Mercurial > repos > iuc > gatk4_mutect2
changeset 8:55e8a08e39e1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
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--- a/gatk4_Mutect2.xml Wed Aug 24 17:58:18 2022 +0000 +++ b/gatk4_Mutect2.xml Tue Feb 03 18:50:29 2026 +0000 @@ -1,4 +1,4 @@ -<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@+galaxy1" profile="18.05"> +<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>- Call somatic SNVs and indels via local assembly of haplotypes</description> <macros> <import>macros.xml</import> @@ -11,16 +11,16 @@ #include source=$pre_gatk_excl_ints_chth# #include source=$pre_gatk_ints_chth# - #set ref_flag='--reference="reference.fa"' + #set ref_flag='-R reference.fa' #if str($reference_source.reference_source_selector) == 'history' ln -s '$reference_source.reference_sequence' reference.fa && samtools faidx reference.fa && - gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" && + gatk CreateSequenceDictionary -R reference.fa -O reference.dict && #else if str($reference_source.reference_source_selector) == 'cached' ln -s '$reference_source.reference_sequence.fields.path' reference.fa && samtools faidx reference.fa && - gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" && + gatk CreateSequenceDictionary -R reference.fa -O reference.dict && #else #set ref_flag='' #end if @@ -44,7 +44,7 @@ #end if #end if - gatk GetSampleName --input="tumor.bam" --output="samplename.txt" && + gatk GetSampleName -I tumor.bam -O samplename.txt && sample=`cat samplename.txt | sed 's/"//g'` && #if str($optional.optional_parameters) == 'yes' @@ -104,7 +104,7 @@ #end if #if $optional.pedigree - --pedigree="$optional.pedigree" + --pedigree "$optional.pedigree" #end if #if $optional.germline_resource @@ -117,28 +117,28 @@ #if $optional.annotation #for $annot in str($optional.annotation).split(',') - --annotation="$annot" + --annotation "$annot" #end for #end if #if $optional.annotation_group #for $annot in str($optional.annotation_group).split(',') - --annotation-group="$annot" + --annotation-group "$annot" #end for #end if #if $optional.annotations_to_exclude #for $annot in str($optional.annotations_to_exclude).split(',') - --annotations-to-exclude="$annot" + --annotations-to-exclude "$annot" #end for #end if #if $optional.founder_id - --founder-id="$optional.founder_id" + --founder-id "$optional.founder_id" #end if #if $optional.normal_sample - --normal-sample="$optional.normal_sample" + --normal-sample "$optional.normal_sample" #end if #if $optional.alleles @@ -146,58 +146,58 @@ #end if #if $optional.f1r2_max_depth: - --f1r2-max-depth="$optional.f1r2_max_depth" + --f1r2-max-depth "$optional.f1r2_max_depth" #end if - #if $optional.f1r2_max_depth: - --f1r2-median-mq="$optional.f1r2_median_mq" + #if $optional.f1r2_median_mq: + --f1r2-median-mq "$optional.f1r2_median_mq" #end if - #if $optional.f1r2_max_depth: - --f1r2-min-bq="$optional.f1r2_min_bq" + #if $optional.f1r2_min_bq: + --f1r2-min-bq "$optional.f1r2_min_bq" #end if #if $optional.interval_merging_rule: - --interval-merging-rule="$optional.interval_merging_rule" + --interval-merging-rule "$optional.interval_merging_rule" #end if #if $optional.interval_set_rule: - --interval-set-rule="$optional.interval_set_rule" + --interval-set-rule "$optional.interval_set_rule" #end if #if $optional.pcr_indel_qual: - --pcr-indel-qual="$optional.pcr_indel_qual" + --pcr-indel-qual "$optional.pcr_indel_qual" #end if #if $optional.pcr_snv_qual: - --pcr-snv-qual="$optional.pcr_snv_qual" + --pcr-snv-qual "$optional.pcr_snv_qual" #end if #if $optional.read_filter #for $filter in str($optional.read_filter).split(',') - --read-filter="$filter" + --read-filter "$filter" #end for #end if #if $optional.disable_read_filter #for $filter in str($optional.disable_read_filter).split(',') - --disable-read-filter="$filter" + --disable-read-filter "$filter" #end for #end if - --base-quality-score-threshold="$optional.base_quality_score_threshold" - --af-of-alleles-not-in-resource="$optional.af_of_alleles_not_in_resource" - --downsampling-stride="$optional.downsampling_stride" - --gcs-max-retries="$optional.gcs_max_retries" - --initial-tumor-lod="$optional.initial_tumor_lod" - --max-population-af="$optional.max_population_af" - --max-reads-per-alignment-start="$optional.max_reads_per_alignment_start" - --min-base-quality-score="$optional.min_base_quality_score" - --native-pair-hmm-threads="\${GALAXY_SLOTS:-1}" - --normal-lod="$optional.normal_lod" - --read-validation-stringency="$optional.read_validation_stringency" - --tumor-lod-to-emit="$optional.tumor_lod_to_emit" - --verbosity="ERROR" + --base-quality-score-threshold "$optional.base_quality_score_threshold" + --af-of-alleles-not-in-resource "$optional.af_of_alleles_not_in_resource" + --downsampling-stride "$optional.downsampling_stride" + --gcs-max-retries "$optional.gcs_max_retries" + --initial-tumor-lod "$optional.initial_tumor_lod" + --max-population-af "$optional.max_population_af" + --max-reads-per-alignment-start "$optional.max_reads_per_alignment_start" + --min-base-quality-score "$optional.min_base_quality_score" + --native-pair-hmm-threads "\${GALAXY_SLOTS:-1}" + --normal-lod "$optional.normal_lod" + --read-validation-stringency "$optional.read_validation_stringency" + --tumor-lod-to-emit "$optional.tumor_lod_to_emit" + --verbosity "ERROR" $optional.lenient $optional.annotate_with_num_discovered_alleles $optional.add_output_sam_program_record @@ -219,41 +219,41 @@ #if str($advanced.advanced_parameters) == 'yes' #if $advanced.kmer_size - --kmer-size="$advanced.kmer_size" + --kmer-size "$advanced.kmer_size" #end if #if $advanced.gvcf_lod_band - --gvcf-lod-band="$advanced.gvcf_lod_band" + --gvcf-lod-band "$advanced.gvcf_lod_band" #end if #if $advanced.emit_ref_confidence - --emit-ref-confidence="$advanced.emit_ref_confidence" + --emit-ref-confidence "$advanced.emit_ref_confidence" #end if #if $advanced.max_unpruned_variants - --max-unpruned-variants="$advanced.max_unpruned_variants" + --max-unpruned-variants "$advanced.max_unpruned_variants" #end if - --allele-informative-reads-overlap-margin="$advanced.allele_informative_reads_overlap_margin" - --active-probability-threshold="$advanced.active_probability_threshold" - --assembly-region-padding="$advanced.assembly_region_padding" - --bam-writer-type="$advanced.bam_writer_type" - --max-assembly-region-size="$advanced.max_assembly_region_size" - --max-mnp-distance="$advanced.max_mnp_distance" - --max-num-haplotypes-in-population="$advanced.max_num_haplotypes_in_population" - --max-prob-propagation-distance="$advanced.max_prob_propagation_distance" - --max-suspicious-reads-per-alignment-start="$advanced.max_suspicious_reads_per_alignment_start" - --min-assembly-region-size="$advanced.min_assembly_region_size" - --min-dangling-branch-length="$advanced.min_dangling_branch_length" - --min-pruning="$advanced.min_pruning" - --minimum-allele-fraction="$advanced.minimum_allele_fraction" - --num-pruning-samples="$advanced.num_pruning_samples" - --pair-hmm-gap-continuation-penalty="$advanced.pair_hmm_gap_continuation_penalty" - --callable-depth="$advanced.callable_depth" - --pair-hmm-implementation="$advanced.pair_hmm_implementation" - --pcr-indel-model="$advanced.pcr_indel_model" - --phred-scaled-global-read-mismapping-rate="$advanced.phred_scaled_global_read_mismapping_rate" - --pruning-lod-threshold="$advanced.pruning_lod_threshold" - --smith-waterman="$advanced.smith_waterman" + --allele-informative-reads-overlap-margin "$advanced.allele_informative_reads_overlap_margin" + --active-probability-threshold "$advanced.active_probability_threshold" + --assembly-region-padding "$advanced.assembly_region_padding" + --bam-writer-type "$advanced.bam_writer_type" + --max-assembly-region-size "$advanced.max_assembly_region_size" + --max-mnp-distance "$advanced.max_mnp_distance" + --max-num-haplotypes-in-population "$advanced.max_num_haplotypes_in_population" + --max-prob-propagation-distance "$advanced.max_prob_propagation_distance" + --max-suspicious-reads-per-alignment-start "$advanced.max_suspicious_reads_per_alignment_start" + --min-assembly-region-size "$advanced.min_assembly_region_size" + --min-dangling-branch-length "$advanced.min_dangling_branch_length" + --min-pruning "$advanced.min_pruning" + --minimum-allele-fraction "$advanced.minimum_allele_fraction" + --num-pruning-samples "$advanced.num_pruning_samples" + --pair-hmm-gap-continuation-penalty "$advanced.pair_hmm_gap_continuation_penalty" + --callable-depth "$advanced.callable_depth" + --pair-hmm-implementation "$advanced.pair_hmm_implementation" + --pcr-indel-model "$advanced.pcr_indel_model" + --phred-scaled-global-read-mismapping-rate "$advanced.phred_scaled_global_read_mismapping_rate" + --pruning-lod-threshold "$advanced.pruning_lod_threshold" + --smith-waterman "$advanced.smith_waterman" $advanced.allow_non_unique_kmers_in_ref $advanced.disable_adaptive_pruning $advanced.disable_tool_default_annotations @@ -275,10 +275,10 @@ #if str($outputs.output_parameters) == 'yes' #if str($outputs.debug_assembly) == 'yes' - --assembly-region-out="assembly-region.tab" + --assembly-region-out "assembly-region.tab" #end if #if str($outputs.debug_bam) == 'yes' - --bam-output="debug.bam" + --bam-output "debug.bam" #end if #end if @@ -501,7 +501,6 @@ <option value="STRICT">Strict</option> <option value="LENIENT">Lenient</option> </param> - <param name="sites_only_vcf_output" argument="--sites-only-vcf-output" type="boolean" truevalue="--sites-only-vcf-output" falsevalue="" optional="true" checked="false" label="Sites Only Vcf Output" help="If true, don&apos;t emit genotype fields when writing vcf file output."/> <param name="tumor_lod_to_emit" argument="--tumor-lod-to-emit" type="float" optional="true" value="3.0" label="Tumor Lod To Emit" help="LOD threshold to emit tumor variant to VCF."/> </when> <when value="no" /> @@ -598,7 +597,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs='1'> <conditional name="mode"> <param name="mode_parameters" value="tumor_only"/> <param name="tumor" ftype="bam" value="Mutect2-in1.bam" /> @@ -609,9 +608,13 @@ <param name="optional_parameters" value="no" /> <param name="advanced_parameters" value="no" /> <param name="output_parameters" value="no" /> - <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" /> + <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="48"> + <assert_contents> + <has_n_lines n="90"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs='1'> <conditional name="mode"> <param name="mode_parameters" value="tumor_only"/> <param name="tumor" ftype="bam" value="Mutect2-in2.bam" /> @@ -620,14 +623,18 @@ <param name="gzipped_output" value="false" /> <param name="reference_source_selector" value="history" /> <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" /> - <param name="seqdict_source" value="history" /> + <param name="seqdict_source_selector" value="history" /> <param name="seqdict_sequence" value="Mutect2-in2.dict" /> <param name="optional_parameters" value="no" /> <param name="advanced_parameters" value="no" /> <param name="output_parameters" value="no" /> - <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" /> + <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="48"> + <assert_contents> + <has_n_lines n="128"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs='1'> <conditional name="mode"> <param name="mode_parameters" value="tumor_only"/> <param name="tumor" ftype="bam" value="Mutect2-in3.bam" /> @@ -640,9 +647,13 @@ <param name="annotation_group" value="StandardMutectAnnotation" /> <param name="advanced_parameters" value="no" /> <param name="output_parameters" value="no" /> - <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="2" /> + <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="48"> + <assert_contents> + <has_n_lines n="67"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs='1'> <conditional name="mode"> <param name="mode_parameters" value="tumor_only"/> <param name="tumor" ftype="bam" value="Mutect2-in4.bam" /> @@ -654,9 +665,13 @@ <param name="optional_parameters" value="no" /> <param name="advanced_parameters" value="no" /> <param name="output_parameters" value="no" /> - <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" /> + <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="48"> + <assert_contents> + <has_n_lines n="85"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs='3'> <conditional name="mode"> <param name="mode_parameters" value="tumor_only"/> <param name="tumor" ftype="bam" value="Mutect2-in5.bam" /> @@ -667,14 +682,17 @@ <param name="optional_parameters" value="no" /> <param name="advanced_parameters" value="no" /> <param name="output_parameters" value="yes" /> - <param name="debug_activity" value="true" /> <param name="debug_assembly" value="true" /> <param name="debug_bam" value="true" /> - <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="2" /> + <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="48"> + <assert_contents> + <has_n_lines n="97"/> + </assert_contents> + </output> <output name="assembly_region_out" file="Mutect2-out5-1.tabular" /> - <output name="bam_output" file="Mutect2-out5.bam" /> + <output name="bam_output" file="Mutect2-out5.bam" ftype="bam" /> </test> - <test> + <test expect_num_outputs='1'> <conditional name="mode"> <param name="mode_parameters" value="somatic"/> <param name="tumor" ftype="bam" value="tumor.bam" /> @@ -686,7 +704,11 @@ <param name="optional_parameters" value="no" /> <param name="advanced_parameters" value="no" /> <param name="output_parameters" value="no" /> - <output name="output_vcf" file="Mutect2-out6.vcf" lines_diff="2" /> + <output name="output_vcf" file="Mutect2-out6.vcf" lines_diff="48"> + <assert_contents> + <has_n_lines n="66"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short @@ -695,10 +717,10 @@ somatic genotyping engine of the original MuTect (`Cibulskis et al., 2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__) with the assembly-based machinery of -`HaplotypeCaller <https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__. +`HaplotypeCaller <https://web.archive.org/web/20230530034638/https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__. This tool is featured in the *Somatic Short Mutation calling Best -Practice Workflow*. See `this article <https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__ +Practice Workflow*. See `this article <https://web.archive.org/web/20230228153229/https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__ for an overview of what traditional somatic calling entails, with usage examples. For the latest pipeline scripts, see the `Mutect2 WDL scripts directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__.
