRO=0;QA=12248;QR=64514;RO=1839;RPL=205;RPP=26.1623;RPPR=43.4228;RPR=144;RUN=1;SAF=175;SAP=3.01652;SAR=174;SRF=924;SRP=3.10594;SRR=915;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11249C>T|p.Thr3750Ile|11249/21291|11249/21291|3750/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2189:1839,349:1839:64514:349:12248:-369.053,0,-4782.23 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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169 NC_045512.2 11522 . T G 3.80427E-13 . AB=0.132833;ABP=2656.4;AC=1;AF=0.5;AN=2;AO=301;CIGAR=1X;DP=2266;DPB=2266;DPRA=0;EPP=3.07523;EPPR=3.19725;GTI=0;LEN=1;MEANALT=2;MQM=49.5449;MQMR=51.4249;NS=1;NUMALT=1;ODDS=255.329;PAIRED=0.993355;PAIREDR=0.987264;PAO=0;PQA=0;PQR=0;PRO=0;QA=10440;QR=68620;RO=1963;RPL=176;RPP=21.7744;RPPR=13.4185;RPR=125;RUN=1;SAF=150;SAP=3.01751;SAR=151;SRF=989;SRP=3.2592;SRR=974;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11257T>G|p.Phe3753Val|11257/21291|11257/21291|3753/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2266:1963,301:1963:68620:301:10440:-194.762,0,-5142.94 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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170 NC_045512.2 11593 . TC GA 1.75387E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=31;CIGAR=2X;DP=2530;DPB=2530;DPRA=0;EPP=3.08035;EPPR=4.33407;GTI=0;LEN=2;MEANALT=3;MQM=42.6452;MQMR=52.4405;NS=1;NUMALT=1;ODDS=3169.29;PAIRED=0.83871;PAIREDR=0.990381;PAO=0;PQA=0;PQR=0;PRO=0;QA=1093;QR=87869;RO=2495;RPL=7;RPP=23.254;RPPR=103.029;RPR=24;RUN=1;SAF=14;SAP=3.64073;SAR=17;SRF=1238;SRP=3.32449;SRR=1257;TYPE=complex;ANN=GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11328_11329delTCinsGA|p.Gln3777Lys|11328/21291|11328/21291|3776/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2530:2495,31:2495:87869:31:1093:0,-680.809,-7515.53 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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171 NC_045512.2 11952 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=40;CIGAR=1X;DP=3760;DPB=3760;DPRA=0;EPP=3.87889;EPPR=17.5825;GTI=0;LEN=1;MEANALT=1;MQM=37.075;MQMR=52.3812;NS=1;NUMALT=1;ODDS=4814.2;PAIRED=1;PAIREDR=0.988441;PAO=0;PQA=0;PQR=0;PRO=0;QA=1331;QR=131082;RO=3720;RPL=2;RPP=73.366;RPPR=302.263;RPR=38;RUN=1;SAF=20;SAP=3.0103;SAR=20;SRF=1889;SRP=4.97396;SRR=1831;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11687A>T|p.Asn3896Ile|11687/21291|11687/21291|3896/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3760:3720,40:3720:131082:40:1331:0,-1040.87,-11225.6 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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172 NC_045512.2 12165 . C T 7.43742E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=48;CIGAR=1X;DP=4731;DPB=4731;DPRA=0;EPP=3.0103;EPPR=5.62303;GTI=0;LEN=1;MEANALT=3;MQM=48.1042;MQMR=52.3067;NS=1;NUMALT=1;ODDS=5980.48;PAIRED=1;PAIREDR=0.995722;PAO=0;PQA=0;PQR=0;PRO=0;QA=1663;QR=163625;RO=4675;RPL=31;RPP=11.8771;RPPR=191.484;RPR=17;RUN=1;SAF=23;SAP=3.19126;SAR=25;SRF=2325;SRP=3.3006;SRR=2350;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11900C>T|p.Ala3967Val|11900/21291|11900/21291|3967/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4731:4675,48:4675:163625:48:1663:0,-1284.97,-13991 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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173 NC_045512.2 12395 . G A 4.42388E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=28;CIGAR=1X;DP=2722;DPB=2722;DPRA=0;EPP=3.0103;EPPR=8.70195;GTI=0;LEN=1;MEANALT=2;MQM=48.5714;MQMR=52.3105;NS=1;NUMALT=1;ODDS=3439.94;PAIRED=1;PAIREDR=0.995542;PAO=0;PQA=0;PQR=0;PRO=0;QA=1004;QR=93798;RO=2692;RPL=10;RPP=7.97367;RPPR=28.5679;RPR=18;RUN=1;SAF=14;SAP=3.0103;SAR=14;SRF=1323;SRP=4.71715;SRR=1369;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12130G>A|p.Ala4044Thr|12130/21291|12130/21291|4044/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2722:2692,28:2692:93798:28:1004:0,-736.807,-8035.4 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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174 NC_045512.2 12421 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=34;CIGAR=1X;DP=2716;DPB=2716;DPRA=0;EPP=3.0103;EPPR=7.0963;GTI=0;LEN=1;MEANALT=3;MQM=52;MQMR=51.0175;NS=1;NUMALT=1;ODDS=3350.88;PAIRED=1;PAIREDR=0.990668;PAO=0;PQA=0;PQR=0;PRO=0;QA=1216;QR=93869;RO=2679;RPL=26;RPP=23.7032;RPPR=139.93;RPR=8;RUN=1;SAF=17;SAP=3.0103;SAR=17;SRF=1326;SRP=3.60119;SRR=1353;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12156A>G|p.Ala4052Ala|12156/21291|12156/21291|4052/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2716:2679,34:2679:93869:34:1216:0,-710.041,-7872.24 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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175 NC_045512.2 12543 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=41;CIGAR=1X;DP=3019;DPB=3019;DPRA=0;EPP=3.06326;EPPR=8.53125;GTI=0;LEN=1;MEANALT=2;MQM=48.9756;MQMR=52.692;NS=1;NUMALT=1;ODDS=3704.8;PAIRED=0.95122;PAIREDR=0.993618;PAO=0;PQA=0;PQR=0;PRO=0;QA=1456;QR=104157;RO=2977;RPL=19;RPP=3.48696;RPPR=63.0916;RPR=22;RUN=1;SAF=22;SAP=3.48696;SAR=19;SRF=1517;SRP=5.38017;SRR=1460;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12278C>T|p.Ser4093Leu|12278/21291|12278/21291|4093/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3019:2977,41:2977:104157:41:1456:0,-788.671,-8910.43 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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176 NC_045512.2 13061 . G A 9.19732E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=53;CIGAR=1X;DP=3822;DPB=3822;DPRA=0;EPP=3.37904;EPPR=9.37237;GTI=0;LEN=1;MEANALT=3;MQM=49.0943;MQMR=50.8974;NS=1;NUMALT=1;ODDS=4686.48;PAIRED=1;PAIREDR=0.975817;PAO=0;PQA=0;PQR=0;PRO=0;QA=1858;QR=132219;RO=3763;RPL=45;RPP=59.0998;RPPR=63.9621;RPR=8;RUN=1;SAF=25;SAP=3.37904;SAR=28;SRF=1861;SRP=3.98034;SRR=1902;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12796G>A|p.Val4266Ile|12796/21291|12796/21291|4266/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3822:3763,53:3763:132219:53:1858:0,-995.615,-11086.3 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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177 NC_045512.2 13105 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=105;CIGAR=1X;DP=3664;DPB=3664;DPRA=0;EPP=3.03098;EPPR=4.13971;GTI=0;LEN=1;MEANALT=3;MQM=48.1048;MQMR=51.373;NS=1;NUMALT=1;ODDS=3921.12;PAIRED=0.961905;PAIREDR=0.978059;PAO=0;PQA=0;PQR=0;PRO=0;QA=3675;QR=124917;RO=3555;RPL=50;RPP=3.52732;RPPR=26.2368;RPR=55;RUN=1;SAF=51;SAP=3.19643;SAR=54;SRF=1812;SRP=5.91842;SRR=1743;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12840C>T|p.Tyr4280Tyr|12840/21291|12840/21291|4280/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3664:3555,105:3555:124917:105:3675:0,-801.229,-10358.9 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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178 NC_045512.2 13162 . TACACACACT TACACACT 0.0 . AB=0.112724;ABP=3863.02;AC=1;AF=0.5;AN=2;AO=334;CIGAR=1M2D7M;DP=2963;DPB=2897.9;DPRA=0;EPP=3.03631;EPPR=3.61938;GTI=0;LEN=2;MEANALT=21;MQM=50.9461;MQMR=53.5356;NS=1;NUMALT=1;ODDS=846.644;PAIRED=0.982036;PAIREDR=0.993844;PAO=3.5;PQA=96;PQR=96;PRO=3.5;QA=10732;QR=90583;RO=2599;RPL=178;RPP=6.15698;RPPR=30.3822;RPR=156;RUN=1;SAF=164;SAP=3.24435;SAR=170;SRF=1308;SRP=3.25176;SRR=1291;TYPE=del;ANN=TACACACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12904_12905delAC|p.Thr4302fs|12904/21291|12904/21291|4302/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2963:2599,334:2599:90583:334:10732:-71.6702,0,-7021.49 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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179 NC_045512.2 13514 . G A 4.65288E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=729;DPB=729;DPRA=0;EPP=3.0103;EPPR=3.15953;GTI=0;LEN=1;MEANALT=1;MQM=51.4375;MQMR=52.5203;NS=1;NUMALT=1;ODDS=839.999;PAIRED=1;PAIREDR=0.995792;PAO=0;PQA=0;PQR=0;PRO=0;QA=524;QR=24566;RO=713;RPL=6;RPP=5.18177;RPPR=53.6912;RPR=10;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=362;SRP=3.37881;SRR=351;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13250G>A|p.Gly4417Asp|13250/21291|13250/21291|4417/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:729:713,16:713:24566:16:524:0,-173.44,-2080.17 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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180 NC_045512.2 13617 . G A 12992.0 . AB=0.366918;ABP=288.526;AC=1;AF=0.5;AN=2;AO=681;CIGAR=1X;DP=1856;DPB=1856;DPRA=0;EPP=4.6971;EPPR=11.4063;GTI=0;LEN=1;MEANALT=3;MQM=50.1747;MQMR=49.3816;NS=1;NUMALT=1;ODDS=2991.51;PAIRED=1;PAIREDR=0.986219;PAO=0;PQA=0;PQR=0;PRO=0;QA=22360;QR=40233;RO=1161;RPL=354;RPP=5.33483;RPPR=1474.54;RPR=327;RUN=1;SAF=324;SAP=6.48274;SAR=357;SRF=609;SRP=9.08706;SRR=552;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13353G>A|p.Lys4451Lys|13353/21291|13353/21291|4451/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1856:1161,681:1161:40233:681:22360:-1335.68,0,-2783.93 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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181 NC_045512.2 13625 . ATG AG 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=1M1D1M;DP=1903;DPB=1889;DPRA=0;EPP=3.0608;EPPR=6.04849;GTI=0;LEN=1;MEANALT=2;MQM=45.0698;MQMR=49.6837;NS=1;NUMALT=1;ODDS=2220.17;PAIRED=1;PAIREDR=0.989779;PAO=0.5;PQA=16;PQR=16;PRO=0.5;QA=1368;QR=65600;RO=1859;RPL=0;RPP=96.3836;RPPR=658.308;RPR=43;RUN=1;SAF=22;SAP=3.0608;SAR=21;SRF=946;SRP=4.28235;SRR=913;TYPE=del;ANN=AG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13362delT|p.Asp4454fs|13362/21291|13362/21291|4454/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1903:1859,43:1859:65600:43:1368:0,-462.878,-5360.42 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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182 NC_045512.2 13837 . C T 1.77195E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=88;CIGAR=1X;DP=3272;DPB=3272;DPRA=0;EPP=3.0103;EPPR=10.8209;GTI=0;LEN=1;MEANALT=2;MQM=49.4205;MQMR=52.6368;NS=1;NUMALT=1;ODDS=3549.8;PAIRED=1;PAIREDR=0.994031;PAO=0;PQA=0;PQR=0;PRO=0;QA=3060;QR=110447;RO=3183;RPL=37;RPP=7.84676;RPPR=68.1483;RPR=51;RUN=1;SAF=43;SAP=3.109;SAR=45;SRF=1567;SRP=4.64828;SRR=1616;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13573C>T|p.His4525Tyr|13573/21291|13573/21291|4525/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3272:3183,88:3183:110447:88:3060:0,-725.794,-9296.11 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
183 NC_045512.2 13884 . ATA AA 5.23755E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=38;CIGAR=1M1D1M;DP=3158;DPB=3145.33;DPRA=0;EPP=3.23888;EPPR=12.2236;GTI=0;LEN=1;MEANALT=3;MQM=39.8947;MQMR=52.8608;NS=1;NUMALT=1;ODDS=3980.02;PAIRED=1;PAIREDR=0.994867;PAO=0;PQA=0;PQR=0;PRO=0;QA=1235;QR=110028;RO=3117;RPL=35;RPP=61.5258;RPPR=7.35812;RPR=3;RUN=1;SAF=17;SAP=3.9246;SAR=21;SRF=1529;SRP=5.43535;SRR=1588;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13621delT|p.Tyr4541fs|13621/21291|13621/21291|4541/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3158:3117,38:3117:110028:38:1235:0,-855.492,-9476.37 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
184 NC_045512.2 13948 . G T 2626.9 . AB=0.192751;ABP=1925.83;AC=1;AF=0.5;AN=2;AO=452;CIGAR=1X;DP=2345;DPB=2345;DPRA=0;EPP=6.77675;EPPR=40.6702;GTI=0;LEN=1;MEANALT=2;MQM=48.3606;MQMR=50.5876;NS=1;NUMALT=1;ODDS=604.866;PAIRED=1;PAIREDR=0.993118;PAO=0;PQA=0;PQR=0;PRO=0;QA=15755;QR=66219;RO=1889;RPL=442;RPP=899.579;RPPR=13.3849;RPR=10;RUN=1;SAF=212;SAP=6.77675;SAR=240;SRF=915;SRP=7.01183;SRR=974;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13684G>T|p.Asp4562Tyr|13684/21291|13684/21291|4562/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2345:1889,452:1889:66219:452:15755:-591.959,0,-4884.54 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
185 NC_045512.2 14343 . T C 2.52654E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=243;CIGAR=1X;DP=3163;DPB=3163;DPRA=0;EPP=3.01924;EPPR=13.9019;GTI=0;LEN=1;MEANALT=2;MQM=48.0741;MQMR=53.283;NS=1;NUMALT=1;ODDS=1944.19;PAIRED=0.987654;PAIREDR=0.994176;PAO=0;PQA=0;PQR=0;PRO=0;QA=8382;QR=101644;RO=2919;RPL=136;RPP=10.5256;RPPR=4.51672;RPR=107;RUN=1;SAF=124;SAP=3.2337;SAR=119;SRF=1486;SRP=5.09994;SRR=1433;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14079T>C|p.Cys4693Cys|14079/21291|14079/21291|4693/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3163:2919,243:2919:101644:243:8382:0,-256.43,-8135.24 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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186 NC_045512.2 14408 . C T 85570.9 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2863;CIGAR=1X;DP=2866;DPB=2866;DPRA=0;EPP=6.02063;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=51.4149;MQMR=52;NS=1;NUMALT=1;ODDS=3935.49;PAIRED=0.991966;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=100761;QR=108;RO=3;RPL=1519;RPP=26.2382;RPPR=3.73412;RPR=1344;RUN=1;SAF=1438;SAP=3.13848;SAR=1425;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14144C>T|p.Pro4715Leu|14144/21291|14144/21291|4715/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:2866:3,2863:3:108:2863:100761:-8563.93,-852.723,0 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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187 NC_045512.2 14599 . C T 10548.1 . AB=0.325339;ABP=511.234;AC=1;AF=0.5;AN=2;AO=624;CIGAR=1X;DP=1918;DPB=1918;DPRA=0;EPP=4.1378;EPPR=15.144;GTI=0;LEN=1;MEANALT=2;MQM=45.7196;MQMR=51.9281;NS=1;NUMALT=1;ODDS=2428.8;PAIRED=0.983974;PAIREDR=0.992266;PAO=0;PQA=0;PQR=0;PRO=0;QA=22070;QR=44878;RO=1293;RPL=147;RPP=381.974;RPPR=21.5258;RPR=477;RUN=1;SAF=324;SAP=5.01474;SAR=300;SRF=649;SRP=3.05229;SRR=644;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14335C>T|p.Leu4779Leu|14335/21291|14335/21291|4779/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1918:1293,624:1293:44878:624:22070:-1154.93,0,-3270.18 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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188 NC_045512.2 14676 . C T 4.51306E-13 . AB=0.129404;ABP=3423.16;AC=1;AF=0.5;AN=2;AO=371;CIGAR=1X;DP=2867;DPB=2867;DPRA=0;EPP=3.06298;EPPR=4.0168;GTI=0;LEN=1;MEANALT=3;MQM=50.1213;MQMR=52.666;NS=1;NUMALT=1;ODDS=370.612;PAIRED=0.994609;PAIREDR=0.989575;PAO=0;PQA=0;PQR=0;PRO=0;QA=13140;QR=85679;RO=2494;RPL=194;RPP=4.70182;RPPR=46.6975;RPR=177;RUN=1;SAF=190;SAP=3.4844;SAR=181;SRF=1273;SRP=5.36461;SRR=1221;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14412C>T|p.Pro4804Pro|14412/21291|14412/21291|4804/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2867:2494,371:2494:85679:371:13140:-229.956,0,-6526.74 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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189 NC_045512.2 14925 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=1720;DPB=1720;DPRA=0;EPP=3.52123;EPPR=14.8804;GTI=0;LEN=1;MEANALT=2;MQM=52.1912;MQMR=50.3628;NS=1;NUMALT=1;ODDS=1662.43;PAIRED=1;PAIREDR=0.992126;PAO=0;PQA=0;PQR=0;PRO=0;QA=2343;QR=57307;RO=1651;RPL=10;RPP=76.5849;RPPR=99.6033;RPR=58;RUN=1;SAF=36;SAP=3.52123;SAR=32;SRF=819;SRP=3.23258;SRR=832;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14661C>T|p.Val4887Val|14661/21291|14661/21291|4887/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1720:1651,68:1651:57307:68:2343:0,-314.394,-4648.27 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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190 NC_045512.2 14960 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=42;CIGAR=1X;DP=1845;DPB=1845;DPRA=0;EPP=3.0103;EPPR=4.84214;GTI=0;LEN=1;MEANALT=1;MQM=49.7381;MQMR=51.802;NS=1;NUMALT=1;ODDS=2084.32;PAIRED=1;PAIREDR=0.988353;PAO=0;PQA=0;PQR=0;PRO=0;QA=1500;QR=63751;RO=1803;RPL=16;RPP=8.18047;RPPR=133.372;RPR=26;RUN=1;SAF=21;SAP=3.0103;SAR=21;SRF=915;SRP=3.88828;SRR=888;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14696A>T|p.Asn4899Ile|14696/21291|14696/21291|4899/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1845:1803,42:1803:63751:42:1500:0,-430.383,-5341.54 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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191 NC_045512.2 15081 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=19;CIGAR=1X;DP=1823;DPB=1823;DPRA=0;EPP=3.12459;EPPR=3.49285;GTI=0;LEN=1;MEANALT=3;MQM=48.7368;MQMR=52.8733;NS=1;NUMALT=1;ODDS=2311.42;PAIRED=1;PAIREDR=0.986667;PAO=0;PQA=0;PQR=0;PRO=0;QA=628;QR=61997;RO=1800;RPL=12;RPP=5.8675;RPPR=27.3356;RPR=7;RUN=1;SAF=10;SAP=3.12459;SAR=9;SRF=897;SRP=3.05373;SRR=903;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14817C>A|p.Ala4939Ala|14817/21291|14817/21291|4939/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1823:1800,19:1800:61997:19:628:0,-496.547,-5321.06 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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192 NC_045512.2 15099 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1724;DPB=1724;DPRA=0;EPP=3.0103;EPPR=3.87276;GTI=0;LEN=1;MEANALT=2;MQM=54.1;MQMR=53.9871;NS=1;NUMALT=1;ODDS=2154.41;PAIRED=1;PAIREDR=0.9953;PAO=0;PQA=0;PQR=0;PRO=0;QA=661;QR=57848;RO=1702;RPL=8;RPP=4.74748;RPPR=3.03071;RPR=12;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=831;SRP=5.05164;SRR=871;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14835A>G|p.Arg4945Arg|14835/21291|14835/21291|4945/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1724:1702,20:1702:57848:20:661:0,-459.131,-5019.76 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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193 NC_045512.2 15112 . G A 