Mercurial > repos > dfornika > snippy
annotate test-data/out/snps.raw.vcf @ 1:e7e5da92d0ab draft
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
| author | dfornika |
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| date | Fri, 18 Jan 2019 19:35:46 -0500 |
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| rev | line source |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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1 ##fileformat=VCFv4.2 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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2 ##fileDate=20190118 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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3 ##source=freeBayes v1.2.0-dirty |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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4 ##reference=reference/ref.fa |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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5 ##contig=<ID=Wildtype,length=197394> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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6 ##phasing=none |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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7 ##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Wildtype:0-13379" |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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8 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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changeset
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9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff
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18 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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44 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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45 ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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46 ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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49 ##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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50 ##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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51 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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52 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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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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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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54 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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55 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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56 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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57 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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58 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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59 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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60 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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61 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT out |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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62 Wildtype 24388 . A G 673.635 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=22;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=4.58955;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=35.1036;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=785;QR=0;RO=0;RPL=16;RPP=12.8806;RPPR=0;RPR=6;RUN=1;SAF=9;SAP=4.58955;SAR=13;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:22:0,22:0:0:22:785:-70.9652,-6.62266,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
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63 Wildtype 29479 . T G 673.562 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=21;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=3.1137;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=33.7174;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=776;QR=0;RO=0;RPL=10;RPP=3.1137;RPPR=0;RPR=11;RUN=1;SAF=7;SAP=8.07707;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:21:0,21:0:0:21:776:-70.1607,-6.32163,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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64 Wildtype 38250 . C G 596.915 . AB=0.555556;ABP=4.21667;AC=1;AF=0.5;AN=2;AO=25;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=17.6895;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=110.085;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=892;QR=738;RO=20;RPL=15;RPP=5.18177;RPPR=3.0103;RPR=10;RUN=1;SAF=10;SAP=5.18177;SAR=15;SRF=11;SRP=3.44459;SRR=9;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:45:20,25:20:738:25:892:-67.0371,0,-53.1992 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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65 Wildtype 47299 . T A 772.746 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=25;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=10.0459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=39.2625;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=921;QR=0;RO=0;RPL=21;RPP=28.1125;RPPR=0;RPR=4;RUN=1;SAF=10;SAP=5.18177;SAR=15;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:25:0,25:0:0:25:921:-83.2013,-7.52575,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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66 Wildtype 102969 . G C 548.461 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=18;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=29.5585;PAIRED=0.666667;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=637;QR=0;RO=0;RPL=11;RPP=4.9405;RPPR=0;RPR=7;RUN=1;SAF=9;SAP=3.0103;SAR=9;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:18:0,18:0:0:18:637:-57.6434,-5.41854,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