--- a/macros.xml Wed Aug 24 17:58:18 2022 +0000 +++ b/macros.xml Tue Feb 03 18:50:29 2026 +0000 @@ -1,13 +1,14 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">4.1.7.0</token> - <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</token> + <token name="@TOOL_VERSION@">4.6.2.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">24.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">gatk4</requirement> - <requirement type="package" version="0.2.5">tabix</requirement> - <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="@TOOL_VERSION@">gatk4</requirement> + <requirement type="package" version="1.11">tabix</requirement> + <requirement type="package" version="1.23">samtools</requirement> <yield /> </requirements> </xml> @@ -654,6 +655,52 @@ <!--#end if--> <!--</template>--> + <token name="@GATK_LINK_REF@"><![CDATA[ + ## 1. Link Reference Genome + #if $reference_source.reference_source_selector == "history": + ln -s '$reference_source.reference_sequence' reference.fa && + samtools faidx reference.fa && + #else: + ln -s '$reference_source.reference_sequence.fields.path' reference.fa && + ln -s '${reference_source.reference_sequence.fields.path}.fai' reference.fa.fai && + #end if + + ## Ensure dictionary exists + gatk CreateSequenceDictionary -R reference.fa && + ]]></token> + + <xml name="gatk_ref_source"> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="cached">Locally cached</option> + <option value="history" selected="true">History</option> + </param> + <when value="cached"> + <param name="reference_sequence" type="select" label="Reference" help="Select reference genome"> + <options from_data_table="all_fasta" /> + </param> + </when> + <when value="history"> + <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Select reference genome from history" /> + </when> + </conditional> + </xml> + + <xml name="gatk_param_intervals"> + <param name="intervals" argument="-L" type="data" format="picard_interval_list" optional="true" label="Interval List" help="One or more genomic intervals over which to operate." /> + </xml> + + <xml name="gatk_param_known_sites"> + <param argument="--known-sites" type="data" format="vcf_bgzip" multiple="true" label="Known Sites" help="VCF file(s) (e.g., dbSNP, Mills) masking known sites." /> + </xml> + + <xml name="gatk_param_use_original_qualities"> + <param argument="--use-original-qualities" type="boolean" truevalue="--use-original-qualities" falsevalue="" checked="true" label="Use Original Qualities" help="Use the OQ tag if present." /> + </xml> + + <xml name="gatk_param_add_output_sam_program_record"> + <param argument="--add-output-sam-program-record" type="boolean" truevalue="--add-output-sam-program-record" falsevalue="" checked="true" label="Add Output SAM Program Record" help="Adds an extra PG tag to the header." /> + </xml> <!--Citations--> <xml name="citations">
--- a/test-data/Mutect2-out1.vcf Wed Aug 24 17:58:18 2022 +0000 +++ b/test-data/Mutect2-out1.vcf Tue Feb 03 18:50:29 2026 +0000 @@ -4,6 +4,7 @@ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=FAD,Number=R,Type=Integer,Description="Count of fragments supporting each allele."> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles"> @@ -11,18 +12,19 @@ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> -##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input tumor.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.7.0",Date="May 8, 2020 3:30:52 PM CEST"> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input tumor.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --trim-to-haplotype true --exact-matching false --flow-use-t0-tag false --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --keep-boundary-flows false --genotype-pon-sites false --genotype-germline-sites false --genotype-germline-sites-fraction 1.0 --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --permutect-ref-downsample 10 --permutect-alt-downsample 20 --permutect-non-artifact-ratio 1 --permutect-dataset-mode ILLUMINA --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --base-qual-correction-factor 5 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --flow-mode NONE --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --use-pdhmm false --use-pdhmm-overlap-optimization false --make-determined-haps-from-pd-code false --print-pileupcalling-status false --fallback-gga-if-pdhmm-fails true --pileup-detection-enable-indel-pileup-calling false --pileup-detection-active-region-phred-threshold 0.0 --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.1 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-snp-basequality-filter 12 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --pileup-detection-filter-assembly-alt-bad-read-tolerance 0.0 --pileup-detection-edit-distance-read-badness-for-assembly-filtering-threshold 0.12 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.6.2.0",Date="February 2, 2026, 12:29:00?AM GMT"> ##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |."> ##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site"> ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of potential somatic events in the assembly region"> +##INFO=<ID=ECNTH,Number=A,Type=Integer,Description="Number of somatic events in best supporting haplotype for each alt allele"> ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> -##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> -##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> -##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality by allele"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length by allele"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality by allele"> ##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> -##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Log 10 odds of artifact in normal with same allele fraction as tumor"> ##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> @@ -42,52 +44,47 @@ ##source=Mutect2 ##tumor_sample=SRR8525881 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 -K03455 4098 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;MBQ=0,34;MFRL=0,158;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=3.58 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,1:0,0,1,0 -K03455 4145 . T C . . AS_SB_TABLE=0,0|3,1;DP=4;ECNT=13;MBQ=0,27;MFRL=0,242;MMQ=60,60;MPOS=39;POPAF=7.30;TLOD=17.40 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,4:0.800:4:0,1:0,3:0,0,3,1 -K03455 4190 . A G . . AS_SB_TABLE=2,0|11,2;DP=15;ECNT=13;MBQ=38,37;MFRL=290,303;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=54.51 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:2,13:0.800:15:0,4:1,9:0|1:4190_A_G:4190:2,0,11,2 -K03455 4209 . GC AC,AA . . AS_SB_TABLE=1,0|4,0|13,2;DP=20;ECNT=13;MBQ=37,35,36;MFRL=200,295,303;MMQ=60,60,60;MPOS=10,36;POPAF=7.30,7.30;TLOD=13.46,61.35 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:1,4,15:0.238,0.667:20:1,2,4:0,2,11:1,0,17,2 -K03455 4233 . T C . . AS_SB_TABLE=18,4|5,1;DP=28;ECNT=13;MBQ=38,39;MFRL=267,268;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=19.09 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:22,6:0.261:28:7,2:13,4:1|0:4190_A_G:4190:18,4,5,1 -K03455 4250 . G A . . AS_SB_TABLE=32,5|2,2;DP=42;ECNT=13;MBQ=37,28;MFRL=281,206;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=6.73 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,4:0.124:41:16,3:19,1:32,5,2,2 -K03455 4259 . T A . . AS_SB_TABLE=7,1|30,6;DP=45;ECNT=13;MBQ=35,35;MFRL=259,280;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=151.55 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:8,36:0.786:44:3,17:5,15:0|1:4259_T_A:4259:7,1,30,6 -K03455 4262 . A T . . AS_SB_TABLE=30,6|7,1;DP=45;ECNT=13;MBQ=37,37;MFRL=280,259;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=26.50 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:36,8:0.214:44:18,3:15,4:1|0:4259_T_A:4259:30,6,7,1 -K03455 4268 . G A . . AS_SB_TABLE=24,7|14,0;DP=45;ECNT=13;MBQ=37,38;MFRL=272,276;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=50.83 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,14:0.349:45:12,8:15,5:24,7,14,0 -K03455 4271 . A G . . AS_SB_TABLE=31,7|10,0;DP=48;ECNT=13;MBQ=37,33;MFRL=259,311;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=33.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:38,10:0.239:48:15,7:18,2:31,7,10,0 -K03455 4277 . C T . . AS_SB_TABLE=10,2|34,6;DP=52;ECNT=13;MBQ=37,37;MFRL=244,280;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=167.14 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:12,40:0.755:52:3,20:5,18:0|1:4259_T_A:4259:10,2,34,6 -K03455 4279 . GT AC,AT . . AS_SB_TABLE=17,2|18,4|9,2;DP=53;ECNT=13;MBQ=36,33,37;MFRL=263,229,272;MMQ=60,60,60;MPOS=34,39;POPAF=7.30,7.30;TLOD=61.69,29.10 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:19,22,11:0.411,0.216:52:8,9,6:9,9,5:17,2,27,6 -K03455 4283 . T C . . AS_SB_TABLE=44,7|2,1;DP=54;ECNT=13;MBQ=35,37;MFRL=272,254;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=6.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:51,3:0.078:54:24,1:23,2:44,7,2,1 -K03455 4310 . C T . . AS_SB_TABLE=25,14|4,3;DP=47;ECNT=15;MBQ=20,20;MFRL=252,254;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=18.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:39,7:0.171:46:21,1:13,4:25,14,4,3 -K03455 4313 . G A . . AS_SB_TABLE=26,16|2,1;DP=45;ECNT=15;MBQ=26,20;MFRL=252,200;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.55 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:42,3:0.073:45:18,1:15,1:26,16,2,1 -K03455 4320 . G A . . AS_SB_TABLE=19,14|6,5;DP=45;ECNT=15;MBQ=20,20;MFRL=252,254;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=46.17 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:33,11:0.263:44:17,1:13,6:19,14,6,5 -K03455 4330 . A G . . AS_SB_TABLE=25,19|3,1;DP=49;ECNT=15;MBQ=20,38;MFRL=250,276;MMQ=60,60;MPOS=60;POPAF=7.30;TLOD=13.53 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:44,4:0.111:48:19,3:20,0:25,19,3,1 -K03455 4334 . A G . . AS_SB_TABLE=27,18|1,4;DP=50;ECNT=15;MBQ=33,36;MFRL=252,254;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=14.29 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:45,5:0.133:50:20,2:22,3:27,18,1,4 -K03455 4340 . A G . . AS_SB_TABLE=15,9|12,15;DP=52;ECNT=15;MBQ=33,20;MFRL=259,252;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=102.69 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:24,27:0.511:51:11,13:12,11:0|1:4340_A_G:4340:15,9,12,15 -K03455 4343 . C A . . AS_SB_TABLE=15,9|11,15;DP=50;ECNT=15;MBQ=33,20;MFRL=259,229;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=102.69 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:24,26:0.511:50:9,12:9,10:0|1:4340_A_G:4340:15,9,11,15 -K03455 4345 . GC AT . . AS_SB_TABLE=21,19|7,7;DP=54;ECNT=15;MBQ=20,37;MFRL=218,251;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=54.30 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:40,14:0.277:54:14,5:15,8:21,19,7,7 -K03455 4346 . C T . . AS_SB_TABLE=17,18|3,1;DP=53;ECNT=15;MBQ=20,26;MFRL=202,276;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=13.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:35,4:0.130:39:13,2:11,0:17,18,3,1 -K03455 4358 . T C . . AS_SB_TABLE=21,22|2,5;DP=51;ECNT=15;MBQ=20,35;MFRL=229,254;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=17.73 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:43,7:0.159:50:15,4:22,3:21,22,2,5 -K03455 4361 . GCT G,ACT . . AS_SB_TABLE=6,3|7,8|11,17;DP=52;ECNT=15;MBQ=36,33,20;MFRL=229,247,208;MMQ=60,60,60;MPOS=32,32;POPAF=7.30,7.30;TLOD=56.30,98.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:9,15,28:0.277,0.532:52:5,4,9:3,9,13:6,3,18,25 -K03455 4364 . A AAG . . AS_SB_TABLE=17,20|7,8;DP=54;ECNT=15;MBQ=33,33;MFRL=209,247;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=55.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,15:0.282:52:17,4:18,9:17,20,7,8 -K03455 4370 . A G . . AS_SB_TABLE=17,17|7,14;DP=56;ECNT=15;MBQ=20,37;MFRL=199,290;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=63.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,21:0.439:55:9,9:16,12:17,17,7,14 -K03455 4376 . C T . . AS_SB_TABLE=10,19|13,13;DP=57;ECNT=15;MBQ=37,20;MFRL=252,244;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=86.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:29,26:0.437:55:9,10:16,13:10,19,13,13 -K03455 4397 . T C . . AS_SB_TABLE=18,19|13,10;DP=66;ECNT=15;MBQ=33,34;MFRL=281,247;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=82.73 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,23:0.394:60:10,9:21,12:18,19,13,10 -K03455 4416 . C T . . AS_SB_TABLE=22,34|6,6;DP=68;ECNT=21;MBQ=37,37;MFRL=270,305;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=37.06 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:56,12:0.197:68:20,5:33,4:22,34,6,6 -K03455 4418 . A G . . AS_SB_TABLE=26,38|1,2;DP=67;ECNT=21;MBQ=37,37;MFRL=284,229;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=6.77 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:64,3:0.062:67:24,3:35,0:26,38,1,2 -K03455 4421 . T C . . AS_SB_TABLE=11,20|16,20;DP=67;ECNT=21;MBQ=34,38;MFRL=263,291;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=142.09 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,36:0.538:67:16,14:12,21:11,20,16,20 -K03455 4424 . T C . . AS_SB_TABLE=13,24|13,15;DP=65;ECNT=21;MBQ=37,38;MFRL=254,295;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=102.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,28:0.444:65:15,9:15,17:13,24,13,15 -K03455 4430 . T C . . AS_SB_TABLE=25,37|1,2;DP=65;ECNT=21;MBQ=37,36;MFRL=280,300;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=7.02 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:62,3:0.063:65:26,2:32,1:25,37,1,2 -K03455 4439 . A G . . AS_SB_TABLE=22,31|3,4;DP=60;ECNT=21;MBQ=38,35;MFRL=287,210;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=21.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:53,7:0.121:60:23,3:26,4:22,31,3,4 -K03455 4442 . AG GA . . AS_SB_TABLE=21,30|3,4;DP=59;ECNT=21;MBQ=37,33;MFRL=287,209;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=18.12 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:51,7:0.142:58:20,2:25,5:21,30,3,4 -K03455 4443 . G A . . AS_SB_TABLE=12,19|11,12;DP=59;ECNT=21;MBQ=35,38;MFRL=276,291;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=78.51 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,23:0.421:54:14,10:13,10:12,19,11,12 -K03455 4448 . C A . . AS_SB_TABLE=22,31|1,2;DP=57;ECNT=21;MBQ=37,20;MFRL=287,126;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=8.91 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:53,3:0.055:56:21,0:27,2:22,31,1,2 -K03455 4449 . C T . . AS_SB_TABLE=13,16|11,15;DP=55;ECNT=21;MBQ=37,38;MFRL=209,322;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=97.76 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:29,26:0.491:55:11,12:16,13:13,16,11,15 -K03455 4460 . T C . . AS_SB_TABLE=22,22|2,5;DP=51;ECNT=21;MBQ=37,37;MFRL=279,321;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=22.02 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:44,7:0.163:51:17,3:24,3:22,22,2,5 -K03455 4465 . T TGGCC . . AS_SB_TABLE=19,20|4,4;DP=50;ECNT=21;MBQ=37,35;MFRL=290,176;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=26.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:39,8:0.155:47:14,6:22,1:19,20,4,4 -K03455 4466 . A G,AGTG . . AS_SB_TABLE=16,17|2,3|4,4;DP=49;ECNT=21;MBQ=37,38,37;MFRL=310,207,176;MMQ=60,60,60;MPOS=20,25;POPAF=7.30,7.30;TLOD=15.50,28.09 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:33,5,8:0.154,0.179:46:12,1,6:16,4,1:16,17,6,7 -K03455 4478 . T C . . AS_SB_TABLE=12,13|5,6;DP=36;ECNT=21;MBQ=37,32;MFRL=323,205;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=44.55 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:25,11:0.306:36:9,6:15,4:12,13,5,6 -K03455 4505 . A G . . AS_SB_TABLE=2,1|11,6;DP=20;ECNT=21;MBQ=39,37;MFRL=394,323;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=72.12 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:3,17:0.818:20:2,6:1,8:2,1,11,6 -K03455 4508 . A T . . AS_SB_TABLE=2,3|10,3;DP=18;ECNT=21;MBQ=39,35;MFRL=287,335;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=52.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,13:0.700:18:3,5:2,8:2,3,10,3 -K03455 4511 . G A . . AS_SB_TABLE=2,1|10,5;DP=18;ECNT=21;MBQ=37,35;MFRL=394,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=62.74 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:3,15:0.800:18:2,5:1,7:2,1,10,5 -K03455 4526 . T C . . AS_SB_TABLE=0,0|11,2;DP=13;ECNT=21;MBQ=0,36;MFRL=0,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=57.35 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,13:0.933:13:0,7:0,6:0,0,11,2 -K03455 4528 . T TCA . . AS_SB_TABLE=10,1|1,1;DP=13;ECNT=21;MBQ=38,37;MFRL=323,421;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=5.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:11,2:0.200:13:5,1:4,1:0|1:4528_T_TCA:4528:10,1,1,1 -K03455 4530 . CTT C . . AS_SB_TABLE=9,1|1,1;DP=13;ECNT=21;MBQ=35,38;MFRL=323,421;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=4,2;RU=T;STR;TLOD=6.12 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:10,2:0.213:12:5,1:4,1:0|1:4528_T_TCA:4528:9,1,1,1 -K03455 4532 . T C . . AS_SB_TABLE=0,0|11,0;DP=13;ECNT=21;MBQ=0,27;MFRL=0,323;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=39.