2.45301E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=22;CIGAR=1X;DP=1742;DPB=1742;DPRA=0;EPP=3.0103;EPPR=7.71074;GTI=0;LEN=1;MEANALT=2;MQM=51.5;MQMR=53.8941;NS=1;NUMALT=1;ODDS=2148.09;PAIRED=1;PAIREDR=0.993601;PAO=0;PQA=0;PQR=0;PRO=0;QA=784;QR=59941;RO=1719;RPL=12;RPP=3.40511;RPPR=4.73965;RPR=10;RUN=1;SAF=11;SAP=3.0103;SAR=11;SRF=842;SRP=4.55774;SRR=877;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14848G>A|p.Ala4950Thr|14848/21291|14848/21291|4950/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1742:1719,22:1719:59941:22:784:0,-454.638,-5189.54 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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194 NC_045512.2 15279 . C T 15999.3 . AB=0.501107;ABP=3.02472;AC=1;AF=0.5;AN=2;AO=679;CIGAR=1X;DP=1355;DPB=1355;DPRA=0;EPP=3.72986;EPPR=5.54368;GTI=0;LEN=1;MEANALT=3;MQM=50.6848;MQMR=52.4911;NS=1;NUMALT=1;ODDS=3683.98;PAIRED=0.997054;PAIREDR=0.997024;PAO=0;PQA=0;PQR=0;PRO=0;QA=23811;QR=23325;RO=672;RPL=353;RPP=5.34167;RPPR=13.1438;RPR=326;RUN=1;SAF=347;SAP=3.72986;SAR=332;SRF=340;SRP=3.21711;SRR=332;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15015C>T|p.His5005His|15015/21291|15015/21291|5005/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1355:672,679:672:23325:679:23811:-1608.52,0,-1621.57 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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195 NC_045512.2 15451 . G A 8929.57 . AB=0.4;ABP=95.515;AC=1;AF=0.5;AN=2;AO=426;CIGAR=1X;DP=1065;DPB=1065;DPRA=0;EPP=3.52004;EPPR=4.50892;GTI=0;LEN=1;MEANALT=1;MQM=48.9977;MQMR=53.4648;NS=1;NUMALT=1;ODDS=2056.11;PAIRED=0.985915;PAIREDR=0.984351;PAO=0;PQA=0;PQR=0;PRO=0;QA=15055;QR=22076;RO=639;RPL=213;RPP=3.0103;RPPR=25.3061;RPR=213;RUN=1;SAF=209;SAP=3.33653;SAR=217;SRF=315;SRP=3.28556;SRR=324;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15187G>A|p.Gly5063Ser|15187/21291|15187/21291|5063/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1065:639,426:639:22076:426:15055:-910.196,0,-1597.03 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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196 NC_045512.2 15610 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=61;CIGAR=1X;DP=2649;DPB=2649;DPRA=0;EPP=3.0459;EPPR=3.03128;GTI=0;LEN=1;MEANALT=2;MQM=49.2623;MQMR=53.041;NS=1;NUMALT=1;ODDS=2973.3;PAIRED=1;PAIREDR=0.993815;PAO=0;PQA=0;PQR=0;PRO=0;QA=2160;QR=90654;RO=2587;RPL=26;RPP=5.89373;RPPR=286.352;RPR=35;RUN=1;SAF=31;SAP=3.0459;SAR=30;SRF=1324;SRP=6.13363;SRR=1263;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15346C>T|p.Gln5116*|15346/21291|15346/21291|5116/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2649:2587,61:2587:90654:61:2160:0,-613.681,-7700.41 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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197 NC_045512.2 15682 . TATT AATA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=62;CIGAR=1X2M1X;DP=3135;DPB=3136;DPRA=0;EPP=3.15039;EPPR=3.32274;GTI=0;LEN=4;MEANALT=6;MQM=44.4677;MQMR=52.7775;NS=1;NUMALT=1;ODDS=3669.8;PAIRED=0.903226;PAIREDR=0.995432;PAO=3;PQA=100;PQR=0;PRO=1;QA=2133;QR=107768;RO=3065;RPL=25;RPP=8.05372;RPPR=14.0802;RPR=37;RUN=1;SAF=31;SAP=3.0103;SAR=31;SRF=1555;SRP=4.44496;SRR=1510;TYPE=complex;ANN=AATA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15418_15421delTATTinsAATA|p.TyrLeu5140AsnMet|15418/21291|15418/21291|5140/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3135:3065,62:3065:107768:62:2133:0,-777.887,-9178.74 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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198 NC_045512.2 15765 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=29;CIGAR=1X;DP=2620;DPB=2620;DPRA=0;EPP=3.08518;EPPR=7.23508;GTI=0;LEN=1;MEANALT=1;MQM=53.8621;MQMR=53.0471;NS=1;NUMALT=1;ODDS=3289.28;PAIRED=1;PAIREDR=0.990351;PAO=0;PQA=0;PQR=0;PRO=0;QA=963;QR=91316;RO=2591;RPL=13;RPP=3.68421;RPPR=13.7118;RPR=16;RUN=1;SAF=14;SAP=3.08518;SAR=15;SRF=1248;SRP=10.574;SRR=1343;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15501A>G|p.Leu5167Leu|15501/21291|15501/21291|5167/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2620:2591,29:2591:91316:29:963:0,-703.357,-7841.25 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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199 NC_045512.2 15924 . C T 6.44918E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=37;CIGAR=1X;DP=3061;DPB=3061;DPRA=0;EPP=3.06899;EPPR=5.95155;GTI=0;LEN=1;MEANALT=1;MQM=41.2703;MQMR=52.1574;NS=1;NUMALT=1;ODDS=3840.84;PAIRED=0.972973;PAIREDR=0.98578;PAO=0;PQA=0;PQR=0;PRO=0;QA=1310;QR=105103;RO=3024;RPL=10;RPP=19.9713;RPPR=26.2761;RPR=27;RUN=1;SAF=18;SAP=3.06899;SAR=19;SRF=1538;SRP=4.95199;SRR=1486;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15660C>T|p.Tyr5220Tyr|15660/21291|15660/21291|5220/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3061:3024,37:3024:105103:37:1310:0,-825.97,-8954.61 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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200 NC_045512.2 16047 . T C 7.54104E-13 . AB=0.115049;ABP=4578.78;AC=1;AF=0.5;AN=2;AO=409;CIGAR=1X;DP=3555;DPB=3555;DPRA=0;EPP=3.27045;EPPR=3.01306;GTI=0;LEN=1;MEANALT=2;MQM=49.6186;MQMR=53.0083;NS=1;NUMALT=1;ODDS=928.295;PAIRED=0.99511;PAIREDR=0.992048;PAO=0;PQA=0;PQR=0;PRO=0;QA=14401;QR=109684;RO=3144;RPL=183;RPP=12.8271;RPPR=10.4806;RPR=226;RUN=1;SAF=206;SAP=3.05808;SAR=203;SRF=1597;SRP=4.73698;SRR=1547;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15783T>C|p.Leu5261Leu|15783/21291|15783/21291|5261/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3555:3144,409:3144:109684:409:14401:-124.324,0,-8453.5 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
201 NC_045512.2 16176 . T C 0.0 . AB=0.113668;ABP=2820.07;AC=1;AF=0.5;AN=2;AO=247;CIGAR=1X;DP=2173;DPB=2173;DPRA=0;EPP=4.49604;EPPR=9.35551;GTI=0;LEN=1;MEANALT=2;MQM=45.5789;MQMR=50.2919;NS=1;NUMALT=1;ODDS=754.39;PAIRED=0.991903;PAIREDR=0.987532;PAO=0;PQA=0;PQR=0;PRO=0;QA=8569;QR=68076;RO=1925;RPL=193;RPP=172.869;RPPR=930.989;RPR=54;RUN=1;SAF=119;SAP=3.7224;SAR=128;SRF=944;SRP=4.55458;SRR=981;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15912T>C|p.Thr5304Thr|15912/21291|15912/21291|5304/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2173:1925,247:1925:68076:247:8569:-17.686,0,-5092.92 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
202 NC_045512.2 16466 . C T 43588.1 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1613;CIGAR=1X;DP=1646;DPB=1646;DPRA=0;EPP=5.98413;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=46.0539;MQMR=52.5455;NS=1;NUMALT=1;ODDS=1904.12;PAIRED=0.989461;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=56743;QR=1140;RO=33;RPL=677;RPP=93.3169;RPPR=22.0271;RPR=936;RUN=1;SAF=821;SAP=4.14248;SAR=792;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16202C>T|p.Pro5401Leu|16202/21291|16202/21291|5401/7096|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:1646:33,1613:33:1140:1613:56743:-4368.86,-393.99,0 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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203 NC_045512.2 16816 . C T 4316.69 . AB=0.255301;ABP=616.196;AC=1;AF=0.5;AN=2;AO=301;CIGAR=1X;DP=1179;DPB=1179;DPRA=0;EPP=3.19065;EPPR=6.96743;GTI=0;LEN=1;MEANALT=1;MQM=47.6346;MQMR=51.0182;NS=1;NUMALT=1;ODDS=993.955;PAIRED=1;PAIREDR=0.989749;PAO=0;PQA=0;PQR=0;PRO=0;QA=10614;QR=30734;RO=878;RPL=107;RPP=57.6145;RPPR=418.756;RPR=194;RUN=1;SAF=154;SAP=3.3638;SAR=147;SRF=427;SRP=4.43486;SRR=451;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16552C>T|p.Gln5518*|16552/21291|16552/21291|5518/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1179:878,301:878:30734:301:10614:-508.866,0,-2253.86 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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204 NC_045512.2 17218 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=35;CIGAR=1X;DP=2615;DPB=2615;DPRA=0;EPP=3.07234;EPPR=4.04173;GTI=0;LEN=1;MEANALT=2;MQM=53.2286;MQMR=53.1377;NS=1;NUMALT=1;ODDS=3202.13;PAIRED=1;PAIREDR=0.993796;PAO=0;PQA=0;PQR=0;PRO=0;QA=1252;QR=91012;RO=2579;RPL=12;RPP=10.5174;RPPR=149.422;RPR=23;RUN=1;SAF=18;SAP=3.07234;SAR=17;SRF=1302;SRP=3.53654;SRR=1277;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16954G>C|p.Asp5652His|16954/21291|16954/21291|5652/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2615:2579,35:2579:91012:35:1252:0,-677.895,-7808.81 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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205 NC_045512.2 17814 . G A 1651.02 . AB=0.17202;ABP=1312.03;AC=1;AF=0.5;AN=2;AO=241;CIGAR=1X;DP=1401;DPB=1401;DPRA=0;EPP=3.09139;EPPR=3.13031;GTI=0;LEN=1;MEANALT=2;MQM=51.8548;MQMR=52.8454;NS=1;NUMALT=1;ODDS=380.16;PAIRED=0.983402;PAIREDR=0.992228;PAO=0;PQA=0;PQR=0;PRO=0;QA=8561;QR=40234;RO=1158;RPL=118;RPP=3.23556;RPPR=37.6939;RPR=123;RUN=1;SAF=120;SAP=3.01931;SAR=121;SRF=590;SRP=3.91789;SRR=568;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17550G>A|p.Leu5850Leu|17550/21291|17550/21291|5850/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1401:1158,241:1158:40234:241:8561:-314.533,0,-3073.09 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
206 NC_045512.2 18564 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=26;CIGAR=1X;DP=2012;DPB=2012;DPRA=0;EPP=3.0103;EPPR=4.27426;GTI=0;LEN=1;MEANALT=1;MQM=38.3077;MQMR=52.5287;NS=1;NUMALT=1;ODDS=2535.91;PAIRED=1;PAIREDR=0.984894;PAO=0;PQA=0;PQR=0;PRO=0;QA=919;QR=69984;RO=1986;RPL=0;RPP=59.4686;RPPR=40.0281;RPR=26;RUN=1;SAF=13;SAP=3.0103;SAR=13;SRF=971;SRP=5.1271;SRR=1015;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18300A>C|p.Lys6100Asn|18300/21291|18300/21291|6100/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2012:1986,26:1986:69984:26:919:0,-543.43,-5961.14 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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207 NC_045512.2 18585 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=34;CIGAR=1X;DP=1713;DPB=1713;DPRA=0;EPP=12.2071;EPPR=3.19799;GTI=0;LEN=1;MEANALT=3;MQM=54.7647;MQMR=52.0816;NS=1;NUMALT=1;ODDS=2102.51;PAIRED=1;PAIREDR=0.991597;PAO=0;PQA=0;PQR=0;PRO=0;QA=599;QR=49685;RO=1666;RPL=24;RPP=15.5282;RPPR=146.677;RPR=10;RUN=1;SAF=33;SAP=68.4099;SAR=1;SRF=784;SRP=15.5282;SRR=882;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18321A>G|p.Val6107Val|18321/21291|18321/21291|6107/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1713:1666,34:1666:49685:34:599:0,-457.977,-4212.18 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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208 NC_045512.2 18589 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=1666;DPB=1666;DPRA=0;EPP=28.0461;EPPR=3.12058;GTI=0;LEN=1;MEANALT=3;MQM=54.6029;MQMR=51.9078;NS=1;NUMALT=1;ODDS=1835.86;PAIRED=1;PAIREDR=0.992476;PAO=0;PQA=0;PQR=0;PRO=0;QA=1260;QR=50241;RO=1595;RPL=48;RPP=28.0461;RPPR=206.91;RPR=20;RUN=1;SAF=68;SAP=150.67;SAR=0;SRF=729;SRP=28.5629;SRR=866;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18325G>T|p.Val6109Phe|18325/21291|18325/21291|6109/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1666:1595,68:1595:50241:68:1260:0,-389.132,-4187.65 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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209 NC_045512.2 18591 . C A,G 0.0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=22,53;CIGAR=1X,1X;DP=1626;DPB=1626;DPRA=0,0;EPP=17.2236,21.0786;EPPR=5.84906;GTI=0;LEN=1,1;MEANALT=3,3;MQM=52.2273,56;MQMR=51.7076;NS=1;NUMALT=2;ODDS=1862.57;PAIRED=0.909091,1;PAIREDR=0.993544;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=349,899;QR=45627;RO=1549;RPL=16,37;RPP=12.8806,21.0786;RPPR=195.963;RPR=6,16;RUN=1,1;SAF=21,53;SAP=42.4916,118.098;SAR=1,0;SRF=701;SRP=33.303;SRR=848;TYPE=snp,snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18327C>A|p.Val6109Val|18327/21291|18327/21291|6109/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1626:1549,22,53:1549:45627:22,53:349,899:0,-442.675,-3865.33,-402.972,-3808.63,-3816.3 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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210 NC_045512.2 18596 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=1X;DP=1560;DPB=1560;DPRA=0;EPP=37.7539;EPPR=7.02588;GTI=0;LEN=1;MEANALT=3;MQM=54.8611;MQMR=51.6866;NS=1;NUMALT=1;ODDS=1910.29;PAIRED=1;PAIREDR=0.994733;PAO=0;PQA=0;PQR=0;PRO=0;QA=597;QR=47340;RO=1519;RPL=30;RPP=37.7539;RPPR=206.189;RPR=6;RUN=1;SAF=34;SAP=64.7766;SAR=2;SRF=706;SRP=19.3771;SRR=813;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18332G>T|p.Trp6111Leu|18332/21291|18332/21291|6111/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1560:1519,36:1519:47340:36:597:0,-415.548,-3982.11 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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211 NC_045512.2 18607 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=37;CIGAR=1X;DP=2032;DPB=2032;DPRA=0;EPP=45.7942;EPPR=35.685;GTI=0;LEN=1;MEANALT=2;MQM=52.7297;MQMR=50.0191;NS=1;NUMALT=1;ODDS=2562.27;PAIRED=1;PAIREDR=0.993967;PAO=0;PQA=0;PQR=0;PRO=0;QA=596;QR=62548;RO=1989;RPL=33;RPP=52.3673;RPPR=39.5716;RPR=4;RUN=1;SAF=36;SAP=74.9036;SAR=1;SRF=984;SRP=3.49176;SRR=1005;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18343T>G|p.Phe6115Val|18343/21291|18343/21291|6115/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2032:1989,37:1989:62548:37:596:0,-558.569,-5124.76 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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212 NC_045512.2 18634 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=30;CIGAR=1X;DP=2484;DPB=2484;DPRA=0;EPP=68.1545;EPPR=20.1139;GTI=0;LEN=1;MEANALT=2;MQM=55.0333;MQMR=49.1239;NS=1;NUMALT=1;ODDS=3237.29;PAIRED=1;PAIREDR=0.991031;PAO=0;PQA=0;PQR=0;PRO=0;QA=541;QR=83732;RO=2453;RPL=30;RPP=68.1545;RPPR=122.241;RPR=0;RUN=1;SAF=30;SAP=68.1545;SAR=0;SRF=1223;SRP=3.05368;SRR=1230;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18370G>T|p.Val6124Leu|18370/21291|18370/21291|6124/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2484:2453,30:2453:83732:30:541:0,-698.736,-6808.01 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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213 NC_045512.2 18977 . A G 0.0 . AB=0.128648;ABP=4723.57;AC=1;AF=0.5;AN=2;AO=507;CIGAR=1X;DP=3941;DPB=3941;DPRA=0;EPP=3.97397;EPPR=3.34491;GTI=0;LEN=1;MEANALT=2;MQM=47.2308;MQMR=50.4512;NS=1;NUMALT=1;ODDS=685.817;PAIRED=1;PAIREDR=0.993009;PAO=0;PQA=0;PQR=0;PRO=0;QA=17828;QR=120870;RO=3433;RPL=192;RPP=67.8076;RPPR=178.682;RPR=315;RUN=1;SAF=262;SAP=4.24808;SAR=245;SRF=1718;SRP=3.01599;SRR=1715;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18713A>G|p.Gln6238Arg|18713/21291|18713/21291|6238/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3941:3433,507:3433:120870:507:17828:-246.189,0,-8997.03 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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214 NC_045512.2 19132 . G T 1.25365E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=135;CIGAR=1X;DP=5691;DPB=5691;DPRA=0;EPP=3.02638;EPPR=3.2745;GTI=0;LEN=1;MEANALT=1;MQM=46.3778;MQMR=52.194;NS=1;NUMALT=1;ODDS=6443.64;PAIRED=0.97037;PAIREDR=0.991901;PAO=0;PQA=0;PQR=0;PRO=0;QA=4554;QR=195166;RO=5556;RPL=89;RPP=32.7514;RPPR=54.7942;RPR=46;RUN=1;SAF=64;SAP=3.79846;SAR=71;SRF=2759;SRP=3.57466;SRR=2797;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18868G>T|p.Glu6290*|18868/21291|18868/21291|6290/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5691:5556,135:5556:195166:135:4554:0,-1352.52,-16428.1 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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215 NC_045512.2 19137 . A C 2.02509E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=114;CIGAR=1X;DP=5642;DPB=5642;DPRA=0;EPP=3.08649;EPPR=3.18362;GTI=0;LEN=1;MEANALT=3;MQM=44.7807;MQMR=52.2286;NS=1;NUMALT=1;ODDS=6562.91;PAIRED=0.964912;PAIREDR=0.991855;PAO=0;PQA=0;PQR=0;PRO=0;QA=3986;QR=194895;RO=5525;RPL=72;RPP=20.1535;RPPR=6.40959;RPR=42;RUN=1;SAF=56;SAP=3.08649;SAR=58;SRF=2750;SRP=3.25594;SRR=2775;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18873A>C|p.Leu6291Phe|18873/21291|18873/21291|6291/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5642:5525,114:5525:194895:114:3986:0,-1386.34,-16434.9 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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216 NC_045512.2 19165 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=172;CIGAR=1X;DP=5857;DPB=5857;DPRA=0;EPP=3.81829;EPPR=8.06357;GTI=0;LEN=1;MEANALT=2;MQM=50.7733;MQMR=52.3231;NS=1;NUMALT=1;ODDS=6177.91;PAIRED=1;PAIREDR=0.993665;PAO=0;PQA=0;PQR=0;PRO=0;QA=6042;QR=200372;RO=5683;RPL=91;RPP=4.27278;RPPR=7.55003;RPR=81;RUN=1;SAF=83;SAP=3.46479;SAR=89;SRF=2791;SRP=6.9081;SRR=2892;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18901A>G|p.Lys6301Glu|18901/21291|18901/21291|6301/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5857:5683,172:5683:200372:172:6042:0,-1250.18,-16760.4 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
217 NC_045512.2 19220 . C T 83946.5 . AB=0.650573;ABP=1067.61;AC=1;AF=0.5;AN=2;AO=3517;CIGAR=1X;DP=5406;DPB=5406;DPRA=0;EPP=3.08501;EPPR=3.47085;GTI=0;LEN=1;MEANALT=3;MQM=48.9795;MQMR=51.3181;NS=1;NUMALT=1;ODDS=8974.42;PAIRED=0.997157;PAIREDR=0.993107;PAO=0;PQA=0;PQR=0;PRO=0;QA=123592;QR=66525;RO=1886;RPL=1966;RPP=109.346;RPPR=12.3363;RPR=1551;RUN=1;SAF=1746;SAP=3.39619;SAR=1771;SRF=945;SRP=3.02872;SRR=941;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18956C>T|p.Ala6319Val|18956/21291|18956/21291|6319/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:5406:1886,3517:1886:66525:3517:123592:-8523.51,0,-4016.27 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
218 NC_045512.2 19245 . C T 7.03964E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=399;CIGAR=1X;DP=5068;DPB=5068;DPRA=0;EPP=3.27697;EPPR=11.8692;GTI=0;LEN=1;MEANALT=2;MQM=46.4637;MQMR=49.5467;NS=1;NUMALT=1;ODDS=3051.2;PAIRED=1;PAIREDR=0.995073;PAO=0;PQA=0;PQR=0;PRO=0;QA=14080;QR=164853;RO=4668;RPL=190;RPP=4.97497;RPPR=471.922;RPR=209;RUN=1;SAF=204;SAP=3.45113;SAR=195;SRF=2293;SRP=6.13819;SRR=2375;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18981C>T|p.Asp6327Asp|18981/21291|18981/21291|6327/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5068:4668,399:4668:164853:399:14080:0,-398.339,-12557.8 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