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67 Wildtype 103048 . T A 659.012 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=23;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=3.86001;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=36.4899;PAIRED=0.913043;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=766;QR=0;RO=0;RPL=8;RPP=7.63648;RPPR=0;RPR=15;RUN=1;SAF=8;SAP=7.63648;SAR=15;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:23:0,23:0:0:23:766:-69.2328,-6.92369,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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68 Wildtype 103379 . GAAAATAGAAAGTTGTTC GAAATAGAAAGTTGTTC 262.515 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=9;CIGAR=1M1D16M;DP=10;DPB=9.55556;DPRA=0;EPP=3.25157;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=18.4681;PAIRED=1;PAIREDR=0;PAO=0.5;PQA=17.5;PQR=17.5;PRO=0.5;QA=310;QR=0;RO=0;RPL=4;RPP=3.25157;RPPR=0;RPR=5;RUN=1;SAF=5;SAP=3.25157;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=del GT:DP:AD:RO:QR:AO:QA:GL 1/1:10:0,9:0:0:9:310:-28.0782,-3.31133,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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69 Wildtype 106602 . T G 679.76 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=22;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=4.58955;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=35.1036;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=790;QR=0;RO=0;RPL=15;RPP=9.32731;RPPR=0;RPR=7;RUN=1;SAF=14;SAP=6.56362;SAR=8;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:22:0,22:0:0:22:790:-71.4106,-6.62266,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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70 Wildtype 106722 . GTTTTTAACTG GTTTTTTAACTG 318.317 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=11;CIGAR=1M1I10M;DP=12;DPB=13;DPRA=0;EPP=3.20771;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=19.8544;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=386;QR=0;RO=0;RPL=6;RPP=3.20771;RPPR=0;RPR=5;RUN=1;SAF=2;SAP=12.6832;SAR=9;SRF=0;SRP=0;SRR=0;TYPE=ins GT:DP:AD:RO:QR:AO:QA:GL 1/1:12:0,11:0:0:11:386:-34.696,-3.31133,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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71 Wildtype 109833 . T A 523.219 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=17;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=3.13803;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=28.1722;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=612;QR=0;RO=0;RPL=11;RPP=6.20364;RPPR=0;RPR=6;RUN=1;SAF=12;SAP=9.26925;SAR=5;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:17:0,17:0:0:17:612:-55.4045,-5.11751,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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72 Wildtype 114540 . ATTGTGAA ATGTGAA 743.241 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=26;CIGAR=1M1D6M;DP=27;DPB=24.125;DPRA=0;EPP=3.34437;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=43.4214;PAIRED=1;PAIREDR=0;PAO=1;PQA=21.5;PQR=21.5;PRO=1;QA=862;QR=0;RO=0;RPL=8;RPP=11.3621;RPPR=0;RPR=18;RUN=1;SAF=14;SAP=3.34437;SAR=12;SRF=0;SRP=0;SRR=0;TYPE=del GT:DP:AD:RO:QR:AO:QA:GL 1/1:27:0,26:0:0:26:862:-77.6409,-9.0309,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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73 Wildtype 129881 . GT AA 591.829 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=19;CIGAR=2X;DP=19;DPB=19;DPRA=0;EPP=4.03889;EPPR=0;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=30.2516;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=686;QR=0;RO=0;RPL=9;RPP=3.12459;RPPR=0;RPR=10;RUN=1;SAF=13;SAP=8.61041;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=mnp GT:DP:AD:RO:QR:AO:QA:GL 1/1:19:0,19:0:0:19:686:-62.0641,-5.71957,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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74 Wildtype 138877 . G C 433.927 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=14;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=24.0133;PAIRED=0.857143;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=507;QR=0;RO=0;RPL=10;RPP=8.59409;RPPR=0;RPR=4;RUN=1;SAF=7;SAP=3.0103;SAR=7;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:14:0,14:0:0:14:507:-45.9644,-4.21442,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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75 Wildtype 138954 . A G 302.917 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=10;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=18.4681;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=354;QR=0;RO=0;RPL=4;RPP=3.87889;RPPR=0;RPR=6;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:10:0,10:0:0:10:354:-32.1976,-3.0103,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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76 Wildtype 160547 . GTCA GCA 553.041 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=19;CIGAR=1M1D2M;DP=19;DPB=14.25;DPRA=0;EPP=4.03889;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=29.5585;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=643;QR=0;RO=0;RPL=7;RPP=5.8675;RPPR=0;RPR=12;RUN=1;SAF=7;SAP=5.8675;SAR=12;SRF=0;SRP=0;SRR=0;TYPE=del GT:DP:AD:RO:QR:AO:QA:GL 1/1:19:0,19:0:0:19:643:-58.1797,-5.71957,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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77 Wildtype 160552 . CTATTAAATAAAATCAACATACAAATCG CATTAAATAAAATCAACATACAAATCG 470.614 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=14;CIGAR=1M1D26M;DP=17;DPB=16.6071;DPRA=0;EPP=3.63072;EPPR=0;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=22.7605;PAIRED=1;PAIREDR=0;PAO=3;PQA=99;PQR=0;PRO=0;QA=452;QR=0;RO=0;RPL=5;RPP=5.49198;RPPR=0;RPR=9;RUN=1;SAF=5;SAP=5.49198;SAR=9;SRF=0;SRP=0;SRR=0;TYPE=del GT:DP:AD:RO:QR:AO:QA:GL 1/1:17:0,14:0:0:14:452:-49.6242,-5.11751,0 |
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e7e5da92d0ab
planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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78 Wildtype 190866 . GTTTTCTTTAAATGTTAG GTTTCTTTAAATGTTAG 508.52 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=17;CIGAR=1M1D16M;DP=17;DPB=16.2778;DPRA=0;EPP=3.13803;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=28.0544;PAIRED=1;PAIREDR=0;PAO=1;PQA=21.5;PQR=21.5;PRO=1;QA=587;QR=0;RO=0;RPL=10;RPP=4.1599;RPPR=0;RPR=7;RUN=1;SAF=9;SAP=3.13803;SAR=8;SRF=0;SRP=0;SRR=0;TYPE=del GT:DP:AD:RO:QR:AO:QA:GL 1/1:17:0,17:0:0:17:587:-53.1441,-6.32163,0 |