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,11:0.926:11:0,6:0,2:0,0,11,0 +K03455 4098 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=5;ECNTH=2;MBQ=0,34;MFRL=0,222;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=7.14 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,2:0.750:2:0,1:0,1:0,2:0,0,2,0 +K03455 4139 . G A . . AS_SB_TABLE=13,1|1,1;DP=16;ECNT=5;ECNTH=3;MBQ=37,27;MFRL=321,321;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=3.04 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:14,2:0.175:16:4,0:8,2:13,2:13,1,1,1 +K03455 4145 . T C . . AS_SB_TABLE=4,0|11,2;DP=17;ECNT=5;ECNTH=2;MBQ=39,33;MFRL=370,326;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=40.51 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:4,13:0.718:17:2,3:2,7:4,12:4,0,11,2 +K03455 4148 . G A . . AS_SB_TABLE=9,2|6,0;DP=17;ECNT=5;ECNTH=3;MBQ=33,38;MFRL=316,338;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=21.00 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:11,6:0.393:17:3,2:6,4:10,6:9,2,6,0 +K03455 4166 . C T . . AS_SB_TABLE=18,2|3,0;DP=23;ECNT=5;ECNTH=3;MBQ=35,37;MFRL=321,447;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=6.40 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:20,3:0.167:23:2,1:11,2:19,3:18,2,3,0 +K03455 4190 . A G . . AS_SB_TABLE=5,0|10,2;DP=17;ECNT=23;ECNTH=9;MBQ=38,38;MFRL=293,295;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=39.32 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:5,12:0.649:17:3,4:2,6:5,10:5,0,10,2 +K03455 4209 . GC AA,AC . . AS_SB_TABLE=0,0|12,2|4,0;DP=18;ECNT=23;ECNTH=8,14;MBQ=0,37,38;MFRL=0,288,310;MMQ=60,60,60;MPOS=41,55;POPAF=7.30,7.30;TLOD=57.24,11.52 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:0,14,4:0.685,0.262:18:0,6,2:0,6,2:0,12,4:0,0,16,2 +K03455 4233 . T C . . AS_SB_TABLE=14,3|4,0;DP=21;ECNT=23;ECNTH=14;MBQ=38,35;MFRL=286,310;MMQ=60,60;MPOS=43;POPAF=7.30;TLOD=12.39 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:17,4:0.238:21:7,2:7,2:15,4:14,3,4,0 +K03455 4259 . T A . . AS_SB_TABLE=4,0|15,5;DP=25;ECNT=23;ECNTH=8;MBQ=33,37;MFRL=294,271;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=83.81 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:4,20:0.792:24:2,10:2,7:4,18:4,0,15,5 +K03455 4262 . A T . . AS_SB_TABLE=15,5|4,0;DP=25;ECNT=23;ECNTH=11;MBQ=28,35;MFRL=271,294;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=12.77 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:20,4:0.208:24:9,1:6,2:18,4:0|1:4262_A_T:4262:15,5,4,0 +K03455 4268 . G A . . AS_SB_TABLE=15,5|4,0;DP=24;ECNT=23;ECNTH=9;MBQ=34,28;MFRL=271,294;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=12.77 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:20,4:0.208:24:9,0:7,2:18,4:15,5,4,0 +K03455 4277 . C T . . AS_SB_TABLE=4,1|15,5;DP=25;ECNT=23;ECNTH=8;MBQ=20,33;MFRL=247,271;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=83.81 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:5,20:0.792:25:1,10:1,7:4,18:1|0:4262_A_T:4262:4,1,15,5 +K03455 4279 . GT AC,AT . . AS_SB_TABLE=4,1|12,3|3,2;DP=25;ECNT=23;ECNTH=8,8;MBQ=20,37,20;MFRL=247,290,184;MMQ=60,60,60;MPOS=34,33;POPAF=7.30,7.30;TLOD=47.62,10.92 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:5,15,5:0.601,0.199:25:1,8,2:2,5,2:4,14,4:4,1,15,5 +K03455 4310 . C T . . AS_SB_TABLE=14,9|3,3;DP=29;ECNT=23;ECNTH=14;MBQ=20,20;MFRL=206,251;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=15.61 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:23,6:0.214:29:10,0:4,3:21,5:14,9,3,3 +K03455 4320 . G A . . AS_SB_TABLE=12,10|3,4;DP=29;ECNT=23;ECNTH=14;MBQ=20,20;MFRL=227,254;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=29.08 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:22,7:0.242:29:9,0:6,4:21,6:12,10,3,4 +K03455 4334 . A G . . AS_SB_TABLE=16,12|1,4;DP=33;ECNT=23;ECNTH=14;MBQ=20,33;MFRL=250,254;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=15.63 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:28,5:0.194:33:9,2:11,3:24,5:16,12,1,4 +K03455 4340 . A G . . AS_SB_TABLE=6,6|11,12;DP=35;ECNT=23;ECNTH=8;MBQ=35,20;MFRL=225,252;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=100.52 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:12,23:0.656:35:3,9:7,7:10,20:0|1:4340_A_G:4340:6,6,11,12 +K03455 4343 . C A . . AS_SB_TABLE=6,6|10,13;DP=35;ECNT=23;ECNTH=8;MBQ=33,20;MFRL=225,252;MMQ=60,60;MPOS=43;POPAF=7.30;TLOD=104.83 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:12,23:0.667:35:3,8:5,6:10,21:0|1:4340_A_G:4340:6,6,10,13 +K03455 4345 . GC AT . . AS_SB_TABLE=12,15|6,6;DP=39;ECNT=23;ECNTH=14;MBQ=20,37;MFRL=197,225;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=49.00 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:27,12:0.314:39:6,3:9,6:23,10:1|0:4340_A_G:4340:12,15,6,6 +K03455 4358 . T C . . AS_SB_TABLE=15,17|2,5;DP=40;ECNT=23;ECNTH=14;MBQ=20,35;MFRL=200,254;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=18.77 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:32,7:0.200:39:7,3:12,3:27,6:15,17,2,5 +K03455 4361 . GCT ACT,G . . AS_SB_TABLE=1,2|11,14|7,7;DP=42;ECNT=23;ECNTH=8,14;MBQ=18,20,34;MFRL=106,209,226;MMQ=60,60,60;MPOS=33,37;POPAF=7.30,7.30;TLOD=101.07,53.78 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:3,25,14:0.615,0.308:42:0,5,4:0,9,7:2,23,11:1,2,18,21 +K03455 4364 . A AAG . . AS_SB_TABLE=12,16|8,7;DP=44;ECNT=23;ECNTH=14;MBQ=33,31;MFRL=206,205;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=56.51 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:28,15:0.333:43:7,4:12,7:25,12:12,16,8,7 +K03455 4370 . A G . . AS_SB_TABLE=11,13|7,13;DP=46;ECNT=23;ECNTH=8;MBQ=20,37;MFRL=191,291;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=64.83 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:24,20:0.538:44:6,5:9,9:17,20:11,13,7,13 +K03455 4376 . C T . . AS_SB_TABLE=9,17|10,12;DP=49;ECNT=23;ECNTH=14;MBQ=37,20;MFRL=267,204;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=76.44 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:26,22:0.404:48:4,6:11,9:24,16:9,17,10,12 +K03455 4397 . T C . . AS_SB_TABLE=17,18|13,9;DP=62;ECNT=23;ECNTH=14;MBQ=32,33;MFRL=290,247;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=79.03 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:35,22:0.386:57:5,8:14,10:31,19:17,18,13,9 +K03455 4416 . C T . . AS_SB_TABLE=16,21|2,1;DP=40;ECNT=19;ECNTH=7;MBQ=37,20;MFRL=281,287;MMQ=60,60;MPOS=9;POPAF=7.30;TLOD=8.03 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:37,3:0.103:40:13,0:18,1:34,3:16,21,2,1 +K03455 4421 . T C . . AS_SB_TABLE=3,5|15,17;DP=40;ECNT=19;ECNTH=9;MBQ=34,38;MFRL=218,289;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=135.40 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:8,32:0.802:40:4,11:1,16:7,30:3,5,15,17 +K03455 4424 . T C . . AS_SB_TABLE=4,7|14,15;DP=40;ECNT=19;ECNTH=9;MBQ=20,38;MFRL=206,291;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=111.14 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:11,29:0.748:40:4,8:1,16:9,28:4,7,14,15 +K03455 4439 . A G . . AS_SB_TABLE=15,17|1,2;DP=35;ECNT=19;ECNTH=6;MBQ=38,20;MFRL=291,126;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=8.08 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:32,3:0.088:35:11,1:16,1:30,2:15,17,1,2 +K03455 4442 . AG GA . . AS_SB_TABLE=13,15|3,4;DP=35;ECNT=19;ECNTH=6;MBQ=39,33;MFRL=297,209;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=21.88 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:28,7:0.235:35:11,1:13,5:25,7:13,15,3,4 +K03455 4443 . G A . . AS_SB_TABLE=3,5|11,11;DP=35;ECNT=19;ECNTH=9;MBQ=38,38;MFRL=258,297;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=80.00 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:8,22:0.726:30:3,9:3,8:7,20:3,5,11,11 +K03455 4448 . C A . . AS_SB_TABLE=14,17|1,2;DP=34;ECNT=19;ECNTH=9;MBQ=38,20;MFRL=290,126;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=9.60 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:31,3:0.091:34:10,0:16,1:29,2:14,17,1,2 +K03455 4449 . C T . . AS_SB_TABLE=6,7|9,10;DP=32;ECNT=19;ECNTH=9;MBQ=31,39;MFRL=206,323;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=74.99 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:13,19:0.617:32:4,7:6,10:11,18:6,7,9,10 +K03455 4460 . T C . . AS_SB_TABLE=15,14|0,2;DP=31;ECNT=19;ECNTH=7;MBQ=37,38;MFRL=290,312;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=4.96 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:29,2:0.100:31:9,0:14,2:26,2:15,14,0,2 +K03455 4465 . T TGGCC . . AS_SB_TABLE=13,12|2,3;DP=30;ECNT=19;ECNTH=8;MBQ=37,28;MFRL=290,229;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=13.23 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:25,5:0.148:30:8,2:14,1:23,4:0|1:4465_T_TGGCC:4465:13,12,2,3 +K03455 4466 . A AGTG . . AS_SB_TABLE=12,12|2,3;DP=30;ECNT=19;ECNTH=8;MBQ=38,29;MFRL=307,229;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=13.49 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:24,5:0.153:29:7,2:13,1:22,4:0|1:4465_T_TGGCC:4465:12,12,2,3 +K03455 4478 . T C . . AS_SB_TABLE=11,9|3,2;DP=25;ECNT=19;ECNTH=8;MBQ=38,20;MFRL=323,207;MMQ=60,60;MPOS=57;POPAF=7.30;TLOD=17.41 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:20,5:0.200:25:6,3:13,1:19,4:11,9,3,2 +K03455 4505 . A G . . AS_SB_TABLE=2,1|10,4;DP=17;ECNT=19;ECNTH=9;MBQ=39,38;MFRL=394,329;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=58.83 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:3,14:0.789:17:2,5:1,8:3,14:2,1,10,4 +K03455 4508 . A T . . AS_SB_TABLE=2,2|10,3;DP=17;ECNT=19;ECNTH=9;MBQ=39,35;MFRL=341,335;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=53.87 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:4,13:0.737:17:2,5:2,8:4,13:2,2,10,3 +K03455 4511 . G A . . AS_SB_TABLE=2,1|10,4;DP=17;ECNT=19;ECNTH=9;MBQ=37,36;MFRL=394,329;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=58.91 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:3,14:0.789:17:2,4:1,7:3,14:2,1,10,4 +K03455 4526 . T C . . AS_SB_TABLE=0,0|11,2;DP=13;ECNT=19;ECNTH=9;MBQ=0,36;MFRL=0,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=56.96 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,13:0.933:13:0,7:0,6:0,13:0,0,11,2 +K03455 4528 . T TCA . . AS_SB_TABLE=10,1|1,1;DP=13;ECNT=19;ECNTH=7;MBQ=38,37;MFRL=323,421;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=5.76 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:11,2:0.200:13:5,1:4,1:11,2:0|1:4528_T_TCA:4528:10,1,1,1 +K03455 4530 . CTT C . . AS_SB_TABLE=9,1|1,1;DP=13;ECNT=19;ECNTH=7;MBQ=35,38;MFRL=323,421;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=4,2;RU=T;STR;TLOD=6.12 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:10,2:0.213:12:5,1:4,1:10,2:0|1:4528_T_TCA:4528:9,1,1,1 +K03455 4532 . T C . . AS_SB_TABLE=0,0|11,0;DP=13;ECNT=19;ECNTH=9;MBQ=0,27;MFRL=0,323;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=39.42 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,11:0.926:11:0,6:0,2:0,11:0,0,11,0
--- a/test-data/Mutect2-out2.vcf Wed Aug 24 17:58:18 2022 +0000 +++ b/test-data/Mutect2-out2.vcf Tue Feb 03 18:50:29 2026 +0000 @@ -4,6 +4,7 @@ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=FAD,Number=R,Type=Integer,Description="Count of fragments supporting each allele."> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles"> @@ -11,18 +12,19 @@ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> -##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input tumor.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.7.0",Date="May 8, 2020 3:31:33 PM CEST"> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input tumor.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --trim-to-haplotype true --exact-matching false --flow-use-t0-tag false --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --keep-boundary-flows false --genotype-pon-sites false --genotype-germline-sites false --genotype-germline-sites-fraction 1.0 --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --permutect-ref-downsample 10 --permutect-alt-downsample 20 --permutect-non-artifact-ratio 1 --permutect-dataset-mode ILLUMINA --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --base-qual-correction-factor 5 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --flow-mode NONE --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --use-pdhmm false --use-pdhmm-overlap-optimization false --make-determined-haps-from-pd-code false --print-pileupcalling-status false --fallback-gga-if-pdhmm-fails true --pileup-detection-enable-indel-pileup-calling false --pileup-detection-active-region-phred-threshold 0.0 --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.1 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-snp-basequality-filter 12 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --pileup-detection-filter-assembly-alt-bad-read-tolerance 0.0 --pileup-detection-edit-distance-read-badness-for-assembly-filtering-threshold 0.12 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.6.2.0",Date="February 2, 2026, 12:29:21?AM GMT"> ##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |."> ##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site"> ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of potential somatic events in the assembly region"> +##INFO=<ID=ECNTH,Number=A,Type=Integer,Description="Number of somatic events in best supporting haplotype for each alt allele"> ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> -##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> -##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> -##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality by allele"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length by allele"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality by allele"> ##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> -##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Log 10 odds of artifact in normal with same allele fraction as tumor"> ##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> @@ -42,85 +44,85 @@ ##source=Mutect2 ##tumor_sample=SRR8525881 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 -K03455 4861 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;MBQ=0,37;MFRL=0,400;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=3.88 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,1:0,0:0,0,1,0 -K03455 4918 . G A . . AS_SB_TABLE=4,1|1,5;DP=11;ECNT=13;MBQ=35,32;MFRL=299,328;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=17.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,6:0.538:11:2,1:3,3:4,1,1,5 -K03455 4923 . A G . . AS_SB_TABLE=0,0|6,6;DP=12;ECNT=13;MBQ=0,33;MFRL=0,301;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=53.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,12:0.929:12:0,4:0,6:0,0,6,6 -K03455 4949 . G A . . AS_SB_TABLE=3,3|5,6;DP=17;ECNT=13;MBQ=38,37;MFRL=281,293;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=44.63 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,11:0.667:17:2,3:2,7:0|1:4949_G_A:4949:3,3,5,6 -K03455 4952 . C T . . AS_SB_TABLE=3,3|5,6;DP=19;ECNT=13;MBQ=25,37;MFRL=281,293;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=44.61 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,11:0.667:17:2,3:2,8:0|1:4949_G_A:4949:3,3,5,6 -K03455 4988 . T C . . AS_SB_TABLE=15,13|4,4;DP=36;ECNT=13;MBQ=34,35;MFRL=254,290;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=23.46 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:28,8:0.229:36:10,4:14,3:15,13,4,4 -K03455 4991 . T C . . AS_SB_TABLE=16,15|3,2;DP=36;ECNT=13;MBQ=33,36;MFRL=264,238;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=12.68 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,5:0.171:36:13,2:17,2:16,15,3,2 -K03455 4996 . AC GA . . AS_SB_TABLE=17,16|3,3;DP=40;ECNT=13;MBQ=34,26;MFRL=260,256;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=12.38 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:33,6:0.161:39:11,2:15,3:17,16,3,3 -K03455 4997 . C T,A . . AS_SB_TABLE=6,5|4,3|10,10;DP=40;ECNT=13;MBQ=20,35,38;MFRL=278,158,261;MMQ=60,60,60;MPOS=14,31;POPAF=7.30,7.30;TLOD=21.98,46.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:11,7,20:0.187,0.536:38:6,2,7:3,4,13:6,5,14,13 -K03455 5015 . A G . . AS_SB_TABLE=6,8|16,17;DP=49;ECNT=13;MBQ=27,37;MFRL=245,251;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=138.05 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:14,33:0.728:47:7,9:6,22:6,8,16,17 -K03455 5018 . A G . . AS_SB_TABLE=18,23|4,4;DP=49;ECNT=13;MBQ=34,20;MFRL=260,194;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=21.59 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:41,8:0.173:49:13,2:22,5:18,23,4,4 -K03455 5027 . G A . . AS_SB_TABLE=18,23|4,7;DP=52;ECNT=13;MBQ=37,20;MFRL=260,158;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=33.61 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:41,11:0.208:52:14,2:24,8:0|1:5027_G_A:5027:18,23,4,7 -K03455 5036 . G A . . AS_SB_TABLE=18,22|4,7;DP=52;ECNT=13;MBQ=34,20;MFRL=259,158;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=33.71 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:40,11:0.212:51:13,2:26,8:0|1:5027_G_A:5027:18,22,4,7 -K03455 5076 . A G . . AS_SB_TABLE=11,36|1,8;DP=56;ECNT=29;MBQ=37,20;MFRL=260,190;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=27.26 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:47,9:0.173:56:15,1:29,8:0|1:5076_A_G:5076:11,36,1,8 -K03455 5098 . A G . . AS_SB_TABLE=1,11|10,40;DP=63;ECNT=29;MBQ=20,33;MFRL=198,269;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=196.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,50:0.785:62:0,11:10,27:1,11,10,40 -K03455 5099 . C T . . AS_SB_TABLE=10,41|1,10;DP=63;ECNT=29;MBQ=34,20;MFRL=260,190;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=33.93 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:51,11:0.196:62:10,1:33,8:0|1:5076_A_G:5076:10,41,1,10 -K03455 5121 . C T . . AS_SB_TABLE=7,39|4,13;DP=63;ECNT=29;MBQ=26,20;MFRL=246,260;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=57.