219 NC_045512.2 19333 . G T 18125.6 . AB=0.270052;ABP=1875.49;AC=1;AF=0.5;AN=2;AO=1101;CIGAR=1X;DP=4077;DPB=4077;DPRA=0;EPP=4.05363;EPPR=4.17776;GTI=0;LEN=1;MEANALT=1;MQM=51.0427;MQMR=53.038;NS=1;NUMALT=1;ODDS=4173.56;PAIRED=0.998183;PAIREDR=0.996304;PAO=0;PQA=0;PQR=0;PRO=0;QA=38316;QR=104017;RO=2976;RPL=524;RPP=8.55041;RPPR=31.6159;RPR=577;RUN=1;SAF=565;SAP=4.66898;SAR=536;SRF=1491;SRP=3.03657;SRR=1485;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19069G>T|p.Asp6357Tyr|19069/21291|19069/21291|6357/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4077:2976,1101:2976:104017:1101:38316:-2016.57,0,-7824.46 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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220 NC_045512.2 19452 . T A 3.9056E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=42;CIGAR=1X;DP=3420;DPB=3420;DPRA=0;EPP=3.0103;EPPR=5.3286;GTI=0;LEN=1;MEANALT=2;MQM=47.9048;MQMR=52.6652;NS=1;NUMALT=1;ODDS=4274.34;PAIRED=0.952381;PAIREDR=0.993179;PAO=0;PQA=0;PQR=0;PRO=0;QA=1464;QR=116982;RO=3372;RPL=42;RPP=94.2121;RPPR=206.405;RPR=0;RUN=1;SAF=21;SAP=3.0103;SAR=21;SRF=1689;SRP=3.03348;SRR=1683;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19188T>A|p.Ala6396Ala|19188/21291|19188/21291|6396/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3420:3372,42:3372:116982:42:1464:0,-909.276,-9987.69 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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221 NC_045512.2 19751 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=917;DPB=917;DPRA=0;EPP=3.0103;EPPR=3.09677;GTI=0;LEN=1;MEANALT=2;MQM=40.5833;MQMR=53.469;NS=1;NUMALT=1;ODDS=1151.16;PAIRED=0.833333;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=424;QR=32022;RO=904;RPL=0;RPP=29.068;RPPR=3.3562;RPR=12;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=445;SRP=3.48111;SRR=459;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19487A>T|p.Glu6496Val|19487/21291|19487/21291|6496/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:917:904,12:904:32022:12:424:0,-244.122,-2771.61 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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222 NC_045512.2 19887 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=33;CIGAR=1X;DP=1166;DPB=1166;DPRA=0;EPP=3.0761;EPPR=3.56419;GTI=0;LEN=1;MEANALT=1;MQM=43.4242;MQMR=51.2604;NS=1;NUMALT=1;ODDS=1295.27;PAIRED=1;PAIREDR=0.993822;PAO=0;PQA=0;PQR=0;PRO=0;QA=1115;QR=39736;RO=1133;RPL=27;RPP=32.0291;RPPR=52.6897;RPR=6;RUN=1;SAF=16;SAP=3.0761;SAR=17;SRF=563;SRP=3.10421;SRR=570;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19623A>G|p.Lys6541Lys|19623/21291|19623/21291|6541/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1166:1133,33:1133:39736:33:1115:0,-267.97,-3332.94 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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223 NC_045512.2 19895 . C T 2.14568E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=18;CIGAR=1X;DP=1174;DPB=1174;DPRA=0;EPP=3.0103;EPPR=3.689;GTI=0;LEN=1;MEANALT=2;MQM=43.0556;MQMR=51.1619;NS=1;NUMALT=1;ODDS=1425.78;PAIRED=1;PAIREDR=0.995671;PAO=0;PQA=0;PQR=0;PRO=0;QA=648;QR=40523;RO=1155;RPL=10;RPP=3.49285;RPPR=8.69749;RPR=8;RUN=1;SAF=9;SAP=3.0103;SAR=9;SRF=579;SRP=3.02722;SRR=576;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19631C>T|p.Ala6544Val|19631/21291|19631/21291|6544/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1174:1155,18:1155:40523:18:648:0,-301.243,-3421.08 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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224 NC_045512.2 19983 . CTTTTTTGA CTTTTTGA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=24;CIGAR=1M1D7M;DP=941;DPB=938.667;DPRA=0;EPP=3.0103;EPPR=3.12892;GTI=0;LEN=1;MEANALT=11;MQM=48.125;MQMR=53.5095;NS=1;NUMALT=1;ODDS=1022.39;PAIRED=1;PAIREDR=0.994426;PAO=0.5;PQA=7;PQR=7;PRO=0.5;QA=783;QR=31500;RO=897;RPL=18;RPP=16.0391;RPPR=3.88421;RPR=6;RUN=1;SAF=12;SAP=3.0103;SAR=12;SRF=461;SRP=4.52331;SRR=436;TYPE=del;ANN=CTTTTTGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19725delT|p.Phe6575fs|19725/21291|19725/21291|6575/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:941:897,24:897:31500:24:783:0,-208.308,-2690.68 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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225 NC_045512.2 20088 . T C 5.90698E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=10;CIGAR=1X;DP=976;DPB=976;DPRA=0;EPP=3.0103;EPPR=3.09122;GTI=0;LEN=1;MEANALT=1;MQM=37.6;MQMR=52.7764;NS=1;NUMALT=1;ODDS=1253.65;PAIRED=1;PAIREDR=0.995859;PAO=0;PQA=0;PQR=0;PRO=0;QA=352;QR=33724;RO=966;RPL=10;RPP=24.725;RPPR=10.0597;RPR=0;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=489;SRP=3.334;SRR=477;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19824T>C|p.Gly6608Gly|19824/21291|19824/21291|6608/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:976:966,10:966:33724:10:352:0,-267.733,-2905.83 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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226 NC_045512.2 20633 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=166;CIGAR=1X;DP=2089;DPB=2089;DPRA=0;EPP=4.31842;EPPR=3.71606;GTI=0;LEN=1;MEANALT=1;MQM=48.7711;MQMR=53.5315;NS=1;NUMALT=1;ODDS=1244.15;PAIRED=1;PAIREDR=0.9948;PAO=0;PQA=0;PQR=0;PRO=0;QA=5737;QR=67701;RO=1923;RPL=103;RPP=23.9402;RPPR=24.2045;RPR=63;RUN=1;SAF=81;SAP=3.2196;SAR=85;SRF=961;SRP=3.01143;SRR=962;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20369T>C|p.Val6790Ala|20369/21291|20369/21291|6790/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2089:1923,166:1923:67701:166:5737:0,-153.829,-5451.28 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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227 NC_045512.2 20686 . G A 4.91807E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=1X;DP=1937;DPB=1937;DPRA=0;EPP=3.0103;EPPR=3.06627;GTI=0;LEN=1;MEANALT=1;MQM=47.8333;MQMR=53.9274;NS=1;NUMALT=1;ODDS=2289.62;PAIRED=1;PAIREDR=0.99474;PAO=0;PQA=0;PQR=0;PRO=0;QA=1232;QR=66116;RO=1901;RPL=12;RPP=11.6962;RPPR=11.6562;RPR=24;RUN=1;SAF=18;SAP=3.0103;SAR=18;SRF=941;SRP=3.42266;SRR=960;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20422G>A|p.Ala6808Thr|20422/21291|20422/21291|6808/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1937:1901,36:1901:66116:36:1232:0,-482.402,-5715.89 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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228 NC_045512.2 20897 . C A 4.32142E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=40;CIGAR=1X;DP=1649;DPB=1649;DPRA=0;EPP=3.22745;EPPR=4.1453;GTI=0;LEN=1;MEANALT=1;MQM=47.125;MQMR=51.7551;NS=1;NUMALT=1;ODDS=1885.05;PAIRED=1;PAIREDR=0.986948;PAO=0;PQA=0;PQR=0;PRO=0;QA=1318;QR=55575;RO=1609;RPL=16;RPP=6.48466;RPPR=13.2253;RPR=24;RUN=1;SAF=23;SAP=4.96463;SAR=17;SRF=814;SRP=3.4975;SRR=795;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20633C>A|p.Pro6878Gln|20633/21291|20633/21291|6878/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1649:1609,40:1609:55575:40:1318:0,-397.579,-4648.18 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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229 NC_045512.2 20912 . T A 1.13313E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1786;DPB=1786;DPRA=0;EPP=3.0103;EPPR=3.60678;GTI=0;LEN=1;MEANALT=2;MQM=32.05;MQMR=51.4484;NS=1;NUMALT=1;ODDS=2291.88;PAIRED=0.7;PAIREDR=0.988082;PAO=0;PQA=0;PQR=0;PRO=0;QA=694;QR=62244;RO=1762;RPL=0;RPP=46.4397;RPPR=4.11945;RPR=20;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=902;SRP=5.18424;SRR=860;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20648T>A|p.Leu6883*|20648/21291|20648/21291|6883/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1786:1762,20:1762:62244:20:694:0,-495.972,-5248.21 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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230 NC_045512.2 21004 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=2194;DPB=2194;DPRA=0;EPP=3.52123;EPPR=3.93042;GTI=0;LEN=1;MEANALT=2;MQM=51.5882;MQMR=52.7298;NS=1;NUMALT=1;ODDS=2307.07;PAIRED=1;PAIREDR=0.989171;PAO=0;PQA=0;PQR=0;PRO=0;QA=2334;QR=73971;RO=2124;RPL=21;RPP=24.5973;RPPR=17.7321;RPR=47;RUN=1;SAF=35;SAP=3.13803;SAR=33;SRF=1065;SRP=3.0471;SRR=1059;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20740G>T|p.Ala6914Ser|20740/21291|20740/21291|6914/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2194:2124,68:2124:73971:68:2334:0,-465.125,-6190.18 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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231 NC_045512.2 21137 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=62;CIGAR=1X;DP=3005;DPB=3005;DPRA=0;EPP=3.15039;EPPR=15.2971;GTI=0;LEN=1;MEANALT=2;MQM=48.9839;MQMR=50.9398;NS=1;NUMALT=1;ODDS=3469.52;PAIRED=1;PAIREDR=0.991159;PAO=0;PQA=0;PQR=0;PRO=0;QA=2198;QR=103359;RO=2941;RPL=10;RPP=64.7922;RPPR=102.457;RPR=52;RUN=1;SAF=32;SAP=3.15039;SAR=30;SRF=1478;SRP=3.17643;SRR=1463;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20873A>G|p.Lys6958Arg|20873/21291|20873/21291|6958/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3005:2941,62:2941:103359:62:2198:0,-720.982,-8572.97 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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232 NC_045512.2 21357 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=76;CIGAR=1X;DP=3104;DPB=3104;DPRA=0;EPP=3.46745;EPPR=3.74513;GTI=0;LEN=1;MEANALT=2;MQM=49.4211;MQMR=50.8596;NS=1;NUMALT=1;ODDS=3454.76;PAIRED=0.973684;PAIREDR=0.954726;PAO=0;PQA=0;PQR=0;PRO=0;QA=2692;QR=107210;RO=3026;RPL=35;RPP=4.03889;RPPR=55.3237;RPR=41;RUN=1;SAF=37;SAP=3.12459;SAR=39;SRF=1503;SRP=3.29734;SRR=1523;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21093T>C|p.Asn7031Asn|21093/21291|21093/21291|7031/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3104:3026,76:3026:107210:76:2692:0,-714.996,-8823.97 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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233 NC_045512.2 21408 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=33;CIGAR=1X;DP=3187;DPB=3187;DPRA=0;EPP=3.0761;EPPR=14.653;GTI=0;LEN=1;MEANALT=2;MQM=42.0303;MQMR=50.2262;NS=1;NUMALT=1;ODDS=4058.01;PAIRED=0.909091;PAIREDR=0.961294;PAO=0;PQA=0;PQR=0;PRO=0;QA=1172;QR=111449;RO=3152;RPL=24;RPP=17.8158;RPPR=4.87314;RPR=9;RUN=1;SAF=15;SAP=3.60252;SAR=18;SRF=1597;SRP=4.22555;SRR=1555;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21144T>A|p.Phe7048Leu|21144/21291|21144/21291|7048/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3187:3152,33:3152:111449:33:1172:0,-876.049,-9303.39 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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234 NC_045512.2 21417 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=101;CIGAR=1X;DP=3209;DPB=3209;DPRA=0;EPP=3.54779;EPPR=9.44926;GTI=0;LEN=1;MEANALT=1;MQM=44.9208;MQMR=49.8475;NS=1;NUMALT=1;ODDS=3401.21;PAIRED=0.960396;PAIREDR=0.95045;PAO=0;PQA=0;PQR=0;PRO=0;QA=3474;QR=109181;RO=3108;RPL=70;RPP=35.7114;RPPR=41.2668;RPR=31;RUN=1;SAF=47;SAP=4.06379;SAR=54;SRF=1571;SRP=3.81796;SRR=1537;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21153A>T|p.Lys7051Asn|21153/21291|21153/21291|7051/7096|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3209:3108,101:3108:109181:101:3474:0,-695.817,-8846.14 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
235 NC_045512.2 21575 . C T 4774.91 . AB=0.206853;ABP=1767.56;AC=1;AF=0.5;AN=2;AO=489;CIGAR=1X;DP=2364;DPB=2364;DPRA=0;EPP=3.01474;EPPR=3.27143;GTI=0;LEN=1;MEANALT=3;MQM=47.4703;MQMR=52.6018;NS=1;NUMALT=1;ODDS=1099.46;PAIRED=1;PAIREDR=0.99519;PAO=0;PQA=0;PQR=0;PRO=0;QA=17184;QR=65447;RO=1871;RPL=279;RPP=24.1522;RPPR=8.22021;RPR=210;RUN=1;SAF=242;SAP=3.12132;SAR=247;SRF=936;SRP=3.01146;SRR=935;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.13C>T|p.Leu5Phe|13/3822|13/3822|5/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2364:1871,489:1871:65447:489:17184:-675.122,0,-4947.91 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
236 NC_045512.2 21618 . C G 35360.1 . AB=0.703596;ABP=743.974;AC=1;AF=0.5;AN=2;AO=1448;CIGAR=1X;DP=2058;DPB=2058;DPRA=0;EPP=3.0103;EPPR=3.01387;GTI=0;LEN=1;MEANALT=2;MQM=50.1657;MQMR=52.7011;NS=1;NUMALT=1;ODDS=2619.29;PAIRED=0.998619;PAIREDR=0.996716;PAO=0;PQA=0;PQR=0;PRO=0;QA=50596;QR=21344;RO=609;RPL=790;RPP=29.14;RPPR=25.2634;RPR=658;RUN=1;SAF=688;SAP=10.7844;SAR=760;SRF=298;SRP=3.61289;SRR=311;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.56C>G|p.Thr19Arg|56/3822|56/3822|19/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2058:609,1448:609:21344:1448:50596:-3624.67,0,-1224.54 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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237 NC_045512.2 21650 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=198;CIGAR=1X;DP=1834;DPB=1834;DPRA=0;EPP=4.58955;EPPR=5.81888;GTI=0;LEN=1;MEANALT=1;MQM=45.2424;MQMR=51.4438;NS=1;NUMALT=1;ODDS=807.489;PAIRED=1;PAIREDR=0.997555;PAO=0;PQA=0;PQR=0;PRO=0;QA=6993;QR=57736;RO=1636;RPL=198;RPP=432.962;RPPR=3.27045;RPR=0;RUN=1;SAF=93;SAP=4.58955;SAR=105;SRF=794;SRP=6.06841;SRR=842;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.88A>C|p.Asn30His|88/3822|88/3822|30/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1834:1636,198:1636:57736:198:6993:0,-5.24931,-4377.3 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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238 NC_045512.2 21656 . TTCACACG TACC 6.46099E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=51;CIGAR=1M4D2M1X;DP=1573;DPB=1546.88;DPRA=0;EPP=5.09662;EPPR=5.44218;GTI=0;LEN=4;MEANALT=13;MQM=45.3333;MQMR=51.4031;NS=1;NUMALT=1;ODDS=1644.42;PAIRED=1;PAIREDR=0.997335;PAO=0;PQA=0;PQR=0;PRO=0;QA=1783;QR=52647;RO=1501;RPL=51;RPP=113.755;RPPR=24.1912;RPR=0;RUN=1;SAF=22;SAP=5.09662;SAR=29;SRF=731;SRP=5.21071;SRR=770;TYPE=complex;ANN=ACC|frameshift_variant&missense_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.95_101delTCACACGinsACC|p.Phe32fs|95/3822|95/3822|32/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1573:1501,51:1501:52647:51:1783:0,-323.476,-4349.96 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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239 NC_045512.2 21764 . ATACATGT AT 20265.8 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=744;CIGAR=1M6D1M;DP=744;DPB=186.75;DPRA=0;EPP=6.38425;EPPR=0;GTI=0;LEN=6;MEANALT=1;MQM=49.7083;MQMR=0;NS=1;NUMALT=1;ODDS=1036.01;PAIRED=0.995968;PAIREDR=0;PAO=3;PQA=0;PQR=0;PRO=3;QA=24386;QR=0;RO=0;RPL=373;RPP=3.02197;RPPR=0;RPR=371;RUN=1;SAF=378;SAP=3.43058;SAR=366;SRF=0;SRP=0;SRR=0;TYPE=del;ANN=AT|disruptive_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.204_209delACATGT|p.His69_Val70del|204/3822|204/3822|68/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:744:0,744:0:0:744:24386:-2031.56,-223.966,0 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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240 NC_045512.2 21855 . C T 10363.6 . AB=0.552296;ABP=21.634;AC=1;AF=0.5;AN=2;AO=433;CIGAR=1X;DP=784;DPB=784;DPRA=0;EPP=3.05543;EPPR=3.16496;GTI=0;LEN=1;MEANALT=1;MQM=50.321;MQMR=52.8519;NS=1;NUMALT=1;ODDS=1907.65;PAIRED=0.995381;PAIREDR=0.997151;PAO=0;PQA=0;PQR=0;PRO=0;QA=15293;QR=12291;RO=351;RPL=218;RPP=3.05543;RPPR=4.79821;RPR=215;RUN=1;SAF=222;SAP=3.61711;SAR=211;SRF=176;SRP=3.01649;SRR=175;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.293C>T|p.Ser98Phe|293/3822|293/3822|98/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:784:351,433:351:12291:433:15293:-1046.09,0,-838.198 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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241 NC_045512.2 21974 . G C 6907.42 . AB=0.470907;ABP=8.44339;AC=1;AF=0.5;AN=2;AO=348;CIGAR=1X;DP=739;DPB=739;DPRA=0;EPP=3.40965;EPPR=3.21074;GTI=0;LEN=1;MEANALT=2;MQM=43.75;MQMR=45.7;NS=1;NUMALT=1;ODDS=1590.49;PAIRED=1;PAIREDR=0.94359;PAO=0;PQA=0;PQR=0;PRO=0;QA=12325;QR=13699;RO=390;RPL=257;RPP=174.956;RPPR=8.02139;RPR=91;RUN=1;SAF=169;SAP=3.63429;SAR=179;SRF=196;SRP=3.03257;SRR=194;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.412G>C|p.Asp138His|412/3822|412/3822|138/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:739:390,348:390:13699:348:12325:-716.861,0,-870.869 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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242 NC_045512.2 21979 . ATTTTTGGGTGTTTATTAC ATTTTGGGTGTTTAC,ATTTTTGGGTGTTTAC 10664.2 . AB=0,0;ABP=0,0;AC=0,2;AF=0,1;AN=2;AO=12,482;CIGAR=1M1D10M3D4M,12M3D4M;DP=548;DPB=469.368;DPRA=0,0;EPP=3.73412,3.65904;EPPR=3.0565;GTI=0;LEN=15,3;MEANALT=5,5;MQM=28.9167,42.9523;MQMR=43.6809;NS=1;NUMALT=2;ODDS=308.58;PAIRED=1,0.977178;PAIREDR=0.829787;PAO=0,0.5;PQA=0,12;PQR=12;PRO=0.5;QA=254,13811;QR=1634;RO=47;RPL=2,311;RPP=14.5915,91.3108;RPPR=80.6751;RPR=10,171;RUN=1,1;SAF=7,234;SAP=3.73412,3.89331;SAR=5,248;SRF=24;SRP=3.0565;SRR=23;TYPE=complex,del;ANN=GGGTGTTTAC|frameshift_variant&missense_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.422_431delTGGGTGTTTAinsGGGTGT|p.Leu141fs|422/3822|422/3822|141/1273||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 2/2:548:47,12,482:47:1634:12,482:254,13811:-1068.01,-1064.49,-1177.28,-28.6243,-127.448,0 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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243 NC_045512.2 22028 . GAGTTCAG GG 0.0 . AB=0.118812;ABP=640.37;AC=1;AF=0.5;AN=2;AO=60;CIGAR=1M6D1M;DP=505;DPB=460;DPRA=0;EPP=3.58936;EPPR=11.6375;GTI=0;LEN=6;MEANALT=2;MQM=49.9;MQMR=43.2995;NS=1;NUMALT=1;ODDS=137.724;PAIRED=1;PAIREDR=0.972973;PAO=0;PQA=0;PQR=0;PRO=0;QA=1971;QR=15417;RO=444;RPL=22;RPP=12.2752;RPPR=53.8932;RPR=38;RUN=1;SAF=32;SAP=3.58936;SAR=28;SRF=208;SRP=6.84461;SRR=236;TYPE=del;ANN=GG|disruptive_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.467_472delAGTTCA|p.Glu156_Arg158delinsGly|467/3822|467/3822|156/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:505:444,60:444:15417:60:1971:-19.2725,0,-1029.82 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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244 NC_045512.2 22070 . T G 2.82671E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=1X;DP=415;DPB=415;DPRA=0;EPP=3.20771;EPPR=3.2038;GTI=0;LEN=1;MEANALT=1;MQM=56.8182;MQMR=53.0619;NS=1;NUMALT=1;ODDS=464.115;PAIRED=0.909091;PAIREDR=0.992574;PAO=0;PQA=0;PQR=0;PRO=0;QA=372;QR=14318;RO=404;RPL=0;RPP=26.8965;RPPR=3.0963;RPR=11;RUN=1;SAF=5;SAP=3.20771;SAR=6;SRF=209;SRP=4.06379;SRR=195;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.508T>G|p.Tyr170Asp|508/3822|508/3822|170/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:415:404,11:404:14318:11:372:0,-91.1698,-1211.65 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