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:46,17:0.250:63:8,6:34,9:7,39,4,13 -K03455 5130 . TG CA . . AS_SB_TABLE=3,13|3,37;DP=56;ECNT=29;MBQ=27,37;MFRL=218,249;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=170.80 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:16,40:0.738:56:5,6:9,32:3,13,3,37 -K03455 5131 . G A . . AS_SB_TABLE=0,1|3,13;DP=56;ECNT=29;MBQ=32,20;MFRL=206,216;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=56.78 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,16:0.946:17:0,4:1,9:0,1,3,13 -K03455 5133 . T C . . AS_SB_TABLE=5,34|0,13;DP=52;ECNT=29;MBQ=33,33;MFRL=278,222;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=42.34 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:39,13:0.280:52:7,1:26,11:0|1:5133_T_C:5133:5,34,0,13 -K03455 5137 . GG AA,AG . . AS_SB_TABLE=3,13|1,21|0,13;DP=51;ECNT=29;MBQ=32,39,39;MFRL=218,320,222;MMQ=60,60,60;MPOS=34,39;POPAF=7.30,7.30;TLOD=86.50,42.93 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:16,22,13:0.452,0.274:51:5,4,1:9,17,10:3,13,1,34 -K03455 5146 . AGG A . . AS_SB_TABLE=4,32|0,12;DP=48;ECNT=29;MBQ=37,37;MFRL=286,219;MMQ=60,60;MPOS=43;POPAF=7.30;RPA=4,2;RU=G;STR;TLOD=39.62 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:36,12:0.276:48:8,1:25,11:0|1:5133_T_C:5133:4,32,0,12 -K03455 5147 . G A . . AS_SB_TABLE=3,12|1,20;DP=48;ECNT=29;MBQ=20,37;MFRL=229,331;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=83.42 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:15,21:0.640:36:5,3:9,14:0|1:5147_G_A:5147:3,12,1,20 -K03455 5149 . G A . . AS_SB_TABLE=3,42|1,1;DP=47;ECNT=29;MBQ=36,18;MFRL=257,64;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=4.60 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:45,2:0.043:47:7,0:30,1:3,42,1,1 -K03455 5153 . GGTTT G . . AS_SB_TABLE=3,28|0,12;DP=43;ECNT=29;MBQ=35,37;MFRL=278,219;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=40.38 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:31,12:0.309:43:7,1:22,11:0|1:5133_T_C:5133:3,28,0,12 -K03455 5155 . T C . . AS_SB_TABLE=3,11|0,16;DP=42;ECNT=29;MBQ=27,38;MFRL=221,315;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=62.97 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:14,16:0.601:30:5,2:8,13:0|1:5147_G_A:5147:3,11,0,16 -K03455 5156 . T A . . AS_SB_TABLE=1,17|2,10;DP=42;ECNT=29;MBQ=37,35;MFRL=296,269;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=43.10 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:18,12:0.365:30:2,5:16,7:0|1:5156_T_A:5156:1,17,2,10 -K03455 5157 . T G,C . . AS_SB_TABLE=2,10|0,16|1,1;DP=42;ECNT=29;MBQ=28,37,20;MFRL=269,315,64;MMQ=60,60,60;MPOS=56,5;POPAF=7.30,7.30;TLOD=63.04,5.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:12,16,2:0.584,0.061:30:5,2,0:7,14,2:2,10,1,17 -K03455 5169 . C T . . AS_SB_TABLE=1,19|1,10;DP=31;ECNT=29;MBQ=38,32;MFRL=275,190;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=37.40 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:20,11:0.355:31:2,4:17,7:1,19,1,10 -K03455 5175 . A T . . AS_SB_TABLE=0,15|1,12;DP=28;ECNT=29;MBQ=28,38;MFRL=222,293;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=52.25 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:15,13:0.448:28:3,2:10,11:0|1:5147_G_A:5147:0,15,1,12 -K03455 5177 . G C . . AS_SB_TABLE=1,16|0,10;DP=27;ECNT=29;MBQ=37,35;MFRL=293,219;MMQ=60,60;MPOS=52;POPAF=7.30;TLOD=36.84 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:17,10:0.393:27:4,1:12,9:0|1:5133_T_C:5133:1,16,0,10 -K03455 5179 . CC AA,AC . . AS_SB_TABLE=0,4|1,11|0,10;DP=26;ECNT=29;MBQ=38,38,34;MFRL=339,296,219;MMQ=60,60,60;MPOS=51,61;POPAF=7.30,7.30;TLOD=48.82,37.25 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:4,12,10:0.429,0.393:26:2,2,1:2,10,7:0,4,1,21 -K03455 5189 . G A . . AS_SB_TABLE=1,12|1,11;DP=25;ECNT=29;MBQ=39,39;MFRL=222,296;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=48.64 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,12:0.462:25:4,2:9,10:1,12,1,11 -K03455 5190 . A G . . AS_SB_TABLE=1,19|1,4;DP=25;ECNT=29;MBQ=39,20;MFRL=252,278;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=15.35 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:20,5:0.231:25:3,2:17,2:0|1:5156_T_A:5156:1,19,1,4 -K03455 5196 . T C . . AS_SB_TABLE=1,20|1,3;DP=25;ECNT=29;MBQ=38,20;MFRL=246,339;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=6.08 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:21,4:0.191:25:3,3:18,1:1,20,1,3 -K03455 5220 . G A . . AS_SB_TABLE=2,14|0,7;DP=23;ECNT=29;MBQ=37,37;MFRL=286,222;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=24.08 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:16,7:0.344:23:5,1:11,6:0|1:5220_G_A:5220:2,14,0,7 -K03455 5223 . T A . . AS_SB_TABLE=1,16|1,4;DP=22;ECNT=29;MBQ=37,37;MFRL=257,278;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=17.16 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:17,5:0.269:22:2,3:14,2:0|1:5223_T_A:5223:1,16,1,4 -K03455 5226 . T C . . AS_SB_TABLE=1,15|1,5;DP=22;ECNT=29;MBQ=34,35;MFRL=268,253;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=12.23 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:16,6:0.231:22:4,1:12,5:1,15,1,5 -K03455 5230 . T C . . AS_SB_TABLE=1,15|1,4;DP=21;ECNT=29;MBQ=33,38;MFRL=275,278;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=17.08 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:16,5:0.281:21:2,3:13,2:0|1:5223_T_A:5223:1,15,1,4 -K03455 5233 . G A . . AS_SB_TABLE=2,9|0,5;DP=16;ECNT=29;MBQ=38,38;MFRL=293,216;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=17.95 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:11,5:0.369:16:3,0:7,5:0|1:5220_G_A:5220:2,9,0,5 -K03455 5236 . A G . . AS_SB_TABLE=0,5|2,9;DP=16;ECNT=29;MBQ=37,38;MFRL=216,293;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=40.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,11:0.631:16:0,4:5,6:0,5,2,9 -K03455 5240 . C T . . AS_SB_TABLE=2,10|0,3;DP=15;ECNT=29;MBQ=37,37;MFRL=250,162;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=9.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,3:0.250:15:3,0:8,3:2,10,0,3 -K03455 6822 . GT AC . . AS_SB_TABLE=0,0|2,2;DP=4;ECNT=1;MBQ=0,38;MFRL=0,117;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=7.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,4:0.750:4:0,0:0,4:0,0,2,2 -K03455 6902 . A C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6905 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6911 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6917 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6920 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6923 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6931 . C A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6936 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 7141 . GAATCC G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,0;MFRL=0,310;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 -K03455 7149 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,15;MFRL=0,310;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 -K03455 7151 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,38;MFRL=0,310;MMQ=60,60;MPOS=9;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 -K03455 7154 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,24;MFRL=0,310;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 -K03455 7156 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,25;MFRL=0,310;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 -K03455 7163 . A C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,13;MFRL=0,310;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,0:0,0,0,1 -K03455 7372 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;MBQ=0,34;MFRL=0,451;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=3.58 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7372_T_C:7372:0,0,0,1 -K03455 7392 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;MBQ=0,32;MFRL=0,451;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7372_T_C:7372:0,0,0,1 -K03455 7441 . A ACCT . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=77;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7443 . A AGTG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=82;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7449 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=91;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7452 . GGA G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=94;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7455 . A ATG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=95;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7457 . TGA T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=99;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7460 . CA C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7468 . CC TA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=107;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 -K03455 7478 . C T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=117;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 -K03455 7491 . A T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=118;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 -K03455 7494 . A G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=115;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 -K03455 7508 . GA AG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 -K03455 7541 . C CGA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=68;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7542 . AGT A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=65;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7548 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=61;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7555 . GA AT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7560 . TC GT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=49;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7568 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=41;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7571 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=38;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7581 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=28;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7584 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=25;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7603 . A AGGG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=6;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7604 . T G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=2;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 4861 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;ECNTH=10;MBQ=0,37;MFRL=0,400;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=3.88 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,1:0.667:1:0,1:0,0:0,1:0,0,1,0 +K03455 4918 . G A . . AS_SB_TABLE=4,1|1,4;DP=11;ECNT=14;ECNTH=5;MBQ=37,32;MFRL=260,331;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=13.33 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:5,5:0.499:10:2,1:3,3:5,5:4,1,1,4 +K03455 4923 . A G . . AS_SB_TABLE=0,0|6,6;DP=12;ECNT=14;ECNTH=5;MBQ=0,33;MFRL=0,284;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=52.89 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,12:0.929:12:0,4:0,6:0,12:0,0,6,6 +K03455 4949 . G A . . AS_SB_TABLE=3,3|4,6;DP=16;ECNT=14;ECNTH=5;MBQ=38,38;MFRL=293,258;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=39.87 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:6,10:0.611:16:2,3:2,6:6,10:0|1:4949_G_A:4949:3,3,4,6 +K03455 4952 . C T . . AS_SB_TABLE=3,3|4,6;DP=18;ECNT=14;ECNTH=5;MBQ=33,37;MFRL=293,258;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=39.85 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:6,10:0.611:16:2,3:3,7:6,10:0|1:4949_G_A:4949:3,3,4,6 +K03455 4988 . T C . . AS_SB_TABLE=10,12|4,3;DP=29;ECNT=14;ECNTH=5;MBQ=36,36;MFRL=249,301;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=17.26 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:22,7:0.267:29:7,4:11,2:20,7:10,12,4,3 +K03455 4991 . T C . . AS_SB_TABLE=12,14|2,1;DP=29;ECNT=14;ECNTH=7;MBQ=36,33;MFRL=262,229;MMQ=60,60;MPOS=60;POPAF=7.30;TLOD=6.20 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:26,3:0.137:29:11,1:12,2:24,3:12,14,2,1 +K03455 4996 . AC GA . . AS_SB_TABLE=11,13|3,3;DP=31;ECNT=14;ECNTH=6;MBQ=36,26;MFRL=262,256;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=12.04 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:24,6:0.199:30:8,2:10,2:23,5:11,13,3,3 +K03455 4997 . C T,A . . AS_SB_TABLE=5,5|2,1|7,10;DP=31;ECNT=14;ECNTH=7,6;MBQ=20,31,38;MFRL=282,229,251;MMQ=60,60,60;MPOS=54,31;POPAF=7.30,7.30;TLOD=6.97,36.41 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:10,3,17:0.130,0.542:30:4,1,7:3,2,9:9,3,16:5,5,9,11 +K03455 5015 . A G . . AS_SB_TABLE=5,8|12,16;DP=43;ECNT=14;ECNTH=6;MBQ=33,37;MFRL=260,251;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=104.33 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:13,28:0.700:41:5,8:5,19:11,27:5,8,12,16 +K03455 5018 . A G . . AS_SB_TABLE=15,25|2,1;DP=43;ECNT=14;ECNTH=10;MBQ=34,20;MFRL=259,229;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=5.47 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:40,3:0.094:43:11,1:19,2:37,3:15,25,2,1 +K03455 5027 . G A . . AS_SB_TABLE=14,28|3,1;DP=47;ECNT=14;ECNTH=10;MBQ=33,29;MFRL=254,254;MMQ=60,60;MPOS=43;POPAF=7.30;TLOD=8.72 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:42,4:0.116:46:11,2:22,2:37,4:14,28,3,1 +K03455 5036 . G A . . AS_SB_TABLE=16,28|2,1;DP=47;ECNT=14;ECNTH=10;MBQ=32,20;MFRL=251,229;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=5.52 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:44,3:0.092:47:12,1:23,2:38,3:16,28,2,1 +K03455 5076 . A G . . AS_SB_TABLE=9,38|1,6;DP=54;ECNT=33;ECNTH=13;MBQ=37,20;MFRL=260,158;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=21.83 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:47,7:0.140:54:14,0:24,5:42,6:0|1:5076_A_G:5076:9,38,1,6 +K03455 5098 . A G . . AS_SB_TABLE=1,10|9,41;DP=62;ECNT=33;ECNTH=11;MBQ=32,33;MFRL=206,269;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=196.84 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:11,50:0.799:61:1,10:8,23:10,43:1,10,9,41 +K03455 5099 . C T . . AS_SB_TABLE=9,43|1,8;DP=62;ECNT=33;ECNTH=13;MBQ=33,20;MFRL=269,162;MMQ=60,60;MPOS=48;POPAF=7.30;TLOD=28.29 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:52,9:0.163:61:9,0:27,6:45,8:0|1:5076_A_G:5076:9,43,1,8 +K03455 5121 . C T . . AS_SB_TABLE=6,39|4,13;DP=62;ECNT=33;ECNTH=10;MBQ=32,30;MFRL=251,260;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=58.62 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:45,17:0.255:62:7,5:29,6:40,13:6,39,4,13 +K03455 5130 . TG CA . . AS_SB_TABLE=3,14|4,35;DP=56;ECNT=33;ECNTH=11;MBQ=33,37;MFRL=229,251;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=168.50 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:17,39:0.717:56:4,6:6,27:14,37:3,14,4,35 +K03455 5131 . G A . . AS_SB_TABLE=0,1|3,13;DP=56;ECNT=33;ECNTH=10;MBQ=32,20;MFRL=206,216;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=58.17 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:1,16:0.946:17:0,3:1,6:1,13:0,1,3,13 +K03455 5133 . T C . . AS_SB_TABLE=4,36|2,10;DP=52;ECNT=33;ECNTH=11;MBQ=37,37;MFRL=280,219;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=49.54 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:40,12:0.260:52:7,1:22,9:36,12:0|1:5133_T_C:5133:4,36,2,10 +K03455 5137 . GG AA,AG . . AS_SB_TABLE=3,13|0,23|2,10;DP=51;ECNT=33;ECNTH=11,11;MBQ=32,39,39;MFRL=218,309,219;MMQ=60,60,60;MPOS=36,36;POPAF=7.30,7.30;TLOD=91.94,49.94 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:16,23,12:0.471,0.255:51:3,3,1:6,16,8:13,23,12:3,13,2,33 +K03455 5146 . AGG A . . AS_SB_TABLE=3,34|2,9;DP=48;ECNT=33;ECNTH=11;MBQ=38,38;MFRL=281,216;MMQ=60,60;MPOS=31;POPAF=7.30;RPA=4,2;RU=G;STR;TLOD=46.83 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:37,11:0.255:48:7,1:21,9:34,11:0|1:5133_T_C:5133:3,34,2,9 +K03455 5147 . G A . . AS_SB_TABLE=3,12|0,22;DP=48;ECNT=33;ECNTH=11;MBQ=20,37;MFRL=229,315;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=88.89 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:15,22:0.640:37:3,4:6,13:12,22:3,12,0,22 +K03455 5148 . G GAAAAAT . . AS_SB_TABLE=3,33|2,9;DP=47;ECNT=33;ECNTH=11;MBQ=37,0;MFRL=280,216;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=46.96 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:36,11:0.261:47:6,0:20,0:33,11:0|1:5133_T_C:5133:3,33,2,9 +K03455 5149 . G A . . AS_SB_TABLE=4,41|1,1;DP=47;ECNT=33;ECNTH=11;MBQ=37,18;MFRL=260,64;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=4.60 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:45,2:0.043:47:6,0:25,0:43,1:4,41,1,1 +K03455 5153 . GGTTT G . . AS_SB_TABLE=3,30|2,11;DP=46;ECNT=33;ECNTH=11;MBQ=34,38;MFRL=278,162;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=47.60 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:33,13:0.281:46:5,1:18,9:30,11:0|1:5133_T_C:5133:3,30,2,11 +K03455 5155 . T C . . AS_SB_TABLE=3,11|0,17;DP=45;ECNT=33;ECNTH=11;MBQ=27,37;MFRL=221,299;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=68.15 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:14,17:0.601:31:3,2:5,12:11,17:0|1:5155_T_C:5155:3,11,0,17 +K03455 5156 . T A . . AS_SB_TABLE=1,19|2,10;DP=45;ECNT=33;ECNTH=10;MBQ=38,36;MFRL=287,269;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=42.93 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:20,12:0.354:32:3,3:14,5:19,10:0|1:5156_T_A:5156:1,19,2,10 +K03455 5157 . T G,C . . AS_SB_TABLE=2,11|0,17|1,1;DP=45;ECNT=33;ECNTH=11,11;MBQ=37,37,20;MFRL=278,299,64;MMQ=60,60,60;MPOS=54,5;POPAF=7.30,7.30;TLOD=67.92,5.59 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:13,17,2:0.565,0.059:32:4,2,0:5,13,1:11,17,1:2,11,1,18 +K03455 5169 . C T . . AS_SB_TABLE=1,21|3,8;DP=33;ECNT=33;ECNTH=10;MBQ=38,20;MFRL=252,100;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=33.24 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:22,11:0.290:33:2,2:16,4:21,8:1,21,3,8 +K03455 5175 . A T . . AS_SB_TABLE=2,14|1,13;DP=30;ECNT=33;ECNTH=11;MBQ=32,38;MFRL=199,275;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=57.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:16,14:0.483:30:2,2:9,9:14,13:0|1:5155_T_C:5155:2,14,1,13 +K03455 5177 . G C . . AS_SB_TABLE=1,17|2,9;DP=29;ECNT=33;ECNTH=11;MBQ=37,32;MFRL=286,162;MMQ=60,60;MPOS=57;POPAF=7.30;TLOD=41.57 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:18,11:0.357:29:2,1:10,8:17,9:0|1:5133_T_C:5133:1,17,2,9 +K03455 5179 . CC AA,AC . . AS_SB_TABLE=0,4|1,12|2,9;DP=28;ECNT=33;ECNTH=11,11;MBQ=38,38,20;MFRL=339,293,162;MMQ=60,60,60;MPOS=51,59;POPAF=7.30,7.30;TLOD=54.29,42.03 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:4,13,11:0.464,0.357:28:1,1,1:2,8,6:4,12,9:0,4,3,21 +K03455 5189 . G A . . AS_SB_TABLE=3,11|1,11;DP=26;ECNT=33;ECNTH=11;MBQ=20,39;MFRL=199,296;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=49.94 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:14,12:0.480:26:3,1:8,8:12,11:3,11,1,11 +K03455 5190 . A G . . AS_SB_TABLE=3,18|1,4;DP=26;ECNT=33;ECNTH=10;MBQ=38,20;MFRL=246,278;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=15.46 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:21,5:0.240:26:2,1:14,2:18,5:0|1:5156_T_A:5156:3,18,1,4 +K03455 5196 . T C . . AS_SB_TABLE=3,19|1,3;DP=26;ECNT=33;ECNTH=10;MBQ=37,20;MFRL=234,339;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=6.18 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:22,4:0.198:26:2,2:15,1:19,4:3,19,1,3 +K03455 5220 . G A . . AS_SB_TABLE=1,14|0,7;DP=22;ECNT=33;ECNTH=11;MBQ=37,37;MFRL=293,216;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=24.54 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:15,7:0.348:22:2,0:9,5:14,7:1,14,0,7 +K03455 5223 . T A . . AS_SB_TABLE=1,17|0,4;DP=22;ECNT=33;ECNTH=10;MBQ=37,38;MFRL=252,339;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=12.88 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:18,4:0.217:22:1,1:11,2:17,4:0|1:5223_T_A:5223:1,17,0,4 +K03455 5226 . T C . . AS_SB_TABLE=0,16|1,5;DP=22;ECNT=33;ECNTH=11;MBQ=34,35;MFRL=268,253;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=15.73 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:16,6:0.261:22:1,1:10,4:16,5:0,16,1,5 +K03455 5230 . T C . . AS_SB_TABLE=1,16|0,4;DP=21;ECNT=33;ECNTH=10;MBQ=34,39;MFRL=257,339;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=12.99 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:17,4:0.227:21:1,1:10,2:16,4:0|1:5223_T_A:5223:1,16,0,4 +K03455 5233 . G A . . AS_SB_TABLE=1,9|0,6;DP=16;ECNT=33;ECNTH=11;MBQ=38,38;MFRL=312,189;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=21.55 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:10,6:0.412:16:2,0:6,4:9,6:1,9,0,6 +K03455 5236 . A G . . AS_SB_TABLE=0,6|1,9;DP=16;ECNT=33;ECNTH=10;MBQ=37,38;MFRL=189,312;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=39.55 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:6,10:0.588:16:0,2:4,5:6,9:0,6,1,9 +K03455 5240 . C T . . AS_SB_TABLE=1,10|0,3;DP=14;ECNT=33;ECNTH=13;MBQ=37,37;MFRL=278,162;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=9.35 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:11,3:0.267:14:2,0:7,2:10,3:1,10,0,3 +K03455 6822 . GT AC . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;ECNTH=1;MBQ=0,20;MFRL=0,117;MMQ=60,60;MPOS=79;POPAF=7.30;TLOD=8.52 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,2:0.750:2:0,0:0,2:0,2:0,0,0,2 +K03455 6902 . A C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6905 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6911 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6917 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6920 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6923 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6931 . C A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6936 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 7141 . GAATCC G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=5;MBQ=0,0;MFRL=0,310;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0,1:0|1:7141_GAATCC_G:7141:0,0,0,1 +K03455 7149 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=5;MBQ=0,15;MFRL=0,310;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0,1:0|1:7141_GAATCC_G:7141:0,0,0,1 +K03455 7151 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=5;MBQ=0,38;MFRL=0,310;MMQ=60,60;MPOS=9;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0,1:0|1:7141_GAATCC_G:7141:0,0,0,1 +K03455 7154 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=5;MBQ=0,24;MFRL=0,310;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0,1:0|1:7141_GAATCC_G:7141:0,0,0,1 +K03455 7156 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=5;MBQ=0,25;MFRL=0,310;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0,1:0|1:7141_GAATCC_G:7141:0,0,0,1 +K03455 7372 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;ECNTH=2;MBQ=0,34;MFRL=0,451;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=3.58 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7372_T_C:7372:0,0,0,1 +K03455 7392 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;ECNTH=2;MBQ=0,32;MFRL=0,451;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7372_T_C:7372:0,0,0,1 +K03455 7441 . A ACCT . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=77;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7443 . A AGTG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=82;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7449 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=91;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7452 . GGA G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=94;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7455 . A ATG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=95;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7457 . TGA T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=99;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7460 . CA C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7468 . CC TA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=107;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7478 . C T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=117;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7491 . A T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=118;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7494 . A G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=115;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7508 . GA AG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7541 . C CGA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=68;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7542 . AGT A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=65;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7548 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=61;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7555 . GA AT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7560 . TC GT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=49;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7568 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=41;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7571 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=38;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7581 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=28;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7584 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=25;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7603 . A AGGG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=6;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7604 . T G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=2;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2
--- a/test-data/Mutect2-out3.vcf Wed Aug 24 17:58:18 2022 +0000 +++ b/test-data/Mutect2-out3.vcf Tue Feb 03 18:50:29 2026 +0000 @@ -4,6 +4,7 @@ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=FAD,Number=R,Type=Integer,Description="Count of fragments supporting each allele."> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles"> @@ -11,19 +12,20 @@ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> -##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --normal-lod 2.2 --base-quality-score-threshold 18 --native-pair-hmm-threads 1 --min-base-quality-score 10 --output output.vcf --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --input tumor.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --gcs-max-retries 20 --annotation StrandBiasBySample --annotation BaseQualityHistogram --annotation OrientationBiasReadCounts --annotation-group StandardMutectAnnotation --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.7.0",Date="May 8, 2020 3:32:12 PM CEST"> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --normal-lod 2.2 --base-quality-score-threshold 18 --native-pair-hmm-threads 1 --min-base-quality-score 10 --output output.vcf --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --input tumor.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --gcs-max-retries 20 --annotation StrandBiasBySample --annotation BaseQualityHistogram --annotation OrientationBiasReadCounts --annotation-group StandardMutectAnnotation --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --trim-to-haplotype true --exact-matching false --flow-use-t0-tag false --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --keep-boundary-flows false --genotype-pon-sites false --genotype-germline-sites false --genotype-germline-sites-fraction 1.0 --mitochondria-mode false --permutect-ref-downsample 10 --permutect-alt-downsample 20 --permutect-non-artifact-ratio 1 --permutect-dataset-mode ILLUMINA --base-qual-correction-factor 5 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --flow-mode NONE --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --use-pdhmm false --use-pdhmm-overlap-optimization false --make-determined-haps-from-pd-code false --print-pileupcalling-status false --fallback-gga-if-pdhmm-fails true --pileup-detection-enable-indel-pileup-calling false --pileup-detection-active-region-phred-threshold 0.0 --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.1 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-snp-basequality-filter 12 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --pileup-detection-filter-assembly-alt-bad-read-tolerance 0.0 --pileup-detection-edit-distance-read-badness-for-assembly-filtering-threshold 0.12 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --enable-legacy-assembly-region-trimming false --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.6.2.0",Date="February 2, 2026, 12:29:39?AM GMT"> ##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |."> ##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site"> ##INFO=<ID=BQHIST,Number=A,Type=Integer,Description="Base quality counts for each allele represented sparsely as alternating entries of qualities and counts for each allele.For example [10,1,0,20,0,1] means one ref base with quality 10 and one alt base with quality 20."> ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of potential somatic events in the assembly region"> +##INFO=<ID=ECNTH,Number=A,Type=Integer,Description="Number of somatic events in best supporting haplotype for each alt allele"> ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> -##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> -##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> -##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality by allele"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length by allele"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality by allele"> ##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> -##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Log 10 odds of artifact in normal with same allele fraction as tumor"> ##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> @@ -43,25 +45,23 @@ ##source=Mutect2 ##tumor_sample=SRR8525881 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 -K03455 2652 . G A . . AS_SB_TABLE=0,0|119,14;BQHIST=16,1,0,18,9,0,20,26,0,29,5,0,32,20,0,33,12,0,34,2,0,37,28,0,38,14,0,39,14,0;DP=133;ECNT=6;MBQ=0,33;MFRL=0,271;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=588.26 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,133:0.992:133:0,59:0,62:0|1:2652_G_A:2652:0,0,119,14 -K03455 2660 . T C . . AS_SB_TABLE=0,0|149,17;BQHIST=15,1,0,16,1,0,17,2,0,20,25,0,29,1,0,32,4,0,33,3,0,34,2,0,35,6,0,37,48,0,38,28,0,39,22,0;DP=166;ECNT=6;MBQ=0,37;MFRL=0,272;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=734.40 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,166:0.994:166:0,68:0,71:0|1:2652_G_A:2652:0,0,149,17 -K03455 2664 . A G . . AS_SB_TABLE=0,0|152,17;BQHIST=18,0,2,19,0,2,20,0,28,30,0,3,32,0,15,33,0,13,34,0,1,35,0,4,36,0,2,37,0,18,38,0,65,39,0,14;DP=169;ECNT=6;MBQ=0,37;MFRL=0,271;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=586.40 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,169:0.994:169:0,82:0,81:0,0,152,17 -K03455 2669 . G A . . AS_SB_TABLE=0,0|159,19;BQHIST=16,1,0,18,1,0,19,2,0,20,33,0,29,1,0,32,5,0,33,9,0,34,3,0,36,1,0,37,46,0,38,45,0,39,31,0;DP=181;ECNT=6;MBQ=0,37;MFRL=0,272;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=772.57 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,178:0.994:178:0,86:0,88:0|1:2652_G_A:2652:0,0,159,19 -K03455 2677 . A G . . AS_SB_TABLE=166,19|3,1;BQHIST=15,3,0,17,1,0,18,1,0,19,4,0,20,36,2,33,6,0,34,9,0,36,3,0,37,29,0,38,36,0,39,57,2;DP=190;ECNT=6;MBQ=38,30;MFRL=271,240;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=5.33 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:185,4:0.023:189:85,2:91,2:166,19,3,1 -K03455 2720 . T C . . AS_SB_TABLE=0,0|255,45;BQHIST=14,3,0,16,11,0,17,1,0,18,21,0,20,65,0,30,1,0,32,2,0,33,25,0,34,9,0,36,13,0,37,82,0,38,24,0,39,41,0;DP=345;ECNT=6;MBQ=0,36;MFRL=0,262;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=1056.74 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,300:0.996:300:0,120:0,142:0,0,255,45 -K03455 2797 . G A . . AS_SB_TABLE=0,0|328,159;BQHIST=15,2,0,16,2,0,17,1,0,18,21,0,20,184,0,32,5,0,33,20,0,35,7,0,36,8,0,37,55,0,38,61,0,39,109,0;DP=509;ECNT=12;MBQ=0,35;MFRL=0,247;MMQ=60,60;MPOS=43;POPAF=7.30;TLOD=1690.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,487:0.998:487:0,240:0,209:0,0,328,159 -K03455 2831 . A T . . AS_SB_TABLE=297,202|0,17;BQHIST=14,5,0,15,11,0,16,2,1,17,47,3,18,12,10,19,3,0,20,137,0,29,2,0,30,5,1,31,6,0,32,10,0,33,40,2,34,14,0,36,5,0,37,52,0,38,43,0,39,102,0;DP=532;ECNT=12;MBQ=33,18;MFRL=240,262;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=4.43 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:499,17:0.024:516:221,1:195,2:297,202,0,17 -K03455 2848 . T TA . . AS_SB_TABLE=8,5|304,260;BQHIST=14,0,2,15,0,18,16,0,11,17,0,1,19,0,1,20,6,239,27,0,1,29,0,1,30,1,14,31,0,1,32,0,14,33,2,24,34,0,12,35,0,1,36,0,20,37,0,48,38,1,71,39,3,81;DP=599;ECNT=12;MBQ=30,30;MFRL=257,246;MMQ=60,60;MPOS=33;POPAF=7.30;RPA=6,7;RU=A;STR;TLOD=1270.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,564:0.983:577:6,264:7,263:8,5,304,260 -K03455 2849 . A AG . . AS_SB_TABLE=314,267|4,4;BQHIST=14,0,7,15,0,1,16,0,3,17,0,1,18,0,16,19,1,0,20,2,269,27,0,1,29,0,2,30,1,8,31,0,2,32,0,4,33,0,18,34,1,6,35,0,4,36,0,33,37,1,40,38,0,101,39,2,62;DP=597;ECNT=12;MBQ=20,32;MFRL=245,276;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=3.17 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:581,8:0.012:589:285,2:265,5:314,267,4,4 -K03455 2872 . T A . . AS_SB_TABLE=267,300|25,0;BQHIST=14,1,2,15,2,0,16,0,11,17,6,6,18,15,51,19,0,38,20,0,167,27,1,1,29,0,16,30,0,3,31,0,9,32,0,22,33,0,29,34,0,12,35,0,12,36,0,9,37,0,78,38,0,48,39,0,53;DP=628;ECNT=12;MBQ=29,18;MFRL=240,283;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.43 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:567,25:0.023:592:225,1:234,0:267,300,25,0 -K03455 2874 . C T . . AS_SB_TABLE=1,0|300,303;BQHIST=16,0,6,17,1,5,18,0,54,19,0,13,20,0,199,29,0,4,30,0,2,31,0,11,32,0,32,33,0,41,34,0,13,35,0,13,36,0,11,37,0,87,38,0,54,39,0,51;DP=606;ECNT=12;MBQ=17,32;MFRL=360,241;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=2043.53 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,603:0.997:604:0,265:0,253:1,0,300,303 -K03455 2882 . G T . . AS_SB_TABLE=1,0|295,283;BQHIST=14,2,0,16,6,0,17,6,0,18,21,0,19,12,0,20,195,0,29,2,0,30,4,0,31,4,1,32,3,0,33,25,0,34,1,0,35,21,0,36,11,0,37,85,0,38,52,0,39,112,0;DP=579;ECNT=12;MBQ=31,35;MFRL=360,246;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1927.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,578:0.997:579:1,259:0,256:1,0,295,283 -K03455 2889 . G A . . AS_SB_TABLE=289,272|7,1;BQHIST=14,0,11,15,0,1,16,0,4,17,0,5,18,0,13,19,0,17,20,0,190,29,1,1,30,0,3,31,0,1,32,0,7,33,2,31,34,1,4,35,0,9,36,0,15,37,1,79,38,1,72,39,2,95,40,0,1;DP=580;ECNT=12;MBQ=33,36;MFRL=249,291;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=9.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:561,8:0.018:569:248,4:260,4:289,272,7,1 -K03455 2891 . A G . . AS_SB_TABLE=286,269|5,4;BQHIST=14,0,1,16,6,0,17,9,0,18,18,0,19,8,0,20,179,6,30,1,0,31,4,0,32,8,0,33,25,1,34,2,0,35,26,0,36,7,1,37,78,0,38,85,0,39,89,0;DP=576;ECNT=12;MBQ=35,20;MFRL=249,231;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=8.78 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:555,9:0.013:564:243,4:261,4:286,269,5,4 -K03455 2894 . T C . . AS_SB_TABLE=0,0|291,273;BQHIST=14,1,0,15,5,0,16,4,0,17,13,0,18,33,0,19,4,0,20,162,0,27,1,0,29,3,0,30,5,0,31,1,0,32,6,0,33,25,0,34,12,0,35,5,0,36,8,0,37,83,0,38,69,0,39,116,0;DP=564;ECNT=12;MBQ=0,35;MFRL=0,250;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1813.95 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,564:0.998:564:0,243:0,253:0,0,291,273 -K03455 2906 . C T . . AS_SB_TABLE=0,0|246,262;BQHIST=16,0,2,18,0,4,19,0,10,20,0,145,30,0,2,31,0,2,32,0,3,33,0,21,34,0,3,35,0,19,36,0,11,37,0,61,38,0,79,39,0,146;DP=508;ECNT=12;MBQ=0,37;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2411.23 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,508:0.998:508:0,232:0,260:0|1:2906_C_T:2906:0,0,246,262 -K03455 2913 . G A . . AS_SB_TABLE=0,0|245,260;BQHIST=18,5,0,19,5,0,20,134,0,29,1,0,30,2,0,31,2,0,32,2,0,33,17,0,34,1,0,35,6,0,36,2,0,37,64,0,38,68,0,39,184,0,40,4,0;DP=505;ECNT=12;MBQ=0,38;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2402.33 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,505:0.998:505:0,230:0,257:0|1:2906_C_T:2906:0,0,245,260 -K03455 2987 . C T . . AS_SB_TABLE=0,0|86,133;BQHIST=16,0,3,17,0,3,19,0,11,20,0,15,30,0,2,31,0,9,32,0,7,33,0,31,34,0,8,35,0,9,36,0,1,37,0,47,38,0,34,39,0,39;DP=223;ECNT=4;MBQ=0,37;MFRL=0,264;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=847.