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245 NC_045512.2 22218 . GTTTTTCG GTTTTCG 6.08732E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1M1D6M;DP=973;DPB=971.75;DPRA=0;EPP=3.0103;EPPR=3.15721;GTI=0;LEN=1;MEANALT=7;MQM=53.0833;MQMR=53.0095;NS=1;NUMALT=1;ODDS=1193.66;PAIRED=1;PAIREDR=0.988372;PAO=1;PQA=34;PQR=34;PRO=1;QA=406;QR=32735;RO=946;RPL=2;RPP=14.5915;RPPR=39.4525;RPR=10;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=463;SRP=3.92847;SRR=483;TYPE=del;ANN=GTTTTCG|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.661delT|p.Ser221fs|661/3822|661/3822|221/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:973:946,12:946:32735:12:406:0,-251.995,-2798.42 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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246 NC_045512.2 22282 . TTTACTTGCT TT 1.8708E-13 . AB=0.146825;ABP=2733.21;AC=1;AF=0.5;AN=2;AO=370;CIGAR=1M8D1M;DP=2520;DPB=2226.5;DPRA=0;EPP=3.03378;EPPR=34.8149;GTI=0;LEN=8;MEANALT=10;MQM=46.7216;MQMR=49.7873;NS=1;NUMALT=1;ODDS=261.116;PAIRED=0.97027;PAIREDR=0.989247;PAO=11.5;PQA=371.5;PQR=443.5;PRO=13.5;QA=11823;QR=75374;RO=2139;RPL=204;RPP=11.4849;RPPR=2756.8;RPR=166;RUN=1;SAF=176;SAP=4.91181;SAR=194;SRF=1146;SRP=26.7747;SRR=993;TYPE=del;ANN=TT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.723_730delACTTGCTT|p.Leu241fs|723/3822|723/3822|241/1273||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/1:2520:2139,370:2139:75374:370:11823:-194.926,0,-5543.52 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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247 NC_045512.2 22315 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=357;CIGAR=1X;DP=4311;DPB=4311;DPRA=0;EPP=3.30835;EPPR=18.922;GTI=0;LEN=1;MEANALT=3;MQM=48.1261;MQMR=49.6176;NS=1;NUMALT=1;ODDS=2556.05;PAIRED=0.985994;PAIREDR=0.992901;PAO=0;PQA=0;PQR=0;PRO=0;QA=12323;QR=138793;RO=3944;RPL=57;RPP=362.179;RPPR=1298.6;RPR=300;RUN=1;SAF=185;SAP=4.03825;SAR=172;SRF=2048;SRP=15.7308;SRR=1896;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.753T>G|p.Pro251Pro|753/3822|753/3822|251/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4311:3944,357:3944:138793:357:12323:0,-302.488,-10551.5 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
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changeset
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248 NC_045512.2 22600 . ATTTGC ATTGC 4.14663E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=275;CIGAR=1M1D4M;DP=5420;DPB=5374.17;DPRA=0;EPP=11.6093;EPPR=8.62691;GTI=0;LEN=1;MEANALT=12;MQM=50.6836;MQMR=52.2494;NS=1;NUMALT=1;ODDS=4743.11;PAIRED=1;PAIREDR=0.995893;PAO=0;PQA=0;PQR=0;PRO=0;QA=8676;QR=179526;RO=5113;RPL=253;RPP=424.363;RPPR=1086.16;RPR=22;RUN=1;SAF=121;SAP=11.6093;SAR=154;SRF=2497;SRP=9.02442;SRR=2616;TYPE=del;ANN=ATTGC|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1041delT|p.Phe347fs|1041/3822|1041/3822|347/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5420:5113,275:5113:179526:275:8676:0,-851.108,-14682.4 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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249 NC_045512.2 22643 . TGT ACA 1.12947E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=66;CIGAR=3X;DP=3250;DPB=3250;DPRA=0;EPP=3.1419;EPPR=4.04925;GTI=0;LEN=3;MEANALT=3;MQM=42.2879;MQMR=53.4939;NS=1;NUMALT=1;ODDS=3785.89;PAIRED=0.924242;PAIREDR=0.996854;PAO=0;PQA=0;PQR=0;PRO=0;QA=2317;QR=110756;RO=3179;RPL=27;RPP=7.74806;RPPR=167.685;RPR=39;RUN=1;SAF=31;SAP=3.53672;SAR=35;SRF=1582;SRP=3.16399;SRR=1597;TYPE=complex;ANN=ACA|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1081_1083delTGTinsACA|p.Cys361Thr|1081/3822|1081/3822|361/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3250:3179,66:3179:110756:66:2317:0,-800.501,-9497.37 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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250 NC_045512.2 22852 . A G 0.0 . AB=0.143746;ABP=3193.32;AC=1;AF=0.5;AN=2;AO=416;CIGAR=1X;DP=2894;DPB=2894;DPRA=0;EPP=5.09825;EPPR=10.6047;GTI=0;LEN=1;MEANALT=3;MQM=43.2572;MQMR=50.5285;NS=1;NUMALT=1;ODDS=362.403;PAIRED=1;PAIREDR=0.984634;PAO=0;PQA=0;PQR=0;PRO=0;QA=14466;QR=87462;RO=2473;RPL=335;RPP=339.776;RPPR=45.1235;RPR=81;RUN=1;SAF=199;SAP=4.70154;SAR=217;SRF=1207;SRP=6.06687;SRR=1266;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1290A>G|p.Thr430Thr|1290/3822|1290/3822|430/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2894:2473,416:2473:87462:416:14466:-239.51,0,-6540.23 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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251 NC_045512.2 22917 . T G 25609.5 . AB=0.654307;ABP=365.559;AC=1;AF=0.5;AN=2;AO=1147;CIGAR=1X;DP=1753;DPB=1753;DPRA=0;EPP=5.88982;EPPR=3.93066;GTI=0;LEN=1;MEANALT=2;MQM=49.0113;MQMR=53.3858;NS=1;NUMALT=1;ODDS=2887.26;PAIRED=0.975588;PAIREDR=0.993377;PAO=0;PQA=0;PQR=0;PRO=0;QA=37925;QR=20944;RO=604;RPL=580;RPP=3.33025;RPPR=3.71495;RPR=567;RUN=1;SAF=582;SAP=3.55743;SAR=565;SRF=309;SRP=3.71495;SRR=295;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1355T>G|p.Leu452Arg|1355/3822|1355/3822|452/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1753:604,1147:604:20944:1147:37925:-2607.08,0,-1299.49 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
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252 NC_045512.2 22995 . C A 26960.9 . AB=0.637002;ABP=281.467;AC=1;AF=0.5;AN=2;AO=1088;CIGAR=1X;DP=1708;DPB=1708;DPRA=0;EPP=3.13803;EPPR=3.79961;GTI=0;LEN=1;MEANALT=2;MQM=50.7574;MQMR=53.2084;NS=1;NUMALT=1;ODDS=3085.5;PAIRED=0.988051;PAIREDR=0.996769;PAO=0;PQA=0;PQR=0;PRO=0;QA=38250;QR=21584;RO=619;RPL=537;RPP=3.40148;RPPR=4.02412;RPR=551;RUN=1;SAF=541;SAP=3.08215;SAR=547;SRF=306;SRP=3.18219;SRR=313;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1433C>A|p.Thr478Lys|1433/3822|1433/3822|478/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1708:619,1088:619:21584:1088:38250:-2733.04,0,-1376.73 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
253 NC_045512.2 23063 . A T 11471.4 . AB=0.363065;ABP=262.299;AC=1;AF=0.5;AN=2;AO=578;CIGAR=1X;DP=1592;DPB=1592;DPRA=0;EPP=3.0103;EPPR=3.55852;GTI=0;LEN=1;MEANALT=1;MQM=48.7907;MQMR=51.641;NS=1;NUMALT=1;ODDS=2641.38;PAIRED=0.989619;PAIREDR=0.97929;PAO=0;PQA=0;PQR=0;PRO=0;QA=20314;QR=35139;RO=1014;RPL=301;RPP=5.17426;RPPR=3.31867;RPR=277;RUN=1;SAF=288;SAP=3.02533;SAR=290;SRF=504;SRP=3.08739;SRR=510;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1501A>T|p.Asn501Tyr|1501/3822|1501/3822|501/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1592:1014,578:1014:35139:578:20314:-1181.74,0,-2507.13 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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254 NC_045512.2 23271 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=99;CIGAR=1X;DP=3990;DPB=3990;DPRA=0;EPP=3.03223;EPPR=3.54827;GTI=0;LEN=1;MEANALT=2;MQM=47.1616;MQMR=52.3784;NS=1;NUMALT=1;ODDS=4435.23;PAIRED=1;PAIREDR=0.998453;PAO=0;PQA=0;PQR=0;PRO=0;QA=3411;QR=135408;RO=3879;RPL=40;RPP=10.9285;RPPR=125.097;RPR=59;RUN=1;SAF=50;SAP=3.03223;SAR=49;SRF=1984;SRP=7.44449;SRR=1895;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1709C>A|p.Ala570Asp|1709/3822|1709/3822|570/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3990:3879,99:3879:135408:99:3411:0,-922.477,-11401.5 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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255 NC_045512.2 23302 . G C 1478.84 . AB=0.154267;ABP=4370.88;AC=1;AF=0.5;AN=2;AO=649;CIGAR=1X;DP=4207;DPB=4207;DPRA=0;EPP=3.97726;EPPR=3.89208;GTI=0;LEN=1;MEANALT=2;MQM=50.0555;MQMR=53.4027;NS=1;NUMALT=1;ODDS=340.516;PAIRED=0.996918;PAIREDR=0.996625;PAO=0;PQA=0;PQR=0;PRO=0;QA=22618;QR=125381;RO=3556;RPL=295;RPP=14.6573;RPPR=18.2546;RPR=354;RUN=1;SAF=323;SAP=3.04041;SAR=326;SRF=1770;SRP=3.16663;SRR=1786;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1740G>C|p.Gln580His|1740/3822|1740/3822|580/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4207:3556,649:3556:125381:649:22618:-637.692,0,-9696.8 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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256 NC_045512.2 23403 . A G 104667.0 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3570;CIGAR=1X;DP=3572;DPB=3572;DPRA=0;EPP=4.29737;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=50.3319;MQMR=54;NS=1;NUMALT=1;ODDS=4927.87;PAIRED=0.995798;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=124700;QR=72;RO=2;RPL=1945;RPP=65.2957;RPPR=7.35324;RPR=1625;RUN=1;SAF=1745;SAP=6.90314;SAR=1825;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1841A>G|p.Asp614Gly|1841/3822|1841/3822|614/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:3572:2,3570:2:72:3570:124700:-10477.8,-1068.47,0 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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257 NC_045512.2 23472 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=35;CIGAR=1X;DP=2386;DPB=2386;DPRA=0;EPP=25.4075;EPPR=10.5077;GTI=0;LEN=1;MEANALT=2;MQM=53.7429;MQMR=48.1756;NS=1;NUMALT=1;ODDS=3053.41;PAIRED=1;PAIREDR=0.976556;PAO=0;PQA=0;PQR=0;PRO=0;QA=546;QR=77493;RO=2346;RPL=27;RPP=25.4075;RPPR=1331.44;RPR=8;RUN=1;SAF=35;SAP=79.0118;SAR=0;SRF=1114;SRP=15.8984;SRR=1232;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1910C>A|p.Ser637Tyr|1910/3822|1910/3822|637/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2386:2346,35:2346:77493:35:546:0,-668.526,-6266.09 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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258 NC_045512.2 23492 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=22;CIGAR=1X;DP=1868;DPB=1868;DPRA=0;EPP=42.4916;EPPR=19.2094;GTI=0;LEN=1;MEANALT=3;MQM=49.7273;MQMR=46.6534;NS=1;NUMALT=1;ODDS=2434.25;PAIRED=1;PAIREDR=0.973842;PAO=0;PQA=0;PQR=0;PRO=0;QA=327;QR=61631;RO=1835;RPL=21;RPP=42.4916;RPPR=2188.54;RPR=1;RUN=1;SAF=22;SAP=50.7827;SAR=0;SRF=857;SRP=20.3359;SRR=978;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1930C>A|p.Gln644Lys|1930/3822|1930/3822|644/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1868:1835,22:1835:61631:22:327:0,-529.793,-4862.4 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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259 NC_045512.2 23575 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=456;DPB=456;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=27.8333;MQMR=51.192;NS=1;NUMALT=1;ODDS=580.51;PAIRED=1;PAIREDR=0.991071;PAO=0;PQA=0;PQR=0;PRO=0;QA=208;QR=15391;RO=448;RPL=4;RPP=4.45795;RPPR=5.35627;RPR=2;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=229;SRP=3.495;SRR=219;TYPE=snp;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2013C>T|p.Cys671Cys|2013/3822|2013/3822|671/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:456:448,6:448:15391:6:208:0,-124.875,-1294.11 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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260 NC_045512.2 23604 . C G 15167.8 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=536;CIGAR=1X;DP=536;DPB=536;DPRA=0;EPP=3.0265;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=49.2929;MQMR=0;NS=1;NUMALT=1;ODDS=747.659;PAIRED=0.998134;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18474;QR=0;RO=0;RPL=228;RPP=28.9383;RPPR=0;RPR=308;RUN=1;SAF=275;SAP=3.80435;SAR=261;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2042C>G|p.Pro681Arg|2042/3822|2042/3822|681/1273|| GT:DP:AD:RO:QR:AO:QA:GL 1/1:536:0,536:0:0:536:18474:-1523.85,-161.352,0 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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261 NC_045512.2 23746 . A G 1.18854E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=59;CIGAR=1X;DP=618;DPB=618;DPRA=0;EPP=3.93042;EPPR=3.88433;GTI=0;LEN=1;MEANALT=1;MQM=52.9492;MQMR=52.1896;NS=1;NUMALT=1;ODDS=268.144;PAIRED=1;PAIREDR=0.989267;PAO=0;PQA=0;PQR=0;PRO=0;QA=2051;QR=19534;RO=559;RPL=32;RPP=3.93042;RPPR=5.84215;RPR=27;RUN=1;SAF=29;SAP=3.0471;SAR=30;SRF=268;SRP=5.06524;SRR=291;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2184A>G|p.Pro728Pro|2184/3822|2184/3822|728/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:618:559,59:559:19534:59:2051:0,-8.56006,-1510.11 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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262 NC_045512.2 23865 . C T 7.83587E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=325;DPB=325;DPRA=0;EPP=3.0103;EPPR=3.34385;GTI=0;LEN=1;MEANALT=1;MQM=49;MQMR=51.4671;NS=1;NUMALT=1;ODDS=391.092;PAIRED=1;PAIREDR=0.984326;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=11241;RO=319;RPL=0;RPP=16.0391;RPPR=3.56168;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=161;SRP=3.07156;SRR=158;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2303C>T|p.Thr768Ile|2303/3822|2303/3822|768/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:325:319,6:319:11241:6:204:0,-79.3917,-944.349 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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263 NC_045512.2 23887 . CAAAAACACCCAAG CAAAACACCCAAG 4.52052E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1M1D12M;DP=304;DPB=303.714;DPRA=0;EPP=3.0103;EPPR=4.05261;GTI=0;LEN=1;MEANALT=1;MQM=56.75;MQMR=52.8033;NS=1;NUMALT=1;ODDS=380.478;PAIRED=1;PAIREDR=0.963333;PAO=0;PQA=0;PQR=0;PRO=0;QA=144;QR=10487;RO=300;RPL=4;RPP=11.6962;RPPR=3.12611;RPR=0;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=150;SRP=3.0103;SRR=150;TYPE=del;ANN=CAAAACACCCAAG|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2330delA|p.Asn777fs|2330/3822|2330/3822|777/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:304:300,4:300:10487:4:144:0,-78.2128,-896.486 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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264 NC_045512.2 23910 . C T 1.37419E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=401;DPB=401;DPRA=0;EPP=3.0103;EPPR=3.14773;GTI=0;LEN=1;MEANALT=1;MQM=55.1667;MQMR=50.9089;NS=1;NUMALT=1;ODDS=489.483;PAIRED=1;PAIREDR=0.959494;PAO=0;PQA=0;PQR=0;PRO=0;QA=216;QR=13744;RO=395;RPL=2;RPP=4.45795;RPPR=11.3718;RPR=4;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=203;SRP=3.67549;SRR=192;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2348C>T|p.Ala783Val|2348/3822|2348/3822|783/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:401:395,6:395:13744:6:216:0,-100.971,-1131.25 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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265 NC_045512.2 23996 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=555;DPB=555;DPRA=0;EPP=3.0103;EPPR=3.58091;GTI=0;LEN=1;MEANALT=2;MQM=54.6667;MQMR=50.4818;NS=1;NUMALT=1;ODDS=702.743;PAIRED=1;PAIREDR=0.972628;PAO=0;PQA=0;PQR=0;PRO=0;QA=216;QR=19193;RO=548;RPL=0;RPP=16.0391;RPPR=7.06794;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=276;SRP=3.0737;SRR=272;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2434C>T|p.Pro812Ser|2434/3822|2434/3822|812/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:555:548,6:548:19193:6:216:0,-147.202,-1587.52 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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266 NC_045512.2 24110 . A C 9.9567E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=57;CIGAR=1X;DP=569;DPB=569;DPRA=0;EPP=3.9627;EPPR=3.62103;GTI=0;LEN=1;MEANALT=1;MQM=47.2807;MQMR=48.4238;NS=1;NUMALT=1;ODDS=274.15;PAIRED=1;PAIREDR=0.935547;PAO=0;PQA=0;PQR=0;PRO=0;QA=2023;QR=18082;RO=512;RPL=0;RPP=126.784;RPPR=3.02726;RPR=57;RUN=1;SAF=31;SAP=3.9627;SAR=26;SRF=253;SRP=3.16298;SRR=259;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2548A>C|p.Ile850Leu|2548/3822|2548/3822|850/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:569:512,57:512:18082:57:2023:0,-5.64707,-1298.89 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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267 NC_045512.2 24201 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=542;DPB=542;DPRA=0;EPP=3.73412;EPPR=3.21144;GTI=0;LEN=1;MEANALT=2;MQM=50.9167;MQMR=52.3214;NS=1;NUMALT=1;ODDS=625.015;PAIRED=1;PAIREDR=0.964083;PAO=0;PQA=0;PQR=0;PRO=0;QA=428;QR=18455;RO=529;RPL=11;RPP=21.1059;RPPR=31.2887;RPR=1;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=266;SRP=3.04724;SRR=263;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2639G>A|p.Gly880Asp|2639/3822|2639/3822|880/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:542:529,12:529:18455:12:428:0,-126.755,-1553.36 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
268 NC_045512.2 24320 . CAAAAATTG CAAAATTG 2687.09 . AB=0.320298;ABP=153.634;AC=1;AF=0.5;AN=2;AO=172;CIGAR=1M1D7M;DP=537;DPB=519.222;DPRA=0;EPP=3.46479;EPPR=3.88374;GTI=0;LEN=1;MEANALT=3;MQM=49.6395;MQMR=53.9553;NS=1;NUMALT=1;ODDS=618.726;PAIRED=1;PAIREDR=0.997207;PAO=1;PQA=34.5;PQR=34.5;PRO=1;QA=5084;QR=12491;RO=358;RPL=99;RPP=11.5447;RPPR=3.22866;RPR=73;RUN=1;SAF=84;SAP=3.2123;SAR=88;SRF=175;SRP=3.3985;SRR=183;TYPE=del;ANN=CAAAATTG|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2763delA|p.Lys921fs|2763/3822|2763/3822|921/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:537:358,172:358:12491:172:5084:-291.188,0,-941.405 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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269 NC_045512.2 24329 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=563;DPB=563;DPRA=0;EPP=3.0103;EPPR=3.04539;GTI=0;LEN=1;MEANALT=1;MQM=54.3333;MQMR=52.1598;NS=1;NUMALT=1;ODDS=713.029;PAIRED=1;PAIREDR=0.994614;PAO=0;PQA=0;PQR=0;PRO=0;QA=211;QR=19533;RO=557;RPL=2;RPP=4.45795;RPPR=8.93994;RPR=4;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=271;SRP=3.88747;SRR=286;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2767A>G|p.Ile923Val|2767/3822|2767/3822|923/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:563:557,6:557:19533:6:211:0,-150.179,-1654.98 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
270 NC_045512.2 24410 . G A 7223.05 . AB=0.387777;ABP=106.822;AC=1;AF=0.5;AN=2;AO=368;CIGAR=1X;DP=949;DPB=949;DPRA=0;EPP=3.86001;EPPR=6.84407;GTI=0;LEN=1;MEANALT=2;MQM=45.2799;MQMR=49.4586;NS=1;NUMALT=1;ODDS=1663.17;PAIRED=0.98913;PAIREDR=0.993103;PAO=0;PQA=0;PQR=0;PRO=0;QA=13128;QR=20569;RO=580;RPL=255;RPP=121.993;RPPR=1202.4;RPR=113;RUN=1;SAF=177;SAP=4.16685;SAR=191;SRF=307;SRP=7.33827;SRR=273;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2848G>A|p.Asp950Asn|2848/3822|2848/3822|950/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:949:580,368:580:20569:368:13128:-752.784,0,-1403.38 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
271 NC_045512.2 24506 . T G 13690.0 . AB=0.316547;ABP=653.14;AC=1;AF=0.5;AN=2;AO=704;CIGAR=1X;DP=2224;DPB=2224;DPRA=0;EPP=3.61486;EPPR=3.76653;GTI=0;LEN=1;MEANALT=2;MQM=51.4545;MQMR=52.4332;NS=1;NUMALT=1;ODDS=3152.23;PAIRED=0.992898;PAIREDR=0.99605;PAO=0;PQA=0;PQR=0;PRO=0;QA=24742;QR=53799;RO=1519;RPL=390;RPP=20.8262;RPPR=19.9947;RPR=314;RUN=1;SAF=361;SAP=4.00967;SAR=343;SRF=776;SRP=4.56707;SRR=743;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2944T>G|p.Ser982Ala|2944/3822|2944/3822|982/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2224:1519,704:1519:53799:704:24742:-1445.67,0,-3985.74 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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272 NC_045512.2 24626 . G A 1.2247E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=45;CIGAR=1X;DP=2469;DPB=2469;DPRA=0;EPP=3.05855;EPPR=4.04844;GTI=0;LEN=1;MEANALT=3;MQM=46.8667;MQMR=52.6319;NS=1;NUMALT=1;ODDS=2917.41;PAIRED=1;PAIREDR=0.995451;PAO=0;PQA=0;PQR=0;PRO=0;QA=1578;QR=84277;RO=2418;RPL=27;RPP=6.91895;RPPR=3.52757;RPR=18;RUN=1;SAF=23;SAP=3.05855;SAR=22;SRF=1205;SRP=3.06777;SRR=1213;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3064G>A|p.Ala1022Thr|3064/3822|3064/3822|1022/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2469:2418,45:2418:84277:45:1578:0,-616.766,-7159.4 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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273 NC_045512.2 24794 . G C 4292.7 . AB=0.176533;ABP=3441.96;AC=1;AF=0.5;AN=2;AO=668;CIGAR=1X;DP=3784;DPB=3784;DPRA=0;EPP=3.4784;EPPR=4.48774;GTI=0;LEN=1;MEANALT=3;MQM=49.018;MQMR=52.3277;NS=1;NUMALT=1;ODDS=988.432;PAIRED=1;PAIREDR=0.994534;PAO=0;PQA=0;PQR=0;PRO=0;QA=23418;QR=109332;RO=3110;RPL=267;RPP=61.38;RPPR=173.402;RPR=401;RUN=1;SAF=341;SAP=3.64744;SAR=327;SRF=1584;SRP=5.35912;SRR=1526;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3232G>C|p.Ala1078Pro|3232/3822|3232/3822|1078/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3784:3110,668:3110:109332:668:23418:-815.381,0,-8328.87 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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274 NC_045512.2 24914 . G C 16119.5 . AB=0.236327;ABP=2962;AC=1;AF=0.5;AN=2;AO=1158;CIGAR=1X;DP=4900;DPB=4900;DPRA=0;EPP=3.19782;EPPR=3.53313;GTI=0;LEN=1;MEANALT=2;MQM=50.032;MQMR=52.79;NS=1;NUMALT=1;ODDS=3711.66;PAIRED=0.996546;PAIREDR=0.991974;PAO=0;PQA=0;PQR=0;PRO=0;QA=40628;QR=131352;RO=3738;RPL=527;RPP=23.2924;RPPR=15.0562;RPR=631;RUN=1;SAF=591;SAP=4.09041;SAR=567;SRF=1865;SRP=3.04748;SRR=1873;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3352G>C|p.Asp1118His|3352/3822|3352/3822|1118/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4900:3738,1158:3738:131352:1158:40628:-1933.55,0,-9894.85 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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275 NC_045512.2 24952 . A G 9.54689E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=70;CIGAR=1X;DP=4842;DPB=4842;DPRA=0;EPP=3.0103;EPPR=10.9423;GTI=0;LEN=1;MEANALT=2;MQM=51.7714;MQMR=52.1543;NS=1;NUMALT=1;ODDS=5869.66;PAIRED=1;PAIREDR=0.991824;PAO=0;PQA=0;PQR=0;PRO=0;QA=2463;QR=167916;RO=4770;RPL=37;RPP=3.50664;RPPR=21.9554;RPR=33;RUN=1;SAF=36;SAP=3.13438;SAR=34;SRF=2328;SRP=8.92654;SRR=2442;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3390A>G|p.Ile1130Met|3390/3822|3390/3822|1130/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4842:4770,70:4770:167916:70:2463:0,-1244.69,-14195.3 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
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changeset
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276 NC_045512.2 25047 . C T 6.36456E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=333;CIGAR=1X;DP=4648;DPB=4648;DPRA=0;EPP=3.79933;EPPR=13.3153;GTI=0;LEN=1;MEANALT=2;MQM=46.3183;MQMR=51.3063;NS=1;NUMALT=1;ODDS=3139.76;PAIRED=0.993994;PAIREDR=0.986076;PAO=0;PQA=0;PQR=0;PRO=0;QA=11708;QR=149413;RO=4309;RPL=109;RPP=89.2497;RPPR=163.88;RPR=224;RUN=1;SAF=173;SAP=4.11234;SAR=160;SRF=2131;SRP=4.1235;SRR=2178;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3485C>T|p.Pro1162Leu|3485/3822|3485/3822|1162/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4648:4309,333:4309:149413:333:11708:0,-469.855,-11790.8 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
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277 NC_045512.2 25243 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=69;CIGAR=1X;DP=3225;DPB=3225;DPRA=0;EPP=3.04177;EPPR=3.63033;GTI=0;LEN=1;MEANALT=2;MQM=52.7681;MQMR=52.0352;NS=1;NUMALT=1;ODDS=3678.35;PAIRED=1;PAIREDR=0.993655;PAO=0;PQA=0;PQR=0;PRO=0;QA=2355;QR=108908;RO=3152;RPL=40;RPP=6.81824;RPPR=95.2951;RPR=29;RUN=1;SAF=34;SAP=3.04177;SAR=35;SRF=1538;SRP=6.9895;SRR=1614;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3681A>G|p.Ile1227Met|3681/3822|3681/3822|1227/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3225:3152,69:3152:108908:69:2355:0,-765.93,-9146.09 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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278 NC_045512.2 25244 . G T 8.47644E-13 . AB=0.135368;ABP=3748.16;AC=1;AF=0.5;AN=2;AO=439;CIGAR=1X;DP=3243;DPB=3243;DPRA=0;EPP=4.12324;EPPR=4.37735;GTI=0;LEN=1;MEANALT=3;MQM=48.303;MQMR=52.5899;NS=1;NUMALT=1;ODDS=418.437;PAIRED=0.995444;PAIREDR=0.99429;PAO=0;PQA=0;PQR=0;PRO=0;QA=15155;QR=97802;RO=2802;RPL=270;RPP=53.4686;RPPR=74.6301;RPR=169;RUN=1;SAF=216;SAP=3.25267;SAR=223;SRF=1369;SRP=6.18459;SRR=1433;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3682G>T|p.Val1228Leu|3682/3822|3682/3822|1228/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3243:2802,439:2802:97802:439:15155:-248.813,0,-7498.01 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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279 NC_045512.2 25277 . A T 2.24204E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=49;CIGAR=1X;DP=2415;DPB=2415;DPRA=0;EPP=100.904;EPPR=7.6624;GTI=0;LEN=1;MEANALT=3;MQM=51.7551;MQMR=50.6511;NS=1;NUMALT=1;ODDS=3038.7;PAIRED=0.979592;PAIREDR=0.9932;PAO=0;PQA=0;PQR=0;PRO=0;QA=748;QR=81205;RO=2353;RPL=1;RPP=100.904;RPPR=938.828;RPR=48;RUN=1;SAF=0;SAP=109.412;SAR=49;SRF=1196;SRP=4.41396;SRR=1157;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3715A>T|p.Ser1239Cys|3715/3822|3715/3822|1239/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2415:2353,49:2353:81205:49:748:0,-656.393,-6775.09 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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280 NC_045512.2 25286 . A T 6.2686E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=74;CIGAR=1X;DP=2593;DPB=2593;DPRA=0;EPP=163.699;EPPR=57.3406;GTI=0;LEN=1;MEANALT=2;MQM=50.9459;MQMR=49.8839;NS=1;NUMALT=1;ODDS=3162.15;PAIRED=0.959459;PAIREDR=0.988391;PAO=0;PQA=0;PQR=0;PRO=0;QA=1109;QR=84675;RO=2498;RPL=0;RPP=163.699;RPPR=507.755;RPR=74;RUN=1;SAF=0;SAP=163.699;SAR=74;SRF=1342;SRP=33.0841;SRR=1156;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3724A>T|p.Ser1242Cys|3724/3822|3724/3822|1242/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2593:2498,74:2498:84675:74:1109:0,-674.605,-6923.8 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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281 NC_045512.2 25296 . A C,T 1.83222E-13 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=141,54;CIGAR=1X,1X;DP=2571;DPB=2571;DPRA=0,0;EPP=119.577,88.0998;EPPR=157.455;GTI=0;LEN=1,1;MEANALT=3,3;MQM=50.9149,51.6111;MQMR=49.8522;NS=1;NUMALT=2;ODDS=2652.62;PAIRED=0.957447,0.981481;PAIREDR=0.988632;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=2213,924;QR=80940;RO=2375;RPL=28,4;RPP=114.279,88.0998;RPPR=367.051;RPR=113,50;RUN=1,1;SAF=1,0;SAP=300.564,120.27;SAR=140,54;SRF=1364;SRP=116.941;SRR=1011;TYPE=snp,snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3734A>C|p.Lys1245Thr|3734/3822|3734/3822|1245/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2571:2375,141,54:2375:80940:141,54:2213,924:0,-560.207,-6463.48,-648.053,-6439.04,-6577.52 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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282 NC_045512.2 25297 . GGGC GGGG 1.29702E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=63;CIGAR=3M1X;DP=2484;DPB=2543.75;DPRA=0;EPP=114.996;EPPR=62.0599;GTI=0;LEN=1;MEANALT=9;MQM=50.7937;MQMR=49.9929;NS=1;NUMALT=1;ODDS=2993.64;PAIRED=0.952381;PAIREDR=0.987137;PAO=66;PQA=2152;PQR=2152;PRO=66;QA=1266;QR=82158;RO=2410;RPL=3;RPP=114.996;RPPR=193.667;RPR=60;RUN=1;SAF=0;SAP=139.813;SAR=63;SRF=1322;SRP=52.3469;SRR=1088;TYPE=snp;ANN=GGGG|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3738C>G|p.Gly1246Gly|3738/3822|3738/3822|1246/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2484:2410,63:2410:82158:63:1266:0,-632.107,-6695.99 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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283 NC_045512.2 25308 . C G,T 1.02822E-13 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=27,37;CIGAR=1X,1X;DP=2591;DPB=2591;DPRA=0,0;EPP=38.4777,74.9036;EPPR=105.533;GTI=0;LEN=1,1;MEANALT=3,3;MQM=47.9259,50.0541;MQMR=50.213;NS=1;NUMALT=2;ODDS=3317.27;PAIRED=0.888889,0.972973;PAIREDR=0.981357;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=392,554;QR=79400;RO=2521;RPL=4,1;RPP=32.0437,74.9036;RPPR=90.6625;RPR=23,36;RUN=1,1;SAF=1,0;SAP=53.2759,83.3548;SAR=26,37;SRF=1425;SRP=96.2441;SRR=1096;TYPE=snp,snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3746C>G|p.Ser1249Cys|3746/3822|3746/3822|1249/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2591:2521,27,37:2521:79400:27,37:392,554:0,-732.46,-6524.72,-721.199,-6495.15,-6510.45 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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284 NC_045512.2 25312 . T G 1.87444E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=29;CIGAR=1X;DP=2594;DPB=2594;DPRA=0;EPP=3.68421;EPPR=76.7412;GTI=0;LEN=1;MEANALT=3;MQM=46.4483;MQMR=50.2856;NS=1;NUMALT=1;ODDS=3381;PAIRED=0.896552;PAIREDR=0.980101;PAO=0;PQA=0;PQR=0;PRO=0;QA=439;QR=80737;RO=2563;RPL=13;RPP=3.68421;RPPR=17.1092;RPR=16;RUN=1;SAF=0;SAP=65.983;SAR=29;SRF=1423;SRP=70.8648;SRR=1140;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3750T>G|p.Cys1250Trp|3750/3822|3750/3822|1250/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2594:2563,29:2563:80737:29:439:0,-743.535,-6638.88 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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285 NC_045512.2 25314 . G T 5.47261E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=98;CIGAR=1X;DP=2511;DPB=2511;DPRA=0;EPP=124.347;EPPR=150.808;GTI=0;LEN=1;MEANALT=2;MQM=49.5816;MQMR=50.4178;NS=1;NUMALT=1;ODDS=2901.26;PAIRED=0.938776;PAIREDR=0.982068;PAO=0;PQA=0;PQR=0;PRO=0;QA=1409;QR=74838;RO=2398;RPL=12;RPP=124.347;RPPR=10.6747;RPR=86;RUN=1;SAF=0;SAP=215.815;SAR=98;SRF=1406;SRP=158.215;SRR=992;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3752G>T|p.Gly1251Val|3752/3822|3752/3822|1251/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2511:2398,98:2398:74838:98:1409:0,-626.065,-6055.73 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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286 NC_045512.2 25316 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=38;CIGAR=1X;DP=2470;DPB=2470;DPRA=0;EPP=17.6392;EPPR=126.463;GTI=0;LEN=1;MEANALT=3;MQM=48.9737;MQMR=50.4211;NS=1;NUMALT=1;ODDS=3112.87;PAIRED=0.973684;PAIREDR=0.979236;PAO=0;PQA=0;PQR=0;PRO=0;QA=605;QR=74347;RO=2408;RPL=10;RPP=21.525;RPPR=4.75613;RPR=28;RUN=1;SAF=1;SAP=77.0689;SAR=37;SRF=1393;SRP=131.859;SRR=1015;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3754T>C|p.Ser1252Pro|3754/3822|3754/3822|1252/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2470:2408,38:2408:74347:38:605:0,-682.516,-6085.67 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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287 NC_045512.2 25323 . GCAAA GAAAT,CAAAA,GAAAA 0.0 . AB=0,0,0;ABP=0,0,0;AC=0,0,0;AF=0,0,0;AN=2;AO=71,67,284;CIGAR=1M1X2M1X,2X3M,1M1X3M;DP=2463;DPB=2473.6;DPRA=0,0,0;EPP=76.4428,38.3048,208.658;EPPR=686.769;GTI=0;LEN=5,2,1;MEANALT=17,17,17;MQM=48.8873,49.7164,50.9155;MQMR=51.4338;NS=1;NUMALT=3;ODDS=1480.75;PAIRED=0.901408,0.955224,0.985915;PAIREDR=0.977006;PAO=9,10,10;PQA=126,247,247;PQR=247;PRO=10;QA=1663,1100,5254;QR=66729;RO=1957;RPL=11,17,60;RPP=76.4428,38.3048,208.658;RPPR=21.475;RPR=60,50,224;RUN=1,1,1;SAF=0,0,0;SAP=157.185,148.499,619.708;SAR=71,67,284;SRF=1463;SRP=1044.87;SRR=494;TYPE=complex,mnp,snp;ANN=GAAAA|stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3762C>A|p.Cys1254*|3762/3822|3762/3822|1254/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2463:1957,71,67,284:1957:66729:71,67,284:1663,1100,5254:0,-464.981,-5396.57,-511.087,-5339.92,-5443.88,-203.076,-5031.91,-5078.01,-5070.55 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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288 NC_045512.2 25331 . G T 1.83222E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=167;CIGAR=1X;DP=2694;DPB=2694;DPRA=0;EPP=135.652;EPPR=242.371;GTI=0;LEN=1;MEANALT=2;MQM=49.7964;MQMR=51.6339;NS=1;NUMALT=1;ODDS=2682.43;PAIRED=0.946108;PAIREDR=0.978884;PAO=0;PQA=0;PQR=0;PRO=0;QA=2950;QR=74828;RO=2510;RPL=33;RPP=135.652;RPPR=260.919;RPR=134;RUN=1;SAF=0;SAP=365.646;SAR=167;SRF=1594;SRP=400.696;SRR=916;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3769G>T|p.Asp1257Tyr|3769/3822|3769/3822|1257/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2694:2510,167:2510:74828:167:2950:0,-546.112,-6035.79 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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289 NC_045512.2 25334 . GAAG CACG,CACC,GACC,CAAG,TAAG,GACG,GAAC 3.16299E-13 . AB=0,0,0,0,0,0,0;ABP=0,0,0,0,0,0,0;AC=0,0,0,0,0,0,0;AF=0,0,0,0,0,0,0;AN=2;AO=70,48,48,67,57,133,35;CIGAR=1X1M1X1M,1X1M2X,2M2X,1X3M,1X3M,2M1X1M,3M1X;DP=2461;DPB=2518;DPRA=0,0,0,0,0,0,0;EPP=57.7314,14.5915,21.1059,42.7126,49.6779,45.4765,35.8306;EPPR=603.572;GTI=0;LEN=4,4,2,1,1,1,1;MEANALT=17,17,17,17,17,17,17;MQM=49.1143,49.9583,46.0833,52.3134,50.9825,51.203,49.3143;MQMR=53.4979;NS=1;NUMALT=7;ODDS=2128.71;PAIRED=0.971429,0.958333,0.979167,1,0.982456,0.977444,0.971429;PAIREDR=0.975873;PAO=0,8.33333,41.5833,0,0,33.25,44.5833;PQA=0,188.333,1318.58,0,0,1130.25,1409.58;PQR=1221.25;PRO=36.25;QA=1249,803,708,1036,910,1875,507;QR=63002;RO=1948;RPL=14,16,14,16,11,41,6;RPP=57.7314,14.5915,21.1059,42.7126,49.6779,45.4765,35.8306;RPPR=494.485;RPR=56,32,34,51,46,92,29;RUN=1,1,1,1,1,1,1;SAF=0,0,0,0,0,0,0;SAP=155.013,107.241,107.241,148.499,126.784,291.816,79.0118;SAR=70,48,48,67,57,133,35;SRF=1469;SRP=1095.55;SRR=479;TYPE=complex,complex,mnp,snp,snp,snp,snp;ANN=TAAG|stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3772G>T|p.Glu1258*|3772/3822|3772/3822|1258/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2461:1948,70,48,48,67,57,133,35:1948:63002:70,48,48,67,57,133,35:1249,803,708,1036,910,1875,507:0,-495.815,-5299.62,-529.806,-5264.1,-5340.23,-539.679,-5273.97,-5307.95,-5350.1,-513.622,-5247.91,-5281.9,-5291.77,-5318.33,-521.963,-5256.25,-5290.24,-5300.11,-5274.06,-5329.68,-458.325,-5192.61,-5226.6,-5236.47,-5210.41,-5218.75,-5243.16,-553.097,-5287.38,-5321.37,-5331.24,-5305.19,-5313.53,-5249.89,-5367.44 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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290 NC_045512.2 25350 . CAGT CT 9.354E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=349;CIGAR=1M2D1M;DP=3349;DPB=3175.5;DPRA=0;EPP=3.76316;EPPR=28.3979;GTI=0;LEN=2;MEANALT=7;MQM=49.7765;MQMR=52.6948;NS=1;NUMALT=1;ODDS=1420.92;PAIRED=0.994269;PAIREDR=0.978268;PAO=0;PQA=0;PQR=68;PRO=2;QA=11744;QR=105020;RO=2991;RPL=33;RPP=501.323;RPPR=873.505;RPR=316;RUN=1;SAF=180;SAP=3.76316;SAR=169;SRF=1504;SRP=3.22011;SRR=1487;TYPE=del;ANN=CT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3789_3790delAG|p.Val1264fs|3789/3822|3789/3822|1263/1273|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3349:2991,349:2991:105020:349:11744:0,-32.0583,-8103.91 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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291 NC_045512.2 25439 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=409;CIGAR=1X;DP=4980;DPB=4980;DPRA=0;EPP=3.14303;EPPR=5.75601;GTI=0;LEN=1;MEANALT=3;MQM=42.0244;MQMR=50.0731;NS=1;NUMALT=1;ODDS=3047.76;PAIRED=0.99511;PAIREDR=0.99387;PAO=0;PQA=0;PQR=0;PRO=0;QA=14327;QR=161011;RO=4568;RPL=229;RPP=15.7577;RPPR=40.8133;RPR=180;RUN=1;SAF=205;SAP=3.01561;SAR=204;SRF=2235;SRP=7.57572;SRR=2333;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.47A>C|p.Lys16Thr|47/828|47/828|16/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4980:4568,409:4568:161011:409:14327:0,-430.196,-12414.4 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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292 NC_045512.2 25469 . C T 90198.9 . AB=0.848337;ABP=4756.25;AC=1;AF=0.5;AN=2;AO=3826;CIGAR=1X;DP=4510;DPB=4510;DPRA=0;EPP=5.48258;EPPR=3.21348;GTI=0;LEN=1;MEANALT=1;MQM=48.1853;MQMR=53.5643;NS=1;NUMALT=1;ODDS=439.848;PAIRED=0.997909;PAIREDR=0.99269;PAO=0;PQA=0;PQR=0;PRO=0;QA=133615;QR=23901;RO=684;RPL=2121;RPP=101.229;RPPR=78.3007;RPR=1705;RUN=1;SAF=1915;SAP=3.01938;SAR=1911;SRF=341;SRP=3.023;SRR=343;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.77C>T|p.Ser26Leu|77/828|77/828|26/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4510:684,3826:684:23901:3826:133615:-9563.49,0,-731.026 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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293 NC_045512.2 25696 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=28.5;MQMR=51.6923;NS=1;NUMALT=1;ODDS=66.8874;PAIRED=0;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=1831;RO=52;RPL=2;RPP=7.35324;RPPR=11.1951;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=27;SRP=3.17734;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.304G>A|p.Glu102Lys|304/828|304/828|102/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:54:52,2:52:1831:2:72:0,-12.7448,-153.498 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