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,219:0.995:219:0,99:0,103:0,0,86,133 -K03455 2992 . T G . . AS_SB_TABLE=74,105|9,0;BQHIST=16,1,0,17,3,0,18,1,7,19,23,0,20,13,1,29,1,0,31,8,0,32,8,0,33,18,1,34,9,0,35,4,0,36,4,0,37,35,0,38,30,0,39,21,0;DP=206;ECNT=4;MBQ=36,18;MFRL=271,260;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.85 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:179,9:0.043:188:74,2:77,0:74,105,9,0 -K03455 3016 . C A . . AS_SB_TABLE=61,27|7,0;BQHIST=14,0,2,15,0,2,18,6,26,29,0,1,30,0,3,32,0,5,33,1,12,34,0,2,35,0,2,36,0,8,37,0,5,38,0,16,39,0,4;DP=100;ECNT=4;MBQ=33,18;MFRL=276,255;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=5.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:88,7:0.081:95:24,1:34,0:61,27,7,0 -K03455 3020 . A G . . AS_SB_TABLE=0,0|65,25;BQHIST=14,0,12,16,0,1,18,0,1,27,0,3,29,0,3,30,0,8,32,0,8,33,0,2,34,0,1,35,0,1,36,0,21,37,0,4,38,0,23,39,0,1;DP=95;ECNT=4;MBQ=0,36;MFRL=0,284;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=324.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,90:0.989:90:0,32:0,43:0,0,65,25 +K03455 2644 . A G . . AS_SB_TABLE=41,9|2,0;BQHIST=20,18,0,32,1,0,37,12,0,38,4,1,39,15,1;DP=61;ECNT=6;ECNTH=6;MBQ=37,39;MFRL=242,292;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=3.99 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:50,2:0.064:52:21,0:21,2:42,2:41,9,2,0 +K03455 2652 . G A . . AS_SB_TABLE=0,0|122,15;BQHIST=16,1,0,18,9,0,20,27,0,29,5,0,32,21,0,33,13,0,34,2,0,37,27,0,38,16,0,39,14,0;DP=137;ECNT=6;ECNTH=5;MBQ=0,33;MFRL=0,266;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=614.56 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,137:0.992:137:0,53:0,59:0,124:0|1:2652_G_A:2652:0,0,122,15 +K03455 2660 . T C . . AS_SB_TABLE=0,0|152,18;BQHIST=15,1,0,16,1,0,17,3,0,20,27,0,29,1,0,32,4,0,33,3,0,34,2,0,35,6,0,37,50,0,38,27,0,39,22,0;DP=170;ECNT=6;ECNTH=5;MBQ=0,37;MFRL=0,269;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=762.96 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,170:0.994:170:0,63:0,68:0,154:0|1:2652_G_A:2652:0,0,152,18 +K03455 2664 . A G . . AS_SB_TABLE=0,0|155,18;BQHIST=18,0,2,19,0,3,20,0,30,30,0,3,32,0,15,33,0,13,34,0,2,35,0,3,36,0,2,37,0,19,38,0,67,39,0,12;DP=173;ECNT=6;ECNTH=5;MBQ=0,37;MFRL=0,267;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=774.91 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,173:0.994:173:0,76:0,76:0,157:0|1:2652_G_A:2652:0,0,155,18 +K03455 2669 . G A . . AS_SB_TABLE=0,0|162,20;BQHIST=16,2,0,18,1,0,19,2,0,20,35,0,29,1,0,32,5,0,33,9,0,34,3,0,36,1,0,37,47,0,38,44,0,39,32,0;DP=185;ECNT=6;ECNTH=5;MBQ=0,37;MFRL=0,271;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=800.27 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,182:0.994:182:0,78:0,82:0,164:0|1:2652_G_A:2652:0,0,162,20 +K03455 2720 . T C . . AS_SB_TABLE=0,0|254,46;BQHIST=14,3,0,16,12,0,17,1,0,18,24,0,20,65,0,30,1,0,32,3,0,33,25,0,34,8,0,36,14,0,37,81,0,38,24,0,39,39,0;DP=348;ECNT=6;ECNTH=5;MBQ=0,36;MFRL=0,259;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=1043.80 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,300:0.996:300:0,106:0,121:0,261:0,0,254,46 +K03455 2797 . G A . . AS_SB_TABLE=0,0|315,161;BQHIST=15,1,0,16,2,0,17,1,0,18,19,0,20,182,0,32,5,0,33,19,0,35,8,0,36,9,0,37,48,0,38,60,0,39,119,0;DP=504;ECNT=9;ECNTH=7;MBQ=0,35;MFRL=0,242;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=1635.75 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,476:0.998:476:0,185:0,168:0,395:0,0,315,161 +K03455 2831 . A T . . AS_SB_TABLE=315,204|0,18;BQHIST=14,0,4,15,0,13,16,1,2,17,3,50,18,11,14,19,0,3,20,0,148,29,0,3,30,1,5,31,0,6,32,0,8,33,2,42,34,0,15,36,0,6,37,0,53,38,0,45,39,0,100;DP=558;ECNT=9;ECNTH=8;MBQ=33,18;MFRL=238,273;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=4.77 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:519,18:0.024:537:182,0:156,0:432,12:315,204,0,18 +K03455 2848 . T TA . . AS_SB_TABLE=14,6|318,254;BQHIST=14,2,0,15,21,2,16,10,0,17,1,0,19,2,0,20,260,9,27,1,0,29,1,0,30,11,2,31,1,0,32,15,0,33,18,3,34,12,0,35,1,0,36,19,1,37,46,1,38,68,0,39,81,2;DP=621;ECNT=9;ECNTH=7;MBQ=20,20;MFRL=270,245;MMQ=60,60;MPOS=32;POPAF=7.30;RPA=6,7;RU=A;STR;TLOD=1153.15 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:20,572:0.982:592:7,179:6,177:14,447:14,6,318,254 +K03455 2872 . T A . . AS_SB_TABLE=267,299|34,0;BQHIST=14,2,1,15,2,0,16,0,12,17,10,5,18,19,51,19,0,35,20,0,173,27,1,1,29,0,16,30,0,1,31,0,7,32,0,24,33,0,31,34,0,12,35,0,10,36,0,10,37,0,79,38,0,43,39,0,54;DP=639;ECNT=9;ECNTH=7;MBQ=29,18;MFRL=240,276;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=9.50 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:566,34:0.031:600:135,1:134,0:468,21:267,299,34,0 +K03455 2874 . C T . . AS_SB_TABLE=0,1|311,300;BQHIST=16,8,0,17,7,0,18,52,0,19,12,0,20,201,0,29,4,0,30,3,0,31,9,0,32,34,0,33,42,0,34,14,0,35,13,0,36,10,0,37,90,1,38,53,0,39,52,0;DP=615;ECNT=9;ECNTH=7;MBQ=37,32;MFRL=235,242;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=2682.59 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:1,611:0.996:612:1,174:0,160:1,505:0|1:2874_C_T:2874:0,1,311,300 +K03455 2882 . G T . . AS_SB_TABLE=4,2|290,266;BQHIST=14,1,0,16,5,1,17,3,2,18,22,0,19,11,0,20,200,0,29,1,1,30,4,0,31,4,1,32,5,0,33,24,0,34,1,0,35,19,0,36,9,0,37,87,0,38,53,0,39,106,0;DP=581;ECNT=9;ECNTH=7;MBQ=17,33;MFRL=276,247;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1871.45 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:6,556:0.994:562:1,167:0,157:4,457:4,2,290,266 +K03455 2894 . T C . . AS_SB_TABLE=0,0|294,271;BQHIST=14,1,0,15,6,0,16,4,0,17,13,0,18,32,0,19,4,0,20,167,0,27,1,0,29,2,0,30,2,0,31,2,0,32,9,0,33,27,0,34,10,0,35,6,0,36,8,0,37,81,0,38,65,0,39,116,0;DP=565;ECNT=9;ECNTH=7;MBQ=0,34;MFRL=0,250;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2595.31 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,565:0.998:565:0,146:0,153:0,476:0|1:2874_C_T:2874:0,0,294,271 +K03455 2906 . C T . . AS_SB_TABLE=0,0|249,259;BQHIST=16,2,0,18,4,0,19,10,0,20,155,0,30,1,0,31,2,0,32,4,0,33,18,0,34,3,0,35,17,0,36,10,0,37,62,0,38,79,0,39,141,0;DP=508;ECNT=9;ECNTH=7;MBQ=0,37;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2422.86 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,508:0.998:508:0,132:0,159:0,440:0|1:2874_C_T:2874:0,0,249,259 +K03455 2913 . G A . . AS_SB_TABLE=0,0|248,257;BQHIST=17,1,0,18,5,0,19,5,0,20,140,0,29,1,0,30,2,0,31,1,0,32,2,0,33,15,0,34,1,0,35,4,0,36,3,0,37,62,0,38,71,0,39,180,0,40,4,0;DP=505;ECNT=9;ECNTH=7;MBQ=0,38;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2413.86 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,505:0.998:505:0,133:0,157:0,438:0|1:2874_C_T:2874:0,0,248,257 +K03455 2987 . C T . . AS_SB_TABLE=0,0|76,130;BQHIST=16,4,0,17,4,0,19,5,0,20,15,0,30,1,0,31,6,0,32,8,0,33,30,0,34,8,0,35,9,0,36,1,0,37,46,0,38,31,0,39,38,0;DP=211;ECNT=5;ECNTH=3;MBQ=0,37;MFRL=0,270;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=782.35 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,206:0.995:206:0,85:0,96:0,199:0,0,76,130 +K03455 3016 . C A . . AS_SB_TABLE=57,28|6,0;BQHIST=14,0,2,15,0,1,18,5,24,20,0,5,29,0,1,30,0,2,32,0,4,33,1,10,34,0,2,35,0,2,36,0,8,37,0,5,38,0,15,39,0,4;DP=95;ECNT=5;ECNTH=3;MBQ=33,18;MFRL=278,272;MMQ=60,60;MPOS=6;POPAF=7.30;TLOD=4.56 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:85,6:0.073:91:23,1:31,0:83,6:57,28,6,0 +K03455 3020 . A G . . AS_SB_TABLE=0,0|59,26;BQHIST=14,0,12,16,0,1,18,0,1,20,0,4,27,0,2,29,0,1,30,0,7,32,0,8,33,0,2,34,0,1,36,0,19,37,0,4,38,0,22,39,0,1;DP=91;ECNT=5;ECNTH=3;MBQ=0,36;MFRL=0,289;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=292.32 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,85:0.988:85:0,30:0,37:0,83:0,0,59,26 +K03455 3036 . A G . . AS_SB_TABLE=16,3|3,0;BQHIST=15,1,0,19,7,2,29,1,0,30,1,0,33,3,0,37,4,1,38,2,0;DP=36;ECNT=5;ECNTH=4;MBQ=30,19;MFRL=289,298;MMQ=60,60;MPOS=0;POPAF=7.30;TLOD=4.59 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,3:0.160:22:7,1:3,0:19,3:0|1:3036_A_G:3036:16,3,3,0 +K03455 3038 . C G . . AS_SB_TABLE=16,3|3,0;BQHIST=14,0,1,19,5,0,30,1,0,32,1,0,33,1,0,35,1,0,37,1,0,38,2,0,39,3,0;DP=22;ECNT=5;ECNTH=4;MBQ=33,14;MFRL=289,298;MMQ=60,60;MPOS=8;POPAF=7.30;TLOD=4.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:19,3:0.166:22:5,0:4,0:19,3:0|1:3036_A_G:3036:16,3,3,0
--- a/test-data/Mutect2-out4.vcf Wed Aug 24 17:58:18 2022 +0000 +++ b/test-data/Mutect2-out4.vcf Tue Feb 03 18:50:29 2026 +0000 @@ -4,6 +4,7 @@ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=FAD,Number=R,Type=Integer,Description="Count of fragments supporting each allele."> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles"> @@ -11,18 +12,19 @@ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> -##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input tumor.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.7.0",Date="May 8, 2020 3:32:53 PM CEST"> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input tumor.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --trim-to-haplotype true --exact-matching false --flow-use-t0-tag false --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --keep-boundary-flows false --genotype-pon-sites false --genotype-germline-sites false --genotype-germline-sites-fraction 1.0 --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --permutect-ref-downsample 10 --permutect-alt-downsample 20 --permutect-non-artifact-ratio 1 --permutect-dataset-mode ILLUMINA --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --base-qual-correction-factor 5 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --flow-mode NONE --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --use-pdhmm false --use-pdhmm-overlap-optimization false --make-determined-haps-from-pd-code false --print-pileupcalling-status false --fallback-gga-if-pdhmm-fails true --pileup-detection-enable-indel-pileup-calling false --pileup-detection-active-region-phred-threshold 0.0 --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.1 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-snp-basequality-filter 12 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --pileup-detection-filter-assembly-alt-bad-read-tolerance 0.0 --pileup-detection-edit-distance-read-badness-for-assembly-filtering-threshold 0.12 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.6.2.0",Date="February 2, 2026, 12:29:59?AM GMT"> ##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |."> ##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site"> ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of potential somatic events in the assembly region"> +##INFO=<ID=ECNTH,Number=A,Type=Integer,Description="Number of somatic events in best supporting haplotype for each alt allele"> ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> -##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> -##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> -##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality by allele"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length by allele"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality by allele"> ##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> -##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Log 10 odds of artifact in normal with same allele fraction as tumor"> ##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> @@ -42,43 +44,42 @@ ##source=Mutect2 ##tumor_sample=SRR8525881 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 -K03455 6822 . GT AC . . AS_SB_TABLE=0,0|2,2;DP=4;ECNT=1;MBQ=0,38;MFRL=0,117;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=7.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,4:0.750:4:0,0:0,4:0,0,2,2 -K03455 6902 . A C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6905 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6911 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6917 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6920 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6923 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6931 . C A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 6936 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 -K03455 7141 . GAATCC G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,0;MFRL=0,310;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 -K03455 7149 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,15;MFRL=0,310;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 -K03455 7151 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,38;MFRL=0,310;MMQ=60,60;MPOS=9;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 -K03455 7154 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,24;MFRL=0,310;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 -K03455 7156 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,25;MFRL=0,310;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0|1:7141_GAATCC_G:7141:0,0,0,1 -K03455 7163 . A C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=14;MBQ=0,13;MFRL=0,310;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,0:0,0,0,1 -K03455 7372 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;MBQ=0,34;MFRL=0,451;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=3.58 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7372_T_C:7372:0,0,0,1 -K03455 7392 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;MBQ=0,32;MFRL=0,451;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7372_T_C:7372:0,0,0,1 -K03455 7441 . A ACCT . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=77;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7443 . A AGTG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=82;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7449 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=91;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7452 . GGA G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=94;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7455 . A ATG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=95;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7457 . TGA T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=99;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7460 . CA C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 -K03455 7468 . CC TA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=107;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 -K03455 7478 . C T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=117;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 -K03455 7491 . A T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=118;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 -K03455 7494 . A G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=115;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 -K03455 7508 . GA AG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 -K03455 7541 . C CGA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=68;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7542 . AGT A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=65;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7548 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=61;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7555 . GA AT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7560 . TC GT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=49;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7568 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=41;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7571 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=38;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7581 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=28;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7584 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=25;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7603 . A AGGG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=6;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 -K03455 7604 . T G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=2;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 6822 . GT AC . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;ECNTH=1;MBQ=0,20;MFRL=0,117;MMQ=60,60;MPOS=79;POPAF=7.30;TLOD=8.52 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,2:0.750:2:0,0:0,2:0,2:0,0,0,2 +K03455 6902 . A C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6905 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6911 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6917 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6920 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6923 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6931 . C A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6936 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=13;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 7141 . GAATCC G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=5;MBQ=0,0;MFRL=0,310;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0,1:0|1:7141_GAATCC_G:7141:0,0,0,1 +K03455 7149 . A G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=5;MBQ=0,15;MFRL=0,310;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,0:0,1:0|1:7141_GAATCC_G:7141:0,0,0,1 +K03455 7151 . C G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=5;MBQ=0,38;MFRL=0,310;MMQ=60,60;MPOS=9;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0,1:0|1:7141_GAATCC_G:7141:0,0,0,1 +K03455 7154 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=5;MBQ=0,24;MFRL=0,310;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0,1:0|1:7141_GAATCC_G:7141:0,0,0,1 +K03455 7156 . G T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=13;ECNTH=5;MBQ=0,25;MFRL=0,310;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,1:0,0:0,1:0|1:7141_GAATCC_G:7141:0,0,0,1 +K03455 7372 . T C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;ECNTH=2;MBQ=0,34;MFRL=0,451;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=3.58 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7372_T_C:7372:0,0,0,1 +K03455 7392 . C T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;ECNTH=2;MBQ=0,32;MFRL=0,451;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7372_T_C:7372:0,0,0,1 +K03455 7441 . A ACCT . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=77;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7443 . A AGTG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=82;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7449 . G A . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=91;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7452 . GGA G . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=94;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7455 . A ATG . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=95;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7457 . TGA T . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=99;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7460 . CA C . . AS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;ECNTH=12;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7468 . CC TA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=107;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7478 . C T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=117;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7491 . A T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=118;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7494 . A G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=115;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7508 . GA AG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=12;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7541 . C CGA . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=68;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7542 . AGT A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=65;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7548 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=61;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7555 . GA AT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7560 . TC GT . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=49;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7568 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=41;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7571 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=38;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7581 . C A . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=28;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7584 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=25;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7603 . A AGGG . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=6;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7604 . T G . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;ECNTH=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=2;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0,1:0|1:7541_C_CGA:7541:0,0,0,2
--- a/test-data/Mutect2-out5-1.tabular Wed Aug 24 17:58:18 2022 +0000 +++ b/test-data/Mutect2-out5-1.tabular Tue Feb 03 18:50:29 2026 +0000 @@ -15,9 +15,9 @@ K03455 1800 1801 end-marker 0.00000 K03455 1800 2057 size=257 -1.00000 K03455 2057 2058 end-marker 0.00000 -K03455 2057 2342 size=285 1.00000 -K03455 2342 2343 end-marker 0.00000 -K03455 2342 2481 size=139 1.00000 +K03455 2057 2346 size=289 1.00000 +K03455 2346 2347 end-marker 0.00000 +K03455 2346 2481 size=135 1.00000 K03455 2481 2482 end-marker 0.00000 K03455 2481 2781 size=300 -1.00000 K03455 2781 2782 end-marker 0.00000
--- a/test-data/Mutect2-out5.vcf Wed Aug 24 17:58:18 2022 +0000 +++ b/test-data/Mutect2-out5.vcf Tue Feb 03 18:50:29 2026 +0000 @@ -4,6 +4,7 @@ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=FAD,Number=R,Type=Integer,Description="Count of fragments supporting each allele."> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles"> @@ -11,18 +12,19 @@ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> -##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --bam-output debug.bam --output output.vcf --assembly-region-out assembly-region.tab --input tumor.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.7.0",Date="May 8, 2020 3:33:33 PM CEST"> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --bam-output debug.bam --output output.vcf --assembly-region-out assembly-region.tab --input tumor.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --trim-to-haplotype true --exact-matching false --flow-use-t0-tag false --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --keep-boundary-flows false --genotype-pon-sites false --genotype-germline-sites false --genotype-germline-sites-fraction 1.0 --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --permutect-ref-downsample 10 --permutect-alt-downsample 20 --permutect-non-artifact-ratio 1 --permutect-dataset-mode ILLUMINA --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --base-qual-correction-factor 5 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --flow-mode NONE --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --use-pdhmm false --use-pdhmm-overlap-optimization false --make-determined-haps-from-pd-code false --print-pileupcalling-status false --fallback-gga-if-pdhmm-fails true --pileup-detection-enable-indel-pileup-calling false --pileup-detection-active-region-phred-threshold 0.0 --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.1 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-snp-basequality-filter 12 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --pileup-detection-filter-assembly-alt-bad-read-tolerance 0.0 --pileup-detection-edit-distance-read-badness-for-assembly-filtering-threshold 0.12 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.6.2.0",Date="February 2, 2026, 12:30:15?AM GMT"> ##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |."> ##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site"> ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of potential somatic events in the assembly region"> +##INFO=<ID=ECNTH,Number=A,Type=Integer,Description="Number of somatic events in best supporting haplotype for each alt allele"> ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> -##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> -##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> -##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality by allele"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length by allele"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality by allele"> ##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> -##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Log 10 odds of artifact in normal with same allele fraction as tumor"> ##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> @@ -42,53 +44,54 @@ ##source=Mutect2 ##tumor_sample=SRR8525881 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 -K03455 2097 . G A . . AS_SB_TABLE=0,0|10,5;DP=15;ECNT=41;MBQ=0,20;MFRL=0,159;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=79.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,15:0.929:15:0,7:0,6:0,0,10,5 -K03455 2106 . T C . . AS_SB_TABLE=9,4|2,2;DP=17;ECNT=41;MBQ=20,30;MFRL=159,90;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=12.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,4:0.266:17:6,1:7,1:9,4,2,2 -K03455 2110 . TA CA,CT . . AS_SB_TABLE=0,0|9,5|3,1;DP=18;ECNT=41;MBQ=0,20,35;MFRL=0,159,161;MMQ=60,60,60;MPOS=44,2;POPAF=7.30,7.30;TLOD=60.04,10.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:0,14,4:0.754,0.187:18:0,6,1:0,8,3:0,0,12,6 -K03455 2118 . A G . . AS_SB_TABLE=3,2|8,3;DP=18;ECNT=41;MBQ=32,20;MFRL=90,160;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=35.11 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,11:0.715:16:1,4:4,6:3,2,8,3 -K03455 2130 . T C . . AS_SB_TABLE=9,5|3,1;DP=18;ECNT=41;MBQ=20,37;MFRL=159,161;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=10.45 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:14,4:0.199:18:4,1:9,3:9,5,3,1 -K03455 2136 . T C . . AS_SB_TABLE=9,5|3,1;DP=18;ECNT=41;MBQ=20,38;MFRL=159,161;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=10.45 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:14,4:0.199:18:4,1:10,2:9,5,3,1 -K03455 2155 . A T . . AS_SB_TABLE=3,2|11,4;DP=20;ECNT=41;MBQ=39,20;MFRL=90,233;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=41.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,15:0.777:20:1,5:4,7:3,2,11,4 -K03455 2169 . A G . . AS_SB_TABLE=0,0|17,6;DP=23;ECNT=41;MBQ=0,34;MFRL=0,232;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=105.32 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,23:0.955:23:0,9:0,13:0,0,17,6 -K03455 2183 . C T . . AS_SB_TABLE=0,0|19,9;DP=28;ECNT=41;MBQ=0,33;MFRL=0,233;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=133.75 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,28:0.962:28:0,9:0,14:0,0,19,9 -K03455 2189 . TA AA,AG . . AS_SB_TABLE=0,0|9,5|10,4;DP=30;ECNT=41;MBQ=0,35,20;MFRL=0,207,265;MMQ=60,60,60;MPOS=21,22;POPAF=7.30,7.30;TLOD=51.22,55.00 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:0,14,14:0.424,0.539:28:0,6,5:0,7,5:0,0,19,9 -K03455 2195 . C G,T . . AS_SB_TABLE=5,4|10,4|5,2;DP=30;ECNT=41;MBQ=37,30,33;MFRL=232,265,241;MMQ=60,60,60;MPOS=19,19;POPAF=7.30,7.30;TLOD=41.44,19.27 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:9,14,7:0.500,0.250:30:3,8,3:5,6,4:5,4,15,6 -K03455 2197 . A G . . AS_SB_TABLE=15,6|5,4;DP=30;ECNT=41;MBQ=31,37;MFRL=248,232;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=29.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:21,9:0.259:30:9,3:8,5:15,6,5,4 -K03455 2200 . ACTC A . . AS_SB_TABLE=16,8|3,2;DP=31;ECNT=41;MBQ=24,36;MFRL=265,232;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=13.22 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:24,5:0.153:29:10,3:7,2:0|1:2200_ACTC_A:2200:16,8,3,2 -K03455 2202 . T C . . AS_SB_TABLE=15,7|2,2;DP=31;ECNT=41;MBQ=34,35;MFRL=257,182;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=5.58 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:22,4:0.166:26:9,1:7,1:0|1:2202_T_C:2202:15,7,2,2 -K03455 2205 . C A . . AS_SB_TABLE=20,9|1,1;DP=31;ECNT=41;MBQ=34,26;MFRL=248,286;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=5.06 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:29,2:0.107:31:13,1:11,0:0|1:2202_T_C:2202:20,9,1,1 -K03455 2213 . A G . . AS_SB_TABLE=4,3|17,7;DP=31;ECNT=41;MBQ=38,37;MFRL=232,265;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=107.32 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:7,24:0.793:31:4,11:2,8:4,3,17,7 -K03455 2214 . G A . . AS_SB_TABLE=17,9|1,1;DP=28;ECNT=41;MBQ=33,26;MFRL=254,286;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=5.06 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:26,2:0.107:28:12,1:10,0:0|1:2214_G_A:2214:17,9,1,1 -K03455 2221 . C A . . AS_SB_TABLE=22,8|3,2;DP=35;ECNT=41;MBQ=34,35;MFRL=251,232;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=12.67 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:30,5:0.114:35:16,1:11,2:0|1:2200_ACTC_A:2200:22,8,3,2 -K03455 2223 . G A . . AS_SB_TABLE=16,3|7,7;DP=34;ECNT=41;MBQ=37,34;MFRL=253,211;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=47.83 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:19,14:0.461:33:12,7:7,6:16,3,7,7 -K03455 2224 . AT GG,CT . . AS_SB_TABLE=11,8|2,2|10,0;DP=33;ECNT=41;MBQ=34,29,38;MFRL=265,207,253;MMQ=60,60,60;MPOS=36,18;POPAF=7.30,7.30;TLOD=9.64,33.76 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:19,4,10:0.091,0.333:33:9,2,7:8,2,3:11,8,12,2 -K03455 2225 . T G . . AS_SB_TABLE=20,7|1,1;DP=33;ECNT=41;MBQ=37,38;MFRL=253,286;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=5.14 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:27,2:0.099:29:16,1:11,1:0|1:2214_G_A:2214:20,7,1,1 -K03455 2226 . A G . . AS_SB_TABLE=3,3|20,7;DP=33;ECNT=41;MBQ=20,37;MFRL=232,253;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=115.36 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,27:0.844:33:3,16:2,9:0|1:2226_A_G:2226:3,3,20,7 -K03455 2230 . A C . . AS_SB_TABLE=3,3|21,7;DP=34;ECNT=41;MBQ=28,37;MFRL=232,253;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=119.79 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,28:0.848:34:2,15:3,11:0|1:2226_A_G:2226:3,3,21,7 -K03455 2234 . A G . . AS_SB_TABLE=3,3|24,10;DP=40;ECNT=41;MBQ=20,37;MFRL=232,245;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=146.51 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,34:0.865:40:1,20:2,11:0|1:2226_A_G:2226:3,3,24,10 -K03455 2235 . AC GA . . AS_SB_TABLE=25,11|2,2;DP=40;ECNT=41;MBQ=35,33;MFRL=247,207;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=9.17 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:36,4:0.081:40:22,1:10,2:0|1:2200_ACTC_A:2200:25,11,2,2 -K03455 2236 . CTG C,GTG . . AS_SB_TABLE=12,2|12,8|1,1;DP=40;ECNT=41;MBQ=38,35,38;MFRL=251,240,286;MMQ=60,60,60;MPOS=16,46;POPAF=7.30,7.30;TLOD=62.15,5.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:14,20,2:0.528,0.083:36:8,12,1:5,8,1:12,2,13,9 -K03455 2239 . TA CC . . AS_SB_TABLE=16,11|12,2;DP=43;ECNT=41;MBQ=36,38;MFRL=232,251;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=49.19 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:27,14:0.368:41:14,9:10,4:16,11,12,2 -K03455 2240 . A ACC . . AS_SB_TABLE=4,3|14,10;DP=43;ECNT=41;MBQ=37,34;MFRL=232,211;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=61.81 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:7,24:0.785:31:3,13:3,9:4,3,14,10 -K03455 2248 . A G . . AS_SB_TABLE=3,2|27,12;DP=44;ECNT=41;MBQ=20,38;MFRL=182,245;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=182.06 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:5,39:0.902:44:2,21:3,15:1|0:2200_ACTC_A:2200:3,2,27,12 -K03455 2250 . T C . . AS_SB_TABLE=27,12|3,2;DP=44;ECNT=41;MBQ=38,37;MFRL=245,182;MMQ=60,60;MPOS=60;POPAF=7.30;TLOD=12.44 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:39,5:0.098:44:23,2:16,3:0|1:2200_ACTC_A:2200:27,12,3,2 -K03455 2258 . GG AA . . AS_SB_TABLE=6,0|26,14;DP=46;ECNT=41;MBQ=39,39;MFRL=216,239;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=159.02 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,40:0.859:46:3,22:3,17:0|1:2258_GG_AA:2258:6,0,26,14 -K03455 2259 . G A . . AS_SB_TABLE=0,0|10,3;DP=46;ECNT=41;MBQ=0,37;MFRL=0,241;MMQ=60,60;MPOS=39;POPAF=7.30;TLOD=13.48 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:0,13:0.961:13:0,5:0,8:1|0:2258_GG_AA:2258:0,0,10,3 -K03455 2282 . C T . . AS_SB_TABLE=32,24|2,2;DP=60;ECNT=41;MBQ=36,20;MFRL=239,182;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=9.01 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:56,4:0.059:60:24,1:24,2:32,24,2,2 -K03455 2285 . C T . . AS_SB_TABLE=30,23|6,3;DP=62;ECNT=41;MBQ=29,38;MFRL=236,205;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=26.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:53,9:0.151:62:24,3:21,4:30,23,6,3 -K03455 2287 . CA AT . . AS_SB_TABLE=32,26|4,3;DP=65;ECNT=41;MBQ=33,37;MFRL=234,285;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=17.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:58,7:0.133:65:25,1:24,2:32,26,4,3 -K03455 2300 . G A . . AS_SB_TABLE=6,6|26,23;DP=63;ECNT=41;MBQ=31,32;MFRL=229,236;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=211.84 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,49:0.796:61:3,20:5,22:6,6,26,23 -K03455 2303 . GCA G . . AS_SB_TABLE=7,8|25,20;DP=61;ECNT=41;MBQ=36,31;MFRL=225,241;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=171.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:15,45:0.735:60:2,18:9,20:7,8,25,20 -K03455 2304 . CAA GTG . . AS_SB_TABLE=6,6|10,9;DP=61;ECNT=41;MBQ=33,20;MFRL=229,235;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=3.47 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,19:0.531:31:4,0:7,3:6,6,10,9 -K03455 2306 . A ATG,G . . AS_SB_TABLE=2,2|26,22|4,4;DP=60;ECNT=41;MBQ=29,32,33;MFRL=182,239,280;MMQ=60,60,60;MPOS=39,19;POPAF=7.30,7.30;TLOD=175.97,22.08 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:4,48,8:0.779,0.164:60:2,20,2:2,23,4:2,2,30,26 -K03455 2315 . A G . . AS_SB_TABLE=19,19|11,9;DP=59;ECNT=41;MBQ=37,38;MFRL=229,244;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=74.64 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:38,20:0.379:58:17,6:15,14:0|1:2315_A_G:2315:19,19,11,9 -K03455 2321 . A C . . AS_SB_TABLE=17,19|11,9;DP=56;ECNT=41;MBQ=34,37;MFRL=229,244;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=75.24 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:36,20:0.392:56:16,6:17,14:0|1:2315_A_G:2315:17,19,11,9 -K03455 2349 . T C . . AS_SB_TABLE=23,24|4,5;DP=56;ECNT=9;MBQ=35,35;MFRL=235,285;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=28.30 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:47,9:0.190:56:19,3:22,5:23,24,4,5 -K03455 2360 . G A . . AS_SB_TABLE=19,20|4,6;DP=49;ECNT=9;MBQ=37,27;MFRL=235,272;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=28.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:39,10:0.229:49:15,3:22,3:19,20,4,6 -K03455 2362 . G A . . AS_SB_TABLE=0,0|21,26;DP=49;ECNT=9;MBQ=0,36;MFRL=0,241;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=181.58 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,47:0.978:47:0,19:0,25:0,0,21,26 -K03455 2372 . A G . . AS_SB_TABLE=16,19|4,5;DP=44;ECNT=9;MBQ=37,36;MFRL=241,259;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=30.36 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:35,9:0.234:44:9,3:17,5:16,19,4,5 -K03455 2374 . G A . . AS_SB_TABLE=12,22|2,2;DP=38;ECNT=9;MBQ=37,35;MFRL=234,284;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=7.75 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,4:0.118:38:8,1:20,2:12,22,2,2 -K03455 2423 . A G . . AS_SB_TABLE=0,13|0,3;DP=16;ECNT=9;MBQ=34,33;MFRL=255,199;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=8.83 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,3:0.226:16:3,0:9,3:0,13,0,3 -K03455 2436 . A G . . AS_SB_TABLE=0,1|0,4;DP=6;ECNT=9;MBQ=16,31;MFRL=255,240;MMQ=60,60;MPOS=4;POPAF=7.30;TLOD=16.53 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,4:0.725:5:0,0:0,4:0,1,0,4 -K03455 2438 . A G . . AS_SB_TABLE=0,3|0,2;DP=6;ECNT=9;MBQ=29,33;MFRL=255,255;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=7.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:3,2:0.430:5:0,0:2,2:0|1:2438_A_G:2438:0,3,0,2 -K03455 2440 . T C . . AS_SB_TABLE=0,3|0,2;DP=6;ECNT=9;MBQ=0,31;MFRL=255,255;MMQ=60,60;MPOS=1;POPAF=7.30;TLOD=7.