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diff
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294 NC_045512.2 25702 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.33068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=50.8525;NS=1;NUMALT=1;ODDS=85.2841;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=2073;RO=61;RPL=0;RPP=5.18177;RPPR=15.8611;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=3.90025;SRR=28;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.310C>A|p.Pro104Thr|310/828|310/828|104/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:62:61,1:61:2073:1:14:0,-17.2639,-174.471 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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295 NC_045512.2 25734 . C A 2.42589E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=68;DPB=68;DPRA=0;EPP=5.18177;EPPR=3.04271;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=50.6716;NS=1;NUMALT=1;ODDS=93.5095;PAIRED=1;PAIREDR=0.940299;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=2355;RO=67;RPL=0;RPP=5.18177;RPPR=23.2666;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=3.30199;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.342C>A|p.Phe114Leu|342/828|342/828|114/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:68:67,1:67:2355:1:14:0,-19.07,-196.772 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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296 NC_045512.2 25750 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=74;DPB=74;DPRA=0;EPP=3.0103;EPPR=3.13094;GTI=0;LEN=1;MEANALT=1;MQM=54.5;MQMR=51.2222;NS=1;NUMALT=1;ODDS=86.3627;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=2546;RO=72;RPL=2;RPP=7.35324;RPPR=6.02623;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=38;SRP=3.49285;SRR=34;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.358T>C|p.Phe120Leu|358/828|358/828|120/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:74:72,2:72:2546:2:72:0,-15.458,-208.988 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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297 NC_045512.2 25785 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=10;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=3.0103;EPPR=3.11887;GTI=0;LEN=1;MEANALT=1;MQM=41.7;MQMR=51.4625;NS=1;NUMALT=1;ODDS=45.1658;PAIRED=1;PAIREDR=0.975;PAO=0;PQA=0;PQR=0;PRO=0;QA=356;QR=2776;RO=80;RPL=2;RPP=10.8276;RPPR=4.74748;RPR=8;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=41;SRP=3.11887;SRR=39;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.393G>T|p.Trp131Cys|393/828|393/828|131/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:90:80,10:80:2776:10:356:0,-0.705101,-211.729 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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298 NC_045512.2 25797 . CAAAAACCCAT CAAAAAACCCAT,CAAAAACCCAC 73.745 . AB=0.1875,0.0208333;ABP=84.4405,194.462;AC=1,0;AF=0.5,0;AN=2;AO=18,2;CIGAR=1M1I10M,10M1X;DP=96;DPB=97.6364;DPRA=0,0;EPP=3.0103,3.0103;EPPR=3.12459;GTI=0;LEN=1,1;MEANALT=2,2;MQM=51.2778,55.5;MQMR=49.3684;NS=1;NUMALT=2;ODDS=16.9804;PAIRED=1,1;PAIREDR=0.973684;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=555,72;QR=2648;RO=76;RPL=8,2;RPP=3.49285,7.35324;RPPR=3.46745;RPR=10,0;RUN=1,1;SAF=9,1;SAP=3.0103,3.0103;SAR=9,1;SRF=39;SRP=3.12459;SRR=37;TYPE=ins,snp;ANN=CAAAAAACCCAT|frameshift_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.410dupA|p.Asn137fs|411/828|411/828|137/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:96:76,18,2:76:2648:18,2:555,72:-20.9576,0,-190.254,-37.9662,-189.807,-233.088 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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299 NC_045512.2 25811 . T A 1.76315E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=3.0103;EPPR=3.21602;GTI=0;LEN=1;MEANALT=1;MQM=54;MQMR=49.9368;NS=1;NUMALT=1;ODDS=118.555;PAIRED=1;PAIREDR=0.978947;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=3323;RO=95;RPL=2;RPP=7.35324;RPPR=5.77607;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=49;SRP=3.21602;SRR=46;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.419T>A|p.Leu140His|419/828|419/828|140/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:97:95,2:95:3323:2:68:0,-22.7518,-268.02 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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300 NC_045512.2 25831 . C T 3.18727E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=30.75;MQMR=54.1733;NS=1;NUMALT=1;ODDS=86.1664;PAIRED=1;PAIREDR=0.973333;PAO=0;PQA=0;PQR=0;PRO=0;QA=144;QR=2659;RO=75;RPL=4;RPP=11.6962;RPPR=6.51361;RPR=0;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=38;SRP=3.03925;SRR=37;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.439C>T|p.Leu147Phe|439/828|439/828|147/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:79:75,4:75:2659:4:144:0,-15.761,-225.561 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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301 NC_045512.2 26042 . CTCAA TTGAG 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=44;CIGAR=1X1M1X1M1X;DP=1484;DPB=1485;DPRA=0;EPP=3.0103;EPPR=3.08455;GTI=0;LEN=5;MEANALT=5;MQM=43.3182;MQMR=53.2568;NS=1;NUMALT=1;ODDS=1592.01;PAIRED=1;PAIREDR=0.993719;PAO=6;PQA=136;PQR=32;PRO=1;QA=1544;QR=50198;RO=1433;RPL=22;RPP=3.0103;RPPR=7.93362;RPR=22;RUN=1;SAF=22;SAP=3.0103;SAR=22;SRF=738;SRP=5.81215;SRR=695;TYPE=complex;ANN=TTGAG|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.650_654delCTCAAinsTTGAG|p.ThrGln217IleGlu|650/828|650/828|217/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1484:1433,44:1433:50198:44:1544:0,-326.758,-4246.55 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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302 NC_045512.2 26057 . A C 1.04572E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=15;CIGAR=1X;DP=1482;DPB=1482;DPRA=0;EPP=3.15506;EPPR=3.02364;GTI=0;LEN=1;MEANALT=2;MQM=47.2667;MQMR=52.9747;NS=1;NUMALT=1;ODDS=1903.72;PAIRED=1;PAIREDR=0.995904;PAO=0;PQA=0;PQR=0;PRO=0;QA=421;QR=49584;RO=1465;RPL=11;RPP=10.1038;RPPR=12.7352;RPR=4;RUN=1;SAF=9;SAP=4.31318;SAR=6;SRF=728;SRP=3.13036;SRR=737;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.665A>C|p.Asp222Ala|665/828|665/828|222/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1482:1465,15:1465:49584:15:421:0,-411.753,-4275.18 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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303 NC_045512.2 26069 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1483;DPB=1483;DPRA=0;EPP=3.0103;EPPR=3.1302;GTI=0;LEN=1;MEANALT=1;MQM=42.8125;MQMR=52.7764;NS=1;NUMALT=1;ODDS=1886.92;PAIRED=0.875;PAIREDR=0.99591;PAO=0;PQA=0;PQR=0;PRO=0;QA=576;QR=51331;RO=1467;RPL=16;RPP=37.7539;RPPR=4.08938;RPR=0;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=725;SRP=3.43808;SRR=742;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.677A>G|p.Glu226Gly|677/828|677/828|226/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1483:1467,16:1467:51331:16:576:0,-402.204,-4405.87 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
304 NC_045512.2 26089 . T A 2.41553E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=1477;DPB=1477;DPRA=0;EPP=3.13803;EPPR=4.17635;GTI=0;LEN=1;MEANALT=1;MQM=41.7647;MQMR=52.7048;NS=1;NUMALT=1;ODDS=1870.29;PAIRED=1;PAIREDR=0.994521;PAO=0;PQA=0;PQR=0;PRO=0;QA=586;QR=49501;RO=1460;RPL=16;RPP=31.7504;RPPR=8.36462;RPR=1;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=746;SRP=4.53331;SRR=714;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.697T>A|p.Tyr233Asn|697/828|697/828|233/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1477:1460,17:1460:49501:17:586:0,-399.573,-4252.67 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
305 NC_045512.2 26108 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1558;DPB=1558;DPRA=0;EPP=3.0103;EPPR=3.3708;GTI=0;LEN=1;MEANALT=1;MQM=51.8125;MQMR=52.0246;NS=1;NUMALT=1;ODDS=1968.1;PAIRED=1;PAIREDR=0.990272;PAO=0;PQA=0;PQR=0;PRO=0;QA=553;QR=52400;RO=1542;RPL=8;RPP=3.0103;RPPR=11.1442;RPR=8;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=768;SRP=3.061;SRR=774;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.716A>T|p.Glu239Val|716/828|716/828|239/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1558:1542,16:1542:52400:16:553:0,-419.335,-4448.58 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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306 NC_045512.2 26141 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=1542;DPB=1542;DPRA=0;EPP=3.13803;EPPR=3.06166;GTI=0;LEN=1;MEANALT=3;MQM=30.8235;MQMR=52.1393;NS=1;NUMALT=1;ODDS=1984.85;PAIRED=0.764706;PAIREDR=0.996058;PAO=0;PQA=0;PQR=0;PRO=0;QA=551;QR=50688;RO=1522;RPL=16;RPP=31.7504;RPPR=7.17062;RPR=1;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=758;SRP=3.06166;SRR=764;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.749A>T|p.Asp250Val|749/828|749/828|250/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1542:1522,17:1522:50688:17:551:0,-430.965,-4315.93 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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307 NC_045512.2 26145 . T C 4.23704E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1538;DPB=1538;DPRA=0;EPP=3.44459;EPPR=3.21656;GTI=0;LEN=1;MEANALT=2;MQM=47.8;MQMR=51.9208;NS=1;NUMALT=1;ODDS=1909.48;PAIRED=1;PAIREDR=0.991425;PAO=0;PQA=0;PQR=0;PRO=0;QA=678;QR=48753;RO=1516;RPL=14;RPP=9.95901;RPPR=34.3849;RPR=6;RUN=1;SAF=9;SAP=3.44459;SAR=11;SRF=758;SRP=3.0103;SRR=758;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.753T>C|p.Gly251Gly|753/828|753/828|251/275|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1538:1516,20:1516:48753:20:678:0,-407.159,-4121.98 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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308 NC_045512.2 26221 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=32;CIGAR=1X;DP=2217;DPB=2217;DPRA=0;EPP=3.28173;EPPR=3.583;GTI=0;LEN=1;MEANALT=2;MQM=48.5312;MQMR=50.4084;NS=1;NUMALT=1;ODDS=2709.72;PAIRED=1;PAIREDR=0.995879;PAO=0;PQA=0;PQR=0;PRO=0;QA=1101;QR=76749;RO=2184;RPL=15;RPP=3.28173;RPPR=759.033;RPR=17;RUN=1;SAF=16;SAP=3.0103;SAR=16;SRF=1104;SRP=3.583;SRR=1080;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-24G>A|||||24| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2217:2184,32:2184:76749:32:1101:0,-576.661,-6377.21 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
309 NC_045512.2 26533 . C T 6.38867E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=52;CIGAR=1X;DP=2958;DPB=2958;DPRA=0;EPP=9.02361;EPPR=16.2327;GTI=0;LEN=1;MEANALT=2;MQM=32.3077;MQMR=51.4386;NS=1;NUMALT=1;ODDS=3622.99;PAIRED=0.692308;PAIREDR=0.993804;PAO=0;PQA=0;PQR=0;PRO=0;QA=1770;QR=101214;RO=2905;RPL=12;RPP=35.7494;RPPR=3.28015;RPR=40;RUN=1;SAF=18;SAP=13.7006;SAR=34;SRF=1471;SRP=4.03362;SRR=1434;TYPE=snp;ANN=T|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.11C>T|p.Ser4Phe|11/669|11/669|4/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2958:2905,52:2905:101214:52:1770:0,-785.764,-8554.41 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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310 NC_045512.2 26542 . CTAT ATAG 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=131;CIGAR=1X2M1X;DP=2947;DPB=2947;DPRA=0;EPP=3.15949;EPPR=17.7373;GTI=0;LEN=4;MEANALT=5;MQM=38.9771;MQMR=51.3038;NS=1;NUMALT=1;ODDS=2841.52;PAIRED=0.755725;PAIREDR=0.99359;PAO=1;PQA=32;PQR=0;PRO=0;QA=4580;QR=99098;RO=2808;RPL=36;RPP=60.7118;RPPR=16.0793;RPR=95;RUN=1;SAF=65;SAP=3.02688;SAR=66;SRF=1418;SRP=3.61658;SRR=1390;TYPE=complex;ANN=ATAG|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.20_23delCTATinsATAG|p.ThrIle7AsnSer|20/669|20/669|7/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2947:2808,131:2808:99098:131:4580:0,-569.035,-8155.39 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
311 NC_045512.2 26554 . A G 1.18733E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=40;CIGAR=1X;DP=3289;DPB=3289;DPRA=0;EPP=3.22745;EPPR=16.114;GTI=0;LEN=1;MEANALT=2;MQM=39.325;MQMR=50.3211;NS=1;NUMALT=1;ODDS=4149.91;PAIRED=0.65;PAIREDR=0.9883;PAO=0;PQA=0;PQR=0;PRO=0;QA=1381;QR=113659;RO=3248;RPL=10;RPP=24.725;RPPR=189.393;RPR=30;RUN=1;SAF=21;SAP=3.22745;SAR=19;SRF=1620;SRP=3.05309;SRR=1628;TYPE=snp;ANN=G|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.32A>G|p.Glu11Gly|32/669|32/669|11/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3289:3248,40:3248:113659:40:1381:0,-898.198,-9489.65 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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312 NC_045512.2 26611 . C G 0.0 . AB=0.134243;ABP=4858.94;AC=1;AF=0.5;AN=2;AO=561;CIGAR=1X;DP=4179;DPB=4179;DPRA=0;EPP=3.19997;EPPR=9.88753;GTI=0;LEN=1;MEANALT=2;MQM=48.8645;MQMR=51.8661;NS=1;NUMALT=1;ODDS=409.84;PAIRED=0.982175;PAIREDR=0.986999;PAO=0;PQA=0;PQR=0;PRO=0;QA=19867;QR=126762;RO=3615;RPL=206;RPP=88.9441;RPPR=79.5669;RPR=355;RUN=1;SAF=285;SAP=3.32383;SAR=276;SRF=1845;SRP=6.38915;SRR=1770;TYPE=snp;ANN=G|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.89C>G|p.Thr30Arg|89/669|89/669|30/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4179:3615,561:3615:126762:561:19867:-380.436,0,-9637.08 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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313 NC_045512.2 26705 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=193;CIGAR=1X;DP=4508;DPB=4508;DPRA=0;EPP=3.29158;EPPR=3.62734;GTI=0;LEN=1;MEANALT=3;MQM=49.8187;MQMR=52.6518;NS=1;NUMALT=1;ODDS=4146.13;PAIRED=0.994819;PAIREDR=0.992577;PAO=0;PQA=0;PQR=0;PRO=0;QA=6785;QR=152705;RO=4311;RPL=116;RPP=20.1233;RPPR=31.3029;RPR=77;RUN=1;SAF=97;SAP=3.02155;SAR=96;SRF=2179;SRP=4.12298;SRR=2132;TYPE=snp;ANN=C|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.183T>C|p.Thr61Thr|183/669|183/669|61/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4508:4311,193:4311:152705:193:6785:0,-781.83,-12614.8 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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314 NC_045512.2 26767 . T C 67526.2 . AB=0.695281;ABP=1322.65;AC=1;AF=0.5;AN=2;AO=2770;CIGAR=1X;DP=3984;DPB=3984;DPRA=0;EPP=6.02371;EPPR=4.62278;GTI=0;LEN=1;MEANALT=2;MQM=50.2946;MQMR=53.2954;NS=1;NUMALT=1;ODDS=5439.65;PAIRED=0.998917;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=96278;QR=42353;RO=1212;RPL=1420;RPP=6.85153;RPPR=11.2949;RPR=1350;RUN=1;SAF=1358;SAP=5.29623;SAR=1412;SRF=599;SRP=3.36146;SRR=613;TYPE=snp;ANN=C|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.245T>C|p.Ile82Thr|245/669|245/669|82/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3984:1212,2770:1212:42353:2770:96278:-6898.83,0,-2508.19 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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315 NC_045512.2 26837 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=44;CIGAR=1X;DP=3100;DPB=3100;DPRA=0;EPP=4.78696;EPPR=3.17023;GTI=0;LEN=1;MEANALT=2;MQM=50.3409;MQMR=51.6887;NS=1;NUMALT=1;ODDS=3775.78;PAIRED=1;PAIREDR=0.997709;PAO=0;PQA=0;PQR=0;PRO=0;QA=1554;QR=105912;RO=3055;RPL=29;RPP=12.6832;RPPR=391.189;RPR=15;RUN=1;SAF=22;SAP=3.0103;SAR=22;SRF=1491;SRP=6.79812;SRR=1564;TYPE=snp;ANN=C|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.315T>C|p.Arg105Arg|315/669|315/669|105/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3100:3055,44:3055:105912:44:1554:0,-800.061,-8955.04 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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316 NC_045512.2 27059 . C T 3.69338E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=299;CIGAR=1X;DP=5267;DPB=5267;DPRA=0;EPP=3.88906;EPPR=4.10568;GTI=0;LEN=1;MEANALT=3;MQM=45.204;MQMR=51.677;NS=1;NUMALT=1;ODDS=4275.32;PAIRED=0.986622;PAIREDR=0.993341;PAO=0;PQA=0;PQR=0;PRO=0;QA=10578;QR=173846;RO=4956;RPL=185;RPP=39.6203;RPPR=25.3893;RPR=114;RUN=1;SAF=148;SAP=3.07566;SAR=151;SRF=2474;SRP=3.03834;SRR=2482;TYPE=snp;ANN=T|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.537C>T|p.Tyr179Tyr|537/669|537/669|179/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5267:4956,299:4956:173846:299:10578:0,-761.739,-14058.3 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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317 NC_045512.2 27115 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=184;CIGAR=1X;DP=4546;DPB=4546;DPRA=0;EPP=3.0103;EPPR=8.93164;GTI=0;LEN=1;MEANALT=2;MQM=48.6087;MQMR=51.3668;NS=1;NUMALT=1;ODDS=4300.67;PAIRED=1;PAIREDR=0.990131;PAO=0;PQA=0;PQR=0;PRO=0;QA=6564;QR=151056;RO=4357;RPL=90;RPP=3.19912;RPPR=3.37362;RPR=94;RUN=1;SAF=90;SAP=3.19912;SAR=94;SRF=2144;SRP=5.38312;SRR=2213;TYPE=snp;ANN=A|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.593G>A|p.Arg198His|593/669|593/669|198/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4546:4357,184:4357:151056:184:6564:0,-827.983,-12351.2 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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318 NC_045512.2 27143 . C T 1.70204E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=272;CIGAR=1X;DP=4401;DPB=4401;DPRA=0;EPP=3.2977;EPPR=6.99475;GTI=0;LEN=1;MEANALT=3;MQM=47.0993;MQMR=50.1321;NS=1;NUMALT=1;ODDS=3329.47;PAIRED=0.992647;PAIREDR=0.987394;PAO=0;PQA=0;PQR=0;PRO=0;QA=9558;QR=143551;RO=4125;RPL=154;RPP=13.3567;RPPR=237.208;RPR=118;RUN=1;SAF=133;SAP=3.2977;SAR=139;SRF=2054;SRP=3.16243;SRR=2071;TYPE=snp;ANN=T|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.621C>T|p.Asn207Asn|621/669|621/669|207/222|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4401:4125,272:4125:143551:272:9558:0,-556.834,-11234.5 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
319 NC_045512.2 27285 . T A 8.19702E-15 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=31;CIGAR=1X;DP=2885;DPB=2885;DPRA=0;EPP=3.08035;EPPR=5.2305;GTI=0;LEN=1;MEANALT=2;MQM=45;MQMR=53.3229;NS=1;NUMALT=1;ODDS=3664.07;PAIRED=1;PAIREDR=0.990182;PAO=0;PQA=0;PQR=0;PRO=0;QA=1108;QR=100423;RO=2852;RPL=0;RPP=70.3259;RPPR=3.99706;RPR=31;RUN=1;SAF=16;SAP=3.08035;SAR=15;SRF=1471;SRP=9.17753;SRR=1381;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.84T>A|p.Asn28Lys|84/186|84/186|28/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2885:2852,31:2852:100423:31:1108:0,-783.645,-8676.19 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
320 NC_045512.2 27291 . TTACA TA 1.11018E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=61;CIGAR=1M3D1M;DP=2674;DPB=2637.6;DPRA=0;EPP=3.0459;EPPR=3.01363;GTI=0;LEN=3;MEANALT=4;MQM=52.6721;MQMR=53.3507;NS=1;NUMALT=1;ODDS=3002.68;PAIRED=1;PAIREDR=0.989639;PAO=0.5;PQA=10.5;PQR=10.5;PRO=0.5;QA=2128;QR=92098;RO=2606;RPL=41;RPP=18.709;RPPR=33.0909;RPR=20;RUN=1;SAF=31;SAP=3.0459;SAR=30;SRF=1312;SRP=3.28028;SRR=1294;TYPE=del;ANN=TA|conservative_inframe_deletion|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.91_93delTAC|p.Tyr31del|91/186|91/186|31/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2674:2606,61:2606:92098:61:2128:0,-619.622,-7867.5 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
321 NC_045512.2 27335 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=78;CIGAR=1X;DP=3108;DPB=3108;DPRA=0;EPP=4.01252;EPPR=6.42569;GTI=0;LEN=1;MEANALT=2;MQM=44.7051;MQMR=53.372;NS=1;NUMALT=1;ODDS=3467.05;PAIRED=0.948718;PAIREDR=0.991411;PAO=0;PQA=0;PQR=0;PRO=0;QA=2703;QR=106229;RO=3027;RPL=39;RPP=3.0103;RPPR=10.3282;RPR=39;RUN=1;SAF=41;SAP=3.45573;SAR=37;SRF=1522;SRP=3.21762;SRR=1505;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.134C>T|p.Thr45Ile|134/186|134/186|45/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3108:3027,78:3027:106229:78:2703:0,-722.646,-9061.78 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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322 NC_045512.2 27344 . AA TT 1.55256E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=95;CIGAR=2X;DP=3040;DPB=3040.5;DPRA=0;EPP=3.21602;EPPR=5.24228;GTI=0;LEN=2;MEANALT=3;MQM=45.7684;MQMR=53.5352;NS=1;NUMALT=1;ODDS=3202.24;PAIRED=0.978947;PAIREDR=0.991505;PAO=1;PQA=36;PQR=0;PRO=0;QA=3335;QR=103633;RO=2943;RPL=40;RPP=8.15326;RPPR=3.01104;RPR=55;RUN=1;SAF=47;SAP=3.03316;SAR=48;SRF=1464;SRP=3.17631;SRR=1479;TYPE=complex;ANN=TT|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.143_144delAAinsTT|p.Lys48Ile|143/186|143/186|48/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3040:2943,95:2943:103633:95:3335:0,-652.573,-8806.08 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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323 NC_045512.2 27354 . A G 1.21024E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=3037;DPB=3037;DPRA=0;EPP=4.1599;EPPR=3.54384;GTI=0;LEN=1;MEANALT=2;MQM=44.5;MQMR=53.3401;NS=1;NUMALT=1;ODDS=3477.58;PAIRED=0.970588;PAIREDR=0.990226;PAO=0;PQA=0;PQR=0;PRO=0;QA=2347;QR=103746;RO=2967;RPL=33;RPP=3.13803;RPPR=3.01689;RPR=35;RUN=1;SAF=32;SAP=3.52123;SAR=36;SRF=1482;SRP=3.01689;SRR=1485;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.153A>G|p.Gln51Gln|153/186|153/186|51/61|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3037:2967,68:2967:103746:68:2347:0,-731.506,-8865.91 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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324 NC_045512.2 27393 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=73;CIGAR=1X;DP=2871;DPB=2871;DPRA=0;EPP=3.04005;EPPR=4.51494;GTI=0;LEN=1;MEANALT=3;MQM=53.1233;MQMR=53.4395;NS=1;NUMALT=1;ODDS=3121.07;PAIRED=1;PAIREDR=0.993916;PAO=0;PQA=0;PQR=0;PRO=0;QA=2586;QR=97778;RO=2794;RPL=38;RPP=3.27802;RPPR=84.5967;RPR=35;RUN=1;SAF=36;SAP=3.04005;SAR=37;SRF=1368;SRP=5.62477;SRR=1426;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1C>T|||||1| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2871:2794,73:2794:97778:73:2586:0,-633.624,-8285.14 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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325 NC_045512.2 27527 . C T 20959.5 . AB=0.321568;ABP=998.011;AC=1;AF=0.5;AN=2;AO=1157;CIGAR=1X;DP=3598;DPB=3598;DPRA=0;EPP=3.16232;EPPR=3.97985;GTI=0;LEN=1;MEANALT=2;MQM=48.0026;MQMR=50.8844;NS=1;NUMALT=1;ODDS=4826.11;PAIRED=0.994814;PAIREDR=0.99672;PAO=0;PQA=0;PQR=0;PRO=0;QA=40472;QR=84380;RO=2439;RPL=514;RPP=34.2423;RPPR=4.81318;RPR=643;RUN=1;SAF=592;SAP=4.3785;SAR=565;SRF=1214;SRP=3.11803;SRR=1225;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.134C>T|p.Pro45Leu|134/366|134/366|45/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3598:2439,1157:2439:84380:1157:40472:-2209.43,0,-6034.2 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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326 NC_045512.2 27566 . G T 5352.15 . AB=0.189077;ABP=3231.63;AC=1;AF=0.5;AN=2;AO=727;CIGAR=1X;DP=3845;DPB=3845;DPRA=0;EPP=3.08497;EPPR=3.59619;GTI=0;LEN=1;MEANALT=2;MQM=46.6768;MQMR=50.3141;NS=1;NUMALT=1;ODDS=1232.38;PAIRED=0.997249;PAIREDR=0.983959;PAO=0;PQA=0;PQR=0;PRO=0;QA=25485;QR=108948;RO=3117;RPL=374;RPP=4.32752;RPPR=10.1169;RPR=353;RUN=1;SAF=373;SAP=4.08857;SAR=354;SRF=1591;SRP=5.95367;SRR=1526;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.173G>T|p.Cys58Phe|173/366|173/366|58/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3845:3117,727:3117:108948:727:25485:-891.399,0,-7962.88 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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327 NC_045512.2 27607 . A T 5075.59 . AB=0.18089;ABP=3640.94;AC=1;AF=0.5;AN=2;AO=744;CIGAR=1X;DP=4113;DPB=4113;DPRA=0;EPP=3.057;EPPR=3.0161;GTI=0;LEN=1;MEANALT=1;MQM=48.8401;MQMR=48.9326;NS=1;NUMALT=1;ODDS=1168.7;PAIRED=0.995968;PAIREDR=0.996438;PAO=0;PQA=0;PQR=0;PRO=0;QA=26185;QR=118988;RO=3369;RPL=355;RPP=6.38425;RPPR=98.548;RPR=389;RUN=1;SAF=375;SAP=3.11537;SAR=369;SRF=1695;SRP=3.29454;SRR=1674;TYPE=snp;ANN=T|stop_gained|HIGH|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.214A>T|p.Lys72*|214/366|214/366|72/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4113:3369,744:3369:118988:744:26185:-910.007,0,-8604.41 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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328 NC_045512.2 27625 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=75;CIGAR=1X;DP=4049;DPB=4049;DPRA=0;EPP=3.03925;EPPR=4.91287;GTI=0;LEN=1;MEANALT=2;MQM=49.64;MQMR=49.5318;NS=1;NUMALT=1;ODDS=4751.09;PAIRED=1;PAIREDR=0.997231;PAO=0;PQA=0;PQR=0;PRO=0;QA=2649;QR=139228;RO=3973;RPL=31;RPP=7.90335;RPPR=56.556;RPR=44;RUN=1;SAF=37;SAP=3.03925;SAR=38;SRF=1999;SRP=3.3519;SRR=1974;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.232C>T|p.Arg78Cys|232/366|232/366|78/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4049:3973,75:3973:139228:75:2649:0,-1000.05,-11370.5 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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329 NC_045512.2 27629 . C A 6085.31 . AB=0.191634;ABP=3399.26;AC=1;AF=0.5;AN=2;AO=788;CIGAR=1X;DP=4112;DPB=4112;DPRA=0;EPP=3.18666;EPPR=6.31437;GTI=0;LEN=1;MEANALT=3;MQM=47.4569;MQMR=50.4522;NS=1;NUMALT=1;ODDS=1401.19;PAIRED=0.997462;PAIREDR=0.996378;PAO=0;PQA=0;PQR=0;PRO=0;QA=27332;QR=115748;RO=3313;RPL=348;RPP=26.3343;RPPR=44.9644;RPR=440;RUN=1;SAF=396;SAP=3.05439;SAR=392;SRF=1671;SRP=3.56152;SRR=1642;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.236C>A|p.Ala79Asp|236/366|236/366|79/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4112:3313,788:3313:115748:788:27332:-982.348,0,-8505.98 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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330 NC_045512.2 27638 . T C 53884.9 . AB=0.555904;ABP=115.422;AC=1;AF=0.5;AN=2;AO=2302;CIGAR=1X;DP=4141;DPB=4141;DPRA=0;EPP=3.31593;EPPR=4.07359;GTI=0;LEN=1;MEANALT=2;MQM=48.9466;MQMR=52.1322;NS=1;NUMALT=1;ODDS=9722.66;PAIRED=0.996959;PAIREDR=0.996736;PAO=0;PQA=0;PQR=0;PRO=0;QA=80818;QR=63827;RO=1838;RPL=1086;RPP=18.952;RPPR=13.4494;RPR=1216;RUN=1;SAF=1166;SAP=3.85927;SAR=1136;SRF=930;SRP=3.58211;SRR=908;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.245T>C|p.Val82Ala|245/366|245/366|82/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4141:1838,2302:1838:63827:2302:80818:-5410.76,0,-4244.12 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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331 NC_045512.2 27652 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=46;CIGAR=1X;DP=4346;DPB=4346;DPRA=0;EPP=4.70971;EPPR=4.53826;GTI=0;LEN=1;MEANALT=2;MQM=46.5435;MQMR=50.996;NS=1;NUMALT=1;ODDS=5527.41;PAIRED=1;PAIREDR=0.996743;PAO=0;PQA=0;PQR=0;PRO=0;QA=1543;QR=149454;RO=4299;RPL=1;RPP=94.401;RPPR=11.1572;RPR=45;RUN=1;SAF=25;SAP=3.76559;SAR=21;SRF=2162;SRP=3.32599;SRR=2137;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.259T>A|p.Phe87Ile|259/366|259/366|87/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4346:4299,46:4299:149454:46:1543:0,-1185.76,-12544.7 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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332 NC_045512.2 27696 . T C 9.00448E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=57;CIGAR=1X;DP=5194;DPB=5194;DPRA=0;EPP=3.0484;EPPR=3.68677;GTI=0;LEN=1;MEANALT=2;MQM=47.6491;MQMR=52.3927;NS=1;NUMALT=1;ODDS=6534.38;PAIRED=1;PAIREDR=0.985592;PAO=0;PQA=0;PQR=0;PRO=0;QA=1986;QR=181866;RO=5136;RPL=28;RPP=3.0484;RPPR=15.8108;RPR=29;RUN=1;SAF=28;SAP=3.0484;SAR=29;SRF=2583;SRP=3.39081;SRR=2553;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.303T>C|p.Phe101Phe|303/366|303/366|101/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:5194:5136,57:5136:181866:57:1986:0,-1404.69,-15506.5 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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333 NC_045512.2 27752 . C T 65709.1 . AB=0.548083;ABP=103.035;AC=1;AF=0.5;AN=2;AO=2730;CIGAR=1X;DP=4981;DPB=4981;DPRA=0;EPP=7.60459;EPPR=11.013;GTI=0;LEN=1;MEANALT=2;MQM=50.2674;MQMR=52.0516;NS=1;NUMALT=1;ODDS=12106.1;PAIRED=0.989377;PAIREDR=0.993769;PAO=0;PQA=0;PQR=0;PRO=0;QA=96766;QR=78943;RO=2247;RPL=1468;RPP=36.7644;RPPR=20.1047;RPR=1262;RUN=1;SAF=1333;SAP=6.2683;SAR=1397;SRF=1104;SRP=4.48018;SRR=1143;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.359C>T|p.Thr120Ile|359/366|359/366|120/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4981:2247,2730:2247:78943:2730:96766:-6594.66,0,-5279.74 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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334 NC_045512.2 27777 . G A 2.06367E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=74;CIGAR=1X;DP=4362;DPB=4362;DPRA=0;EPP=3.0103;EPPR=7.8761;GTI=0;LEN=1;MEANALT=2;MQM=46.5676;MQMR=51.2193;NS=1;NUMALT=1;ODDS=5211.88;PAIRED=1;PAIREDR=0.988567;PAO=0;PQA=0;PQR=0;PRO=0;QA=2614;QR=150803;RO=4286;RPL=49;RPP=19.9126;RPPR=772.005;RPR=25;RUN=1;SAF=36;SAP=3.12768;SAR=38;SRF=2091;SRP=8.49015;SRR=2195;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.22G>A|p.Asp8Asn|22/132|22/132|8/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4362:4286,74:4286:150803:74:2614:0,-1105.72,-12659.9 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
335 NC_045512.2 27857 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1159;DPB=1159;DPRA=0;EPP=3.0103;EPPR=3.05796;GTI=0;LEN=1;MEANALT=2;MQM=46.75;MQMR=48.8033;NS=1;NUMALT=1;ODDS=1424.16;PAIRED=1;PAIREDR=0.924495;PAO=0;PQA=0;PQR=0;PRO=0;QA=528;QR=39898;RO=1139;RPL=10;RPP=5.18177;RPPR=3.10372;RPR=6;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=573;SRP=3.10372;SRR=566;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.102G>A|p.Leu34Leu|102/132|102/132|34/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1159:1139,16:1139:39898:16:528:0,-302.123,-3258.71 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
336 NC_045512.2 27864 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=66;CIGAR=1X;DP=1237;DPB=1237;DPRA=0;EPP=3.53672;EPPR=3.05674;GTI=0;LEN=1;MEANALT=2;MQM=43.9848;MQMR=49.7802;NS=1;NUMALT=1;ODDS=1098.27;PAIRED=0.984848;PAIREDR=0.939264;PAO=0;PQA=0;PQR=0;PRO=0;QA=2278;QR=40992;RO=1169;RPL=1;RPP=137.773;RPPR=9.04547;RPR=65;RUN=1;SAF=34;SAP=3.1419;SAR=32;SRF=587;SRP=3.05674;SRR=582;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.109C>A|p.His37Asn|109/132|109/132|37/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1237:1169,66:1169:40992:66:2278:0,-193.616,-3261.46 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
337 NC_045512.2 27870 . GAAAC TAAAT,TAAAC,GAAAT 28573.3 . AB=0.0133648,0.0196541,0.855346;ABP=2619.44,2552.24,1398.11;AC=0,0,1;AF=0,0,0.5;AN=2;AO=17,25,1088;CIGAR=1X3M1X,1X4M,4M1X;DP=1272;DPB=1277;DPRA=0,0,0;EPP=3.13803,3.09716,3.52123;EPPR=3.26577;GTI=0;LEN=5,1,1;MEANALT=7,7,7;MQM=35.8824,37.32,50.6305;MQMR=52.1103;NS=1;NUMALT=3;ODDS=350.184;PAIRED=0.823529,0.76,0.983456;PAIREDR=0.941176;PAO=12.5,0.5,12;PQA=409,7,402;PQR=0;PRO=0;QA=597,665,38499;QR=4734;RO=136;RPL=1,0,534;RPP=31.7504,57.2971,3.80864;RPPR=3.26577;RPR=16,25,554;RUN=1,1,1;SAF=8,12,550;SAP=3.13803,3.09716,3.2977;SAR=9,13,538;SRF=70;SRP=3.26577;SRR=66;TYPE=complex,snp,snp;ANN=TAAAC|stop_gained|HIGH|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.115G>T|p.Glu39*|115/132|115/132|39/43|| GT:DP:AD:RO:QR:AO:QA:GL 0/3:1272:136,17,25,1088:136:4734:17,25,1088:597,665,38499:-2896.73,-2902.78,-3263.11,-2887.86,-3218.42,-3245.78,0,-330.591,-315.679,-37.9604 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
338 NC_045512.2 27942 . C T 0.0 . AB=0.128987;ABP=1690.03;AC=1;AF=0.5;AN=2;AO=182;CIGAR=1X;DP=1411;DPB=1411;DPRA=0;EPP=3.05802;EPPR=4.49623;GTI=0;LEN=1;MEANALT=1;MQM=45.6429;MQMR=53.1587;NS=1;NUMALT=1;ODDS=303.191;PAIRED=0.983516;PAIREDR=0.981286;PAO=0;PQA=0;PQR=0;PRO=0;QA=6276;QR=43106;RO=1229;RPL=105;RPP=12.3643;RPPR=3.09688;RPR=77;RUN=1;SAF=89;SAP=3.2012;SAR=93;SRF=616;SRP=3.0262;SRR=613;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.49C>T|p.His17Tyr|49/366|49/366|17/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1411:1229,182:1229:43106:182:6276:-65.6317,0,-3323.38 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
|
339 NC_045512.2 27972 . C T 7.85929E-14 . AB=0.114679;ABP=1689.83;AC=1;AF=0.5;AN=2;AO=150;CIGAR=1X;DP=1308;DPB=1308;DPRA=0;EPP=3.0103;EPPR=3.37975;GTI=0;LEN=1;MEANALT=3;MQM=46.5933;MQMR=53.855;NS=1;NUMALT=1;ODDS=387.178;PAIRED=1;PAIREDR=0.987847;PAO=0;PQA=0;PQR=0;PRO=0;QA=5274;QR=39803;RO=1152;RPL=87;RPP=11.3488;RPPR=3.28173;RPR=63;RUN=1;SAF=74;SAP=3.06821;SAR=76;SRF=571;SRP=3.1988;SRR=581;TYPE=snp;ANN=T|stop_gained|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.79C>T|p.Gln27*|79/366|79/366|27/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:1308:1152,150:1152:39803:150:5274:-29.6341,0,-3107.07 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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340 NC_045512.2 27981 . CCA CTACA 2.43493E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=15;CIGAR=1M2I2M;DP=1259;DPB=1269.33;DPRA=0;EPP=3.15506;EPPR=4.91888;GTI=0;LEN=2;MEANALT=4;MQM=47;MQMR=53.2139;NS=1;NUMALT=1;ODDS=1576.8;PAIRED=0.933333;PAIREDR=0.991929;PAO=0.5;PQA=0;PQR=0;PRO=0.5;QA=476;QR=43082;RO=1239;RPL=2;RPP=20.5268;RPPR=14.5091;RPR=13;RUN=1;SAF=7;SAP=3.15506;SAR=8;SRF=615;SRP=3.15226;SRR=624;TYPE=ins;ANN=CTACA|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.88_89insTA|p.Pro30fs|89/366|89/366|30/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1259:1239,15:1239:43082:15:476:0,-335.717,-3717.41 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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341 NC_045512.2 27987 . GTAG GG 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1M2D1M;DP=1259;DPB=1250.5;DPRA=0;EPP=3.13803;EPPR=3.35409;GTI=0;LEN=2;MEANALT=3;MQM=48.1176;MQMR=53.3328;NS=1;NUMALT=1;ODDS=1571.36;PAIRED=0.941176;PAIREDR=0.991115;PAO=0;PQA=0;PQR=0;PRO=0;QA=486;QR=43228;RO=1238;RPL=2;RPP=24.5973;RPPR=31.7481;RPR=15;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=609;SRP=3.71191;SRR=629;TYPE=del;ANN=GG|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.95_96delTA|p.Val32fs|95/366|95/366|32/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1259:1238,17:1238:43228:17:486:0,-336.27,-3738.37 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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342 NC_045512.2 28048 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=133;CIGAR=1X;DP=1234;DPB=1234;DPRA=0;EPP=3.15724;EPPR=3.24894;GTI=0;LEN=1;MEANALT=1;MQM=42.4511;MQMR=52.6803;NS=1;NUMALT=1;ODDS=498.144;PAIRED=1;PAIREDR=0.993642;PAO=0;PQA=0;PQR=0;PRO=0;QA=4623;QR=38646;RO=1101;RPL=56;RPP=10.2104;RPPR=15.3193;RPR=77;RUN=1;SAF=65;SAP=3.15724;SAR=68;SRF=528;SRP=7.00415;SRR=573;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.155G>T|p.Arg52Ile|155/366|155/366|52/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:1234:1101,133:1101:38646:133:4623:0,-20.4073,-2999.34 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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343 NC_045512.2 28095 . A T 1.91419E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=95;CIGAR=1X;DP=2258;DPB=2258;DPRA=0;EPP=3.03316;EPPR=31.6832;GTI=0;LEN=1;MEANALT=1;MQM=36.3368;MQMR=50.2603;NS=1;NUMALT=1;ODDS=2252.59;PAIRED=1;PAIREDR=0.992141;PAO=0;PQA=0;PQR=0;PRO=0;QA=3257;QR=76414;RO=2163;RPL=75;RPP=72.1546;RPPR=1509.51;RPR=20;RUN=1;SAF=46;SAP=3.21602;SAR=49;SRF=1157;SRP=25.9006;SRR=1006;TYPE=snp;ANN=T|stop_gained|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.202A>T|p.Lys68*|202/366|202/366|68/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2258:2163,95:2163:76414:95:3257:0,-455.717,-6188.95 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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344 NC_045512.2 28111 . A G 30254.2 . AB=0.521647;ABP=14.5739;AC=1;AF=0.5;AN=2;AO=1482;CIGAR=1X;DP=2841;DPB=2841;DPRA=0;EPP=22.0524;EPPR=10.6289;GTI=0;LEN=1;MEANALT=2;MQM=47.7821;MQMR=51.2771;NS=1;NUMALT=1;ODDS=6966.29;PAIRED=0.992578;PAIREDR=0.992631;PAO=0;PQA=0;PQR=0;PRO=0;QA=51828;QR=48256;RO=1357;RPL=66;RPP=2673.39;RPPR=281.268;RPR=1416;RUN=1;SAF=796;SAP=20.7396;SAR=686;SRF=701;SRP=6.25071;SRR=656;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.218A>G|p.Tyr73Cys|218/366|218/366|73/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2841:1357,1482:1357:48256:1482:51828:-3367.71,0,-3253.93 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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345 NC_045512.2 28242 . GTTTTAGATTTCA GTTTTAA,GTTTTTAGATTTCA 21929.6 . AB=0.252466,0.0809736;ABP=3348.5,9589.76;AC=1,0;AF=0.5,0;AN=2;AO=1587,509;CIGAR=6M6D1M,1M1I12M;DP=6286;DPB=5604.62;DPRA=0,0;EPP=3.40574,3.11695;EPPR=3.2873;GTI=0;LEN=6,1;MEANALT=21,21;MQM=47.1979,46.4597;MQMR=50.1179;NS=1;NUMALT=2;ODDS=5049.48;PAIRED=0.993699,0.994106;PAIREDR=0.99156;PAO=18.6667,39.1667;PQA=641,1351;PQR=1351;PRO=39.1667;QA=52030,16119;QR=145691;RO=4147;RPL=901,310;RPP=66.2594,55.5736;RPPR=51.0838;RPR=686,199;RUN=1,1;SAF=786,251;SAP=3.31816,3.21934;SAR=801,258;SRF=2052;SRP=3.97848;SRR=2095;TYPE=del,ins;ANN=GTTTTTAGATTTCA|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.353dupT|p.Leu118fs|354/366|354/366|118/121|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:6286:4147,1587,509:4147:145691:1587,509:52030,16119:-2465.57,0,-10582,-2450.21,-9796.04,-13356.8 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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346 NC_045512.2 28270 . TAAAATG TAAATG 162166.0 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6075;CIGAR=1M1D5M;DP=6091;DPB=5242.14;DPRA=0;EPP=3.02781;EPPR=0;GTI=0;LEN=1;MEANALT=13;MQM=46.504;MQMR=0;NS=1;NUMALT=1;ODDS=8426.34;PAIRED=0.985021;PAIREDR=0;PAO=62.5;PQA=2061.5;PQR=2085.5;PRO=63.5;QA=184797;QR=0;RO=0;RPL=2885;RPP=36.2615;RPPR=0;RPR=3190;RUN=1;SAF=3053;SAP=3.3538;SAR=3022;SRF=0;SRP=0;SRR=0;TYPE=del;ANN=TAAATG|frameshift_variant&start_lost|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1delA|p.Met1fs|1/1260|1/1260|1/419||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 1/1:6091:0,6075:0:0:6075:184797:-16226,-1828.76,0 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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347 NC_045512.2 28280 . GAT CTA 78730.3 . AB=0.542129;ABP=100.346;AC=1;AF=0.5;AN=2;AO=3423;CIGAR=3X;DP=6314;DPB=6358.67;DPRA=0;EPP=4.66031;EPPR=4.82376;GTI=0;LEN=3;MEANALT=9;MQM=47.7812;MQMR=44.7071;NS=1;NUMALT=1;ODDS=13474;PAIRED=0.991528;PAIREDR=0.969739;PAO=134;PQA=4677;PQR=0;PRO=0;QA=120731;QR=100878;RO=2875;RPL=2093;RPP=372.325;RPPR=363.649;RPR=1330;RUN=1;SAF=1701;SAP=3.29006;SAR=1722;SRF=1446;SRP=3.22858;SRR=1429;TYPE=mnp;ANN=CTA|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.7_9delGATinsCTA|p.Asp3Leu|7/1260|7/1260|3/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:6314:2875,3423:2875:100878:3423:120731:-7930.42,0,-5908.15 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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348 NC_045512.2 28295 . A G 1.00676E-12 . AB=0.129612;ABP=9012.63;AC=1;AF=0.5;AN=2;AO=980;CIGAR=1X;DP=7561;DPB=7561;DPRA=0;EPP=3.23188;EPPR=3.26911;GTI=0;LEN=1;MEANALT=3;MQM=45.3653;MQMR=46.2847;NS=1;NUMALT=1;ODDS=1467.02;PAIRED=0.945918;PAIREDR=0.96017;PAO=0;PQA=0;PQR=0;PRO=0;QA=34084;QR=230830;RO=6578;RPL=539;RPP=24.2907;RPPR=6.58078;RPR=441;RUN=1;SAF=482;SAP=3.57754;SAR=498;SRF=3262;SRP=3.9729;SRR=3316;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.22A>G|p.Asn8Asp|22/1260|22/1260|8/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:7561:6578,980:6578:230830:980:34084:-382.745,0,-16005.3 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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349 NC_045512.2 28461 . A G 15382.4 . AB=0.361009;ABP=368.81;AC=1;AF=0.5;AN=2;AO=787;CIGAR=1X;DP=2180;DPB=2180;DPRA=0;EPP=4.00636;EPPR=32.7183;GTI=0;LEN=1;MEANALT=2;MQM=48.2071;MQMR=50.8757;NS=1;NUMALT=1;ODDS=3541.92;PAIRED=0.986023;PAIREDR=0.984914;PAO=0;PQA=0;PQR=0;PRO=0;QA=27472;QR=45714;RO=1392;RPL=252;RPP=223.99;RPPR=356.461;RPR=535;RUN=1;SAF=405;SAP=4.4699;SAR=382;SRF=637;SRP=24.7313;SRR=755;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.188A>G|p.Asp63Gly|188/1260|188/1260|63/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:2180:1392,787:1392:45714:787:27472:-1606.4,0,-3204.04 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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350 NC_045512.2 28567 . C T 4.22129E-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=26;CIGAR=1X;DP=2372;DPB=2372;DPRA=0;EPP=3.0103;EPPR=4.08121;GTI=0;LEN=1;MEANALT=2;MQM=50.0769;MQMR=52.7534;NS=1;NUMALT=1;ODDS=2985.45;PAIRED=1;PAIREDR=0.995307;PAO=0;PQA=0;PQR=0;PRO=0;QA=906;QR=81075;RO=2344;RPL=4;RPP=30.0702;RPPR=35.7528;RPR=22;RUN=1;SAF=13;SAP=3.0103;SAR=13;SRF=1173;SRP=3.01401;SRR=1171;TYPE=snp;ANN=T|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.294C>T|p.Asp98Asp|294/1260|294/1260|98/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2372:2344,26:2344:81075:26:906:0,-636.928,-6974.26 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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351 NC_045512.2 28579 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=86;CIGAR=1X;DP=2340;DPB=2340;DPRA=0;EPP=3.1113;EPPR=5.22994;GTI=0;LEN=1;MEANALT=1;MQM=48.9651;MQMR=52.7955;NS=1;NUMALT=1;ODDS=2324.18;PAIRED=1;PAIREDR=0.996894;PAO=0;PQA=0;PQR=0;PRO=0;QA=2951;QR=78442;RO=2254;RPL=40;RPP=3.91929;RPPR=39.2683;RPR=46;RUN=1;SAF=42;SAP=3.1113;SAR=44;SRF=1099;SRP=6.03148;SRR=1155;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.306A>T|p.Lys102Asn|306/1260|306/1260|102/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2340:2254,86:2254:78442:86:2951:0,-458.341,-6586.23 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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352 NC_045512.2 28598 . T C 2.20595E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=27;CIGAR=1X;DP=2328;DPB=2328;DPRA=0;EPP=3.09072;EPPR=3.05658;GTI=0;LEN=1;MEANALT=2;MQM=46.5185;MQMR=52.5028;NS=1;NUMALT=1;ODDS=2914.06;PAIRED=1;PAIREDR=0.996085;PAO=0;PQA=0;PQR=0;PRO=0;QA=942;QR=80683;RO=2299;RPL=16;RPP=5.02092;RPPR=42.7041;RPR=11;RUN=1;SAF=13;SAP=3.09072;SAR=14;SRF=1156;SRP=3.16993;SRR=1143;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.325T>C|p.Tyr109His|325/1260|325/1260|109/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2328:2299,27:2299:80683:27:942:0,-623.497,-6905.87 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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353 NC_045512.2 28881 . GGGG AACC,AACG,TGGG 91355.5 . AB=0.0998312,0.256089,0.638775;ABP=5771.14,2145.96,696.709;AC=0,1,1;AF=0,0.5,0.5;AN=2;AO=414,1062,2649;CIGAR=4X,3X1M,1X3M;DP=4147;DPB=4199.25;DPRA=0,0,0;EPP=3.03128,3.08391,3.30622;EPPR=5.18177;GTI=0;LEN=4,3,1;MEANALT=14,14,14;MQM=48.314,48.1742,48.4179;MQMR=60;NS=1;NUMALT=3;ODDS=3919.48;PAIRED=1,0.997175,1;PAIREDR=1;PAO=10.5,2.5,101;PQA=343,88,3369;PQR=1079;PRO=62;QA=14330,33717,84424;QR=21;RO=1;RPL=203,506,1423;RPP=3.34599,8.12205,34.8233;RPPR=5.18177;RPR=211,556,1226;RUN=1,1,1;SAF=207,534,1330;SAP=3.0103,3.08391,3.10949;SAR=207,528,1319;SRF=0;SRP=5.18177;SRR=1;TYPE=complex,mnp,snp;ANN=TGGG|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.608G>T|p.Arg203Met|608/1260|608/1260|203/419|| GT:DP:AD:RO:QR:AO:QA:GL 2/3:4147:1,414,1062,2649:1:21:414,1062,2649:14330,33717,84424:-9304.73,-8260.38,-8137.34,-6643.97,-5600.91,-6325.87,-2659.48,-1616.42,0,-1863.64 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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354 NC_045512.2 28915 . CG TT,CT 52376.7 . AB=0.0279205,0.547018;ABP=8669.27,88.9772;AC=0,1;AF=0,0.5;AN=2;AO=125,2449;CIGAR=2X,1M1X;DP=4477;DPB=4484;DPRA=0,0;EPP=3.16665,3.56447;EPPR=3.56579;GTI=0;LEN=2,1;MEANALT=7,7;MQM=44.744,46.5545;MQMR=49.2706;NS=1;NUMALT=2;ODDS=9522.4;PAIRED=1,0.998367;PAIREDR=0.996829;PAO=8,6;PQA=264,196;PQR=0;PRO=0;QA=4248,82127;QR=65723;RO=1892;RPL=62,1210;RPP=3.02767,3.756;RPPR=8.96004;RPR=63,1239;RUN=1,1;SAF=64,1220;SAP=3.16665,3.08212;SAR=61,1229;SRF=929;SRP=4.33706;SRR=963;TYPE=mnp,snp;ANN=CT|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.643G>T|p.Gly215Cys|643/1260|643/1260|215/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/2:4477:1892,125,2449:1892:65723:125,2449:4248,82127:-5262.66,-5540.44,-10401,0,-4606.45,-4161 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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355 NC_045512.2 28972 . A G 5.40026E-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=108;CIGAR=1X;DP=4047;DPB=4047;DPRA=0;EPP=3.0103;EPPR=5.63492;GTI=0;LEN=1;MEANALT=1;MQM=44.75;MQMR=46.8825;NS=1;NUMALT=1;ODDS=4445.98;PAIRED=0.981481;PAIREDR=0.995684;PAO=0;PQA=0;PQR=0;PRO=0;QA=3804;QR=138740;RO=3939;RPL=56;RPP=3.332;RPPR=289.586;RPR=52;RUN=1;SAF=52;SAP=3.332;SAR=56;SRF=1921;SRP=8.19725;SRR=2018;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.699A>G|p.Lys233Lys|699/1260|699/1260|233/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:4047:3939,108:3939:138740:108:3804:0,-922.009,-10833.9 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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356 NC_045512.2 28977 . C T 25897.3 . AB=0.383986;ABP=459.997;AC=1;AF=0.5;AN=2;AO=1501;CIGAR=1X;DP=3909;DPB=3909;DPRA=0;EPP=3.91448;EPPR=5.26474;GTI=0;LEN=1;MEANALT=1;MQM=41.2438;MQMR=50.309;NS=1;NUMALT=1;ODDS=5963.07;PAIRED=0.997335;PAIREDR=0.995432;PAO=0;PQA=0;PQR=0;PRO=0;QA=52393;QR=84353;RO=2408;RPL=949;RPP=231.021;RPPR=135.982;RPR=552;RUN=1;SAF=735;SAP=4.40056;SAR=766;SRF=1191;SRP=3.6199;SRR=1217;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.704C>T|p.Ser235Phe|704/1260|704/1260|235/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3909:2408,1501:2408:84353:1501:52393:-2668.08,0,-5930.49 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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357 NC_045512.2 29000 . G T 2875.6 . AB=0.194681;ABP=3047.47;AC=1;AF=0.5;AN=2;AO=732;CIGAR=1X;DP=3760;DPB=3760;DPRA=0;EPP=3.97144;EPPR=12.9956;GTI=0;LEN=1;MEANALT=1;MQM=36.9194;MQMR=48.4699;NS=1;NUMALT=1;ODDS=662.131;PAIRED=0.998634;PAIREDR=0.988771;PAO=0;PQA=0;PQR=0;PRO=0;QA=25394;QR=104500;RO=3028;RPL=449;RPP=84.755;RPPR=22.7716;RPR=283;RUN=1;SAF=356;SAP=4.1969;SAR=376;SRF=1504;SRP=3.29715;SRR=1524;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.727G>T|p.Gly243Cys|727/1260|727/1260|243/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:3760:3028,732:3028:104500:732:25394:-631.313,0,-7432.98 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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changeset
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358 NC_045512.2 29029 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=74;CIGAR=1X;DP=3572;DPB=3572;DPRA=0;EPP=3.47981;EPPR=17.1686;GTI=0;LEN=1;MEANALT=2;MQM=38.5541;MQMR=46.4673;NS=1;NUMALT=1;ODDS=4202.1;PAIRED=0.986486;PAIREDR=0.985702;PAO=0;PQA=0;PQR=0;PRO=0;QA=2455;QR=120356;RO=3497;RPL=47;RPP=14.748;RPPR=272.678;RPR=27;RUN=1;SAF=36;SAP=3.12768;SAR=38;SRF=1756;SRP=3.15001;SRR=1741;TYPE=snp;ANN=C|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.756T>C|p.Ala252Ala|756/1260|756/1260|252/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3572:3497,74:3497:120356:74:2455:0,-898.696,-9450.46 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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359 NC_045512.2 29039 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=149;CIGAR=1X;DP=3516;DPB=3516;DPRA=0;EPP=4.77371;EPPR=20.1454;GTI=0;LEN=1;MEANALT=1;MQM=37.7181;MQMR=47.6341;NS=1;NUMALT=1;ODDS=3473.2;PAIRED=0.973154;PAIREDR=0.985744;PAO=0;PQA=0;PQR=0;PRO=0;QA=5164;QR=118588;RO=3367;RPL=86;RPP=10.7198;RPPR=174.061;RPR=63;RUN=1;SAF=76;SAP=3.14146;SAR=73;SRF=1658;SRP=4.68776;SRR=1709;TYPE=snp;ANN=T|stop_gained|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.766A>T|p.Lys256*|766/1260|766/1260|256/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3516:3367,149:3367:118588:149:5164:0,-709.856,-9327.62 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
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360 NC_045512.2 29049 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=101;CIGAR=1X;DP=3347;DPB=3347;DPRA=0;EPP=6.64375;EPPR=12.4923;GTI=0;LEN=1;MEANALT=2;MQM=43.099;MQMR=49.1378;NS=1;NUMALT=1;ODDS=3614.81;PAIRED=0.960396;PAIREDR=0.990133;PAO=0;PQA=0;PQR=0;PRO=0;QA=3321;QR=110630;RO=3243;RPL=47;RPP=4.06379;RPPR=70.2965;RPR=54;RUN=1;SAF=48;SAP=3.54779;SAR=53;SRF=1609;SRP=3.42879;SRR=1634;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.776G>A|p.Arg259Gln|776/1260|776/1260|259/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/0:3347:3243,101:3243:110630:101:3321:0,-752.738,-8988.5 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
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361 NC_045512.2 29067 . CTAAAGCATACAATGT CT 2.70012E-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=187;CIGAR=1M14D1M;DP=2118;DPB=1955.62;DPRA=0;EPP=3.02191;EPPR=5.31131;GTI=0;LEN=14;MEANALT=13;MQM=48.7647;MQMR=53.2214;NS=1;NUMALT=1;ODDS=1275.56;PAIRED=0.97861;PAIREDR=0.993197;PAO=1;PQA=34;PQR=101;PRO=3;QA=5285;QR=66815;RO=1911;RPL=76;RPP=17.2352;RPPR=87.6977;RPR=111;RUN=1;SAF=98;SAP=3.95088;SAR=89;SRF=986;SRP=7.23848;SRR=925;TYPE=del;ANN=CT|frameshift_variant|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.798_811delAGCATACAATGTAA|p.Lys266fs|798/1260|798/1260|266/419||INFO_REALIGN_3_PRIME GT:DP:AD:RO:QR:AO:QA:GL 0/0:2118:1911,187:1911:66815:187:5285:0,-187.495,-5392.39 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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362 NC_045512.2 29402 . G T 33928.1 . AB=0.380005;ABP=537.172;AC=1;AF=0.5;AN=2;AO=1623;CIGAR=1X;DP=4271;DPB=4271;DPRA=0;EPP=4.13551;EPPR=7.75762;GTI=0;LEN=1;MEANALT=3;MQM=49.4449;MQMR=52.7301;NS=1;NUMALT=1;ODDS=7812.23;PAIRED=0.997535;PAIREDR=0.995079;PAO=0;PQA=0;PQR=0;PRO=0;QA=57174;QR=92750;RO=2642;RPL=779;RPP=8.66309;RPPR=18.6627;RPR=844;RUN=1;SAF=832;SAP=5.25937;SAR=791;SRF=1339;SRP=4.07549;SRR=1303;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1129G>T|p.Asp377Tyr|1129/1260|1129/1260|377/419|| GT:DP:AD:RO:QR:AO:QA:GL 0/1:4271:2642,1623:2642:92750:1623:57174:-3456.1,0,-6754.07 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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363 NC_045512.2 29681 . TTAATCA TTAATCTAATCA 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=59;CIGAR=1M5I6M;DP=2108;DPB=2151.14;DPRA=0;EPP=3.34154;EPPR=24.183;GTI=0;LEN=5;MEANALT=6;MQM=52.322;MQMR=51.6699;NS=1;NUMALT=1;ODDS=2266.18;PAIRED=1;PAIREDR=0.995586;PAO=1;PQA=27.5;PQR=27.5;PRO=1;QA=1893;QR=70994;RO=2039;RPL=34;RPP=5.99147;RPPR=724.345;RPR=25;RUN=1;SAF=31;SAP=3.34154;SAR=28;SRF=963;SRP=16.6089;SRR=1076;TYPE=ins;ANN=TTAATCTAATCA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4302_*4303insTAATC|||||4303| GT:DP:AD:RO:QR:AO:QA:GL 0/0:2108:2039,59:2039:70994:59:1893:0,-462.802,-5912.21 |
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5e8505f27681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
iuc
parents:
diff
changeset
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364 NC_045512.2 29742 . G T 36691.9 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1276;CIGAR=1X;DP=1276;DPB=1276;DPRA=0;EPP=3.69101;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=49.6567;MQMR=0;NS=1;NUMALT=1;ODDS=1773.52;PAIRED=0.996082;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=44133;QR=0;RO=0;RPL=591;RPP=18.0472;RPPR=0;RPR=685;RUN=1;SAF=637;SAP=3.01711;SAR=639;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4358G>T|||||4358| GT:DP:AD:RO:QR:AO:QA:GL 1/1:1276:0,1276:0:0:1276:44133:-3675.72,-384.114,0 |