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:3,2:0.430:5:0,0:0,2:0|1:2438_A_G:2438:0,3,0,2 +K03455 2097 . G A . . AS_SB_TABLE=0,0|10,4;DP=14;ECNT=48;ECNTH=22;MBQ=0,20;MFRL=0,160;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=75.42 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,14:0.923:14:0,6:0,3:0,11:0,0,10,4 +K03455 2106 . T C . . AS_SB_TABLE=9,4|2,0;DP=15;ECNT=48;ECNTH=22;MBQ=20,39;MFRL=159,186;MMQ=60,60;MPOS=39;POPAF=7.30;TLOD=10.57 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:13,2:0.214:15:5,1:5,0:10,2:9,4,2,0 +K03455 2110 . TA CA,CT . . AS_SB_TABLE=0,0|9,4|3,1;DP=17;ECNT=48;ECNTH=22,18;MBQ=0,20,32;MFRL=0,159,161;MMQ=60,60,60;MPOS=46,2;POPAF=7.30,7.30;TLOD=55.66,10.78 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:0,13,4:0.738,0.200:17:0,5,1:0,5,1:0,10,2:0,0,12,5 +K03455 2118 . A G . . AS_SB_TABLE=3,1|9,4;DP=17;ECNT=48;ECNTH=16;MBQ=26,20;MFRL=161,159;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=51.30 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:4,13:0.787:17:1,4:1,4:2,10:3,1,9,4 +K03455 2130 . T C . . AS_SB_TABLE=9,4|3,1;DP=17;ECNT=48;ECNTH=18;MBQ=20,29;MFRL=159,161;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=10.55 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:13,4:0.213:17:4,1:6,1:10,2:9,4,3,1 +K03455 2136 . T C . . AS_SB_TABLE=9,4|3,1;DP=17;ECNT=48;ECNTH=18;MBQ=20,30;MFRL=159,161;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=10.55 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:13,4:0.213:17:4,1:6,1:10,2:9,4,3,1 +K03455 2155 . A T . . AS_SB_TABLE=3,1|11,4;DP=19;ECNT=48;ECNTH=22;MBQ=30,20;MFRL=161,233;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=56.42 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:4,15:0.823:19:1,5:1,5:2,13:3,1,11,4 +K03455 2169 . A G . . AS_SB_TABLE=0,0|17,5;DP=22;ECNT=48;ECNTH=22;MBQ=0,33;MFRL=0,233;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=101.65 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,22:0.952:22:0,9:0,9:0,19:0,0,17,5 +K03455 2183 . C T . . AS_SB_TABLE=0,0|19,9;DP=28;ECNT=48;ECNTH=22;MBQ=0,20;MFRL=0,233;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=142.60 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,28:0.962:28:0,10:0,11:0,24:0,0,19,9 +K03455 2189 . TA AA,AG . . AS_SB_TABLE=0,0|9,5|10,5;DP=31;ECNT=48;ECNTH=17,22;MBQ=0,35,20;MFRL=0,207,265;MMQ=60,60,60;MPOS=21,22;POPAF=7.30,7.30;TLOD=46.96,59.29 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:0,14,15:0.408,0.556:29:0,5,6:0,4,5:0,10,14:0,0,19,10 +K03455 2195 . C G,T . . AS_SB_TABLE=5,5|11,4|4,2;DP=31;ECNT=48;ECNTH=22,18;MBQ=33,30,38;MFRL=207,265,204;MMQ=60,60,60;MPOS=18,23;POPAF=7.30,7.30;TLOD=55.86,17.17 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:10,15,6:0.514,0.210:31:3,8,2:3,6,3:7,14,5:5,5,15,6 +K03455 2197 . A G . . AS_SB_TABLE=15,7|5,4;DP=31;ECNT=48;ECNTH=17;MBQ=31,37;MFRL=245,232;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=29.21 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:22,9:0.250:31:10,3:7,3:20,6:15,7,5,4 +K03455 2200 . ACTC A . . AS_SB_TABLE=16,9|3,3;DP=31;ECNT=48;ECNTH=17;MBQ=22,35;MFRL=265,207;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=17.33 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:25,6:0.179:31:10,2:6,1:22,4:0|1:2200_ACTC_A:2200:16,9,3,3 +K03455 2202 . T C . . AS_SB_TABLE=15,9|1,1;DP=31;ECNT=48;ECNTH=15;MBQ=27,35;MFRL=245,286;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=5.33 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:24,2:0.118:26:9,1:6,1:21,2:0|1:2202_T_C:2202:15,9,1,1 +K03455 2205 . C A . . AS_SB_TABLE=20,11|1,1;DP=33;ECNT=48;ECNTH=15;MBQ=20,26;MFRL=241,286;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=4.96 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:31,2:0.100:33:12,1:8,0:26,2:0|1:2202_T_C:2202:20,11,1,1 +K03455 2213 . A G . . AS_SB_TABLE=4,4|17,7;DP=32;ECNT=48;ECNTH=22;MBQ=20,37;MFRL=232,265;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=107.92 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:8,24:0.767:32:4,10:1,7:6,22:0|1:2213_A_G:2213:4,4,17,7 +K03455 2214 . G A . . AS_SB_TABLE=17,10|1,1;DP=29;ECNT=48;ECNTH=19;MBQ=32,26;MFRL=248,286;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=5.01 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:27,2:0.103:29:11,1:8,0:25,2:17,10,1,1 +K03455 2221 . C A . . AS_SB_TABLE=22,8|3,2;DP=35;ECNT=48;ECNTH=17;MBQ=34,20;MFRL=251,232;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=12.95 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:30,5:0.111:35:16,1:9,1:31,3:0|1:2200_ACTC_A:2200:22,8,3,2 +K03455 2223 . G A . . AS_SB_TABLE=17,4|6,6;DP=34;ECNT=48;ECNTH=22;MBQ=34,33;MFRL=248,250;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=43.41 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:21,12:0.400:33:13,5:6,4:19,12:0|1:2223_G_A:2223:17,4,6,6 +K03455 2224 . AT GG,CT . . AS_SB_TABLE=11,8|2,2|10,0;DP=33;ECNT=48;ECNTH=17,19;MBQ=34,20,38;MFRL=265,207,253;MMQ=60,60,60;MPOS=36,18;POPAF=7.30,7.30;TLOD=9.60,31.07 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:19,4,10:0.088,0.324:33:10,1,7:5,1,3:19,2,10:11,8,12,2 +K03455 2225 . T G . . AS_SB_TABLE=20,7|1,1;DP=33;ECNT=48;ECNTH=15;MBQ=37,38;MFRL=253,286;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=5.35 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:27,2:0.096:29:16,1:8,1:27,2:0|1:2202_T_C:2202:20,7,1,1 +K03455 2226 . A G . . AS_SB_TABLE=3,4|20,6;DP=33;ECNT=48;ECNTH=22;MBQ=20,37;MFRL=232,253;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=123.69 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:7,26:0.818:33:3,15:1,7:5,26:0|1:2213_A_G:2213:3,4,20,6 +K03455 2230 . A C . . AS_SB_TABLE=3,4|21,6;DP=34;ECNT=48;ECNTH=22;MBQ=20,37;MFRL=232,253;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=128.16 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:7,27:0.824:34:3,15:2,8:5,27:0|1:2213_A_G:2213:3,4,21,6 +K03455 2234 . A G . . AS_SB_TABLE=3,4|24,7;DP=38;ECNT=48;ECNTH=22;MBQ=20,37;MFRL=232,248;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=145.81 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:7,31:0.842:38:2,18:1,9:5,31:0|1:2213_A_G:2213:3,4,24,7 +K03455 2235 . AC GA . . AS_SB_TABLE=25,9|2,2;DP=38;ECNT=48;ECNTH=17;MBQ=34,20;MFRL=251,207;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=9.13 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:34,4:0.079:38:20,1:8,1:34,2:0|1:2200_ACTC_A:2200:25,9,2,2 +K03455 2236 . CTG C,GTG . . AS_SB_TABLE=14,1|10,6|1,1;DP=38;ECNT=48;ECNTH=22,15;MBQ=38,34,38;MFRL=253,240,286;MMQ=60,60,60;MPOS=25,46;POPAF=7.30,7.30;TLOD=57.94,5.24 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:15,16,2:0.481,0.083:33:9,8,1:5,5,1:15,16,2:14,1,11,7 +K03455 2239 . TA CC . . AS_SB_TABLE=14,10|14,1;DP=44;ECNT=48;ECNTH=18;MBQ=32,38;MFRL=232,253;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=48.64 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:24,15:0.400:39:11,10:6,4:22,15:14,10,14,1 +K03455 2240 . A ACC . . AS_SB_TABLE=4,5|14,7;DP=44;ECNT=48;ECNTH=22;MBQ=20,34;MFRL=182,235;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=57.61 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:9,21:0.736:30:3,10:3,6:7,20:0|1:2223_G_A:2223:4,5,14,7 +K03455 2248 . A G . . AS_SB_TABLE=3,2|27,13;DP=45;ECNT=48;ECNTH=22;MBQ=20,37;MFRL=182,245;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=186.70 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:5,40:0.905:45:1,19:2,12:3,37:3,2,27,13 +K03455 2250 . T C . . AS_SB_TABLE=27,13|3,2;DP=45;ECNT=48;ECNTH=17;MBQ=37,20;MFRL=245,182;MMQ=60,60;MPOS=60;POPAF=7.30;TLOD=12.39 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:40,5:0.095:45:21,1:13,2:37,3:0|1:2200_ACTC_A:2200:27,13,3,2 +K03455 2258 . GG AA . . AS_SB_TABLE=6,1|25,14;DP=46;ECNT=48;ECNTH=22;MBQ=34,38;MFRL=191,243;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=153.60 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:7,39:0.851:46:3,19:3,12:6,35:0|1:2258_GG_AA:2258:6,1,25,14 +K03455 2259 . G A . . AS_SB_TABLE=0,0|8,5;DP=46;ECNT=48;ECNTH=19;MBQ=0,33;MFRL=0,187;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=14.22 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 1|0:0,13:0.963:13:0,8:0,8:0,19:1|0:2258_GG_AA:2258:0,0,8,5 +K03455 2273 . A G . . AS_SB_TABLE=33,13|0,2;DP=48;ECNT=48;ECNTH=19;MBQ=36,27;MFRL=234,225;MMQ=60,60;MPOS=61;POPAF=7.30;TLOD=3.75 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:46,2:0.065:48:22,1:15,1:42,2:33,13,0,2 +K03455 2282 . C T . . AS_SB_TABLE=31,24|2,2;DP=60;ECNT=48;ECNTH=16;MBQ=20,20;MFRL=241,182;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=9.01 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:55,4:0.060:59:19,0:18,1:46,2:31,24,2,2 +K03455 2285 . C T . . AS_SB_TABLE=30,24|3,3;DP=60;ECNT=48;ECNTH=16;MBQ=20,28;MFRL=236,207;MMQ=60,60;MPOS=52;POPAF=7.30;TLOD=15.47 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:54,6:0.098:60:20,2:17,2:45,4:30,24,3,3 +K03455 2287 . CA AT . . AS_SB_TABLE=32,27|1,1;DP=61;ECNT=48;ECNTH=18;MBQ=20,38;MFRL=232,286;MMQ=60,60;MPOS=52;POPAF=7.30;TLOD=4.18 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:59,2:0.057:61:22,1:17,1:49,2:32,27,1,1 +K03455 2300 . G A . . AS_SB_TABLE=3,4|26,24;DP=57;ECNT=48;ECNTH=22;MBQ=36,34;MFRL=182,236;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=226.05 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:7,50:0.880:57:3,15:1,16:5,43:3,4,26,24 +K03455 2303 . GCA G . . AS_SB_TABLE=4,6|25,20;DP=56;ECNT=48;ECNTH=22;MBQ=28,31;MFRL=204,241;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=181.84 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:10,45:0.812:55:1,15:4,15:8,38:4,6,25,20 +K03455 2304 . CAA GTG . . AS_SB_TABLE=3,4|9,9;DP=56;ECNT=48;ECNTH=18;MBQ=35,31;MFRL=182,232;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.64 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:7,18:0.643:25:3,0:2,3:6,16:3,4,9,9 +K03455 2306 . A ATG,G . . AS_SB_TABLE=2,3|26,22|1,1;DP=55;ECNT=48;ECNTH=22,15;MBQ=20,34,36;MFRL=182,239,286;MMQ=60,60,60;MPOS=39,33;POPAF=7.30,7.30;TLOD=184.31,4.73 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1/2:5,48,2:0.857,0.061:55:2,16,1:1,17,1:3,41,2:2,3,27,23 +K03455 2315 . A G . . AS_SB_TABLE=16,17|11,9;DP=54;ECNT=48;ECNTH=22;MBQ=33,38;MFRL=202,244;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=75.73 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:33,20:0.418:53:12,5:9,10:27,19:0|1:2315_A_G:2315:16,17,11,9 +K03455 2321 . A C . . AS_SB_TABLE=14,17|11,9;DP=51;ECNT=48;ECNTH=22;MBQ=33,37;MFRL=202,244;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=76.39 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:31,20:0.435:51:10,5:9,10:25,19:0|1:2315_A_G:2315:14,17,11,9 +K03455 2349 . T C . . AS_SB_TABLE=16,23|4,5;DP=49;ECNT=9;ECNTH=6;MBQ=35,35;MFRL=235,259;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=26.85 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:39,9:0.211:48:13,3:18,5:36,9:0|1:2349_T_C:2349:16,23,4,5 +K03455 2360 . G A . . AS_SB_TABLE=15,20|3,5;DP=43;ECNT=9;ECNTH=6;MBQ=35,36;MFRL=235,246;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=23.78 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:35,8:0.213:43:11,3:17,3:32,8:0|1:2349_T_C:2349:15,20,3,5 +K03455 2362 . G A . . AS_SB_TABLE=0,0|16,25;DP=43;ECNT=9;ECNTH=3;MBQ=0,36;MFRL=0,235;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=152.64 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,41:0.976:41:0,13:0,21:0,38:0,0,16,25 +K03455 2372 . A G . . AS_SB_TABLE=12,18|4,5;DP=39;ECNT=9;ECNTH=6;MBQ=37,36;MFRL=227,232;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=28.25 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:30,9:0.263:39:3,3:16,5:27,9:12,18,4,5 +K03455 2422 . G A . . AS_SB_TABLE=0,14|0,2;DP=16;ECNT=9;ECNTH=3;MBQ=34,36;MFRL=239,219;MMQ=60,60;MPOS=9;POPAF=7.30;TLOD=5.69 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:14,2:0.167:16:0,0:9,2:14,2:0|1:2422_G_A:2422:0,14,0,2 +K03455 2426 . G A . . AS_SB_TABLE=0,14|0,2;DP=16;ECNT=9;ECNTH=3;MBQ=37,35;MFRL=239,219;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=5.69 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:14,2:0.167:16:0,0:9,2:14,2:0|1:2422_G_A:2422:0,14,0,2 +K03455 2436 . A G . . AS_SB_TABLE=0,0|0,0;DP=3;ECNT=9;ECNTH=4;MBQ=0,31;MFRL=0,255;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=8.49 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.766:2:0,0:0,2:0,2:0|1:2436_A_G:2436:0,0,0,2 +K03455 2438 . A G . . AS_SB_TABLE=0,0|0,0;DP=3;ECNT=9;ECNTH=4;MBQ=0,33;MFRL=0,255;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=8.49 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.766:2:0,0:0,2:0,2:0|1:2436_A_G:2436:0,0,0,2 +K03455 2440 . T C . . AS_SB_TABLE=0,0|0,0;DP=3;ECNT=9;ECNTH=4;MBQ=0,31;MFRL=0,255;MMQ=60,60;MPOS=1;POPAF=7.30;TLOD=8.49 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|1:0,2:0.766:2:0,0:0,2:0,2:0|1:2436_A_G:2436:0,0,0,2
--- a/test-data/Mutect2-out6.vcf Wed Aug 24 17:58:18 2022 +0000 +++ b/test-data/Mutect2-out6.vcf Tue Feb 03 18:50:29 2026 +0000 @@ -4,6 +4,7 @@ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=FAD,Number=R,Type=Integer,Description="Count of fragments supporting each allele."> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles"> @@ -11,18 +12,19 @@ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> -##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample NA12891 --output output.vcf --input tumor.bam --input normal.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.7.0",Date="May 8, 2020 3:34:24 PM CEST"> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample NA12891 --output output.vcf --input tumor.bam --input normal.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --trim-to-haplotype true --exact-matching false --flow-use-t0-tag false --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --keep-boundary-flows false --genotype-pon-sites false --genotype-germline-sites false --genotype-germline-sites-fraction 1.0 --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --permutect-ref-downsample 10 --permutect-alt-downsample 20 --permutect-non-artifact-ratio 1 --permutect-dataset-mode ILLUMINA --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --base-qual-correction-factor 5 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --flow-mode NONE --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --use-pdhmm false --use-pdhmm-overlap-optimization false --make-determined-haps-from-pd-code false --print-pileupcalling-status false --fallback-gga-if-pdhmm-fails true --pileup-detection-enable-indel-pileup-calling false --pileup-detection-active-region-phred-threshold 0.0 --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.1 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-snp-basequality-filter 12 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --pileup-detection-filter-assembly-alt-bad-read-tolerance 0.0 --pileup-detection-edit-distance-read-badness-for-assembly-filtering-threshold 0.12 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.6.2.0",Date="February 2, 2026, 12:30:34?AM GMT"> ##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |."> ##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site"> ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of potential somatic events in the assembly region"> +##INFO=<ID=ECNTH,Number=A,Type=Integer,Description="Number of somatic events in best supporting haplotype for each alt allele"> ##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> -##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> -##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> -##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality by allele"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length by allele"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality by allele"> ##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> -##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Log 10 odds of artifact in normal with same allele fraction as tumor"> ##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> ##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> ##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> @@ -43,22 +45,22 @@ ##tumor_sample=NA12891 ##tumor_sample=NA12892 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891 NA12892 -chr20 862991 . C G . . AS_SB_TABLE=10,7|4,1;DP=22;ECNT=1;MBQ=39,37;MFRL=340,366;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=11.91 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,5:0.491:10:4,3:1,1:1,4,4,1 0/1:12,0:0.071:12:6,0:6,0:9,3,0,0 -chr20 863148 . C CTAT . . AS_SB_TABLE=19,18|4,5;DP=50;ECNT=1;MBQ=38,39;MFRL=351,362;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=1,2;RU=TAT;STR;TLOD=29.75 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:11,9:0.454:20:4,4:6,4:5,6,4,5 0/1:26,0:0.034:26:14,0:11,0:14,12,0,0 -chr20 863271 . A G . . AS_SB_TABLE=24,10|5,4;DP=44;ECNT=1;MBQ=36,37;MFRL=347,359;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=26.85 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:8,9:0.526:17:4,5:4,4:7,1,5,4 0/1:26,0:0.035:26:15,0:10,0:17,9,0,0 -chr20 863508 . A G . . AS_SB_TABLE=24,20|6,6;DP=59;ECNT=1;MBQ=39,40;MFRL=343,355;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=36.80 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:11,12:0.524:23:6,6:4,6:4,7,6,6 0/1:33,0:0.028:33:16,0:16,0:20,13,0,0 -chr20 863706 . C T . . AS_SB_TABLE=7,25|9,11;DP=53;ECNT=2;MBQ=37,39;MFRL=341,345;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=65.75 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,20:0.955:20:0,12:0,7:0,0,9,11 0/1:32,0:0.029:32:9,0:23,0:7,25,0,0 -chr20 863744 . C T . . AS_SB_TABLE=10,24|6,6;DP=48;ECNT=2;MBQ=39,38;MFRL=341,347;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=38.56 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:8,12:0.591:20:5,7:3,5:4,4,6,6 0/1:26,0:0.035:26:10,0:16,0:6,20,0,0 -chr20 863846 . C T . . AS_SB_TABLE=28,10|4,3;DP=48;ECNT=2;MBQ=40,38;MFRL=348,343;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=20.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:17,7:0.309:24:11,5:5,2:14,3,4,3 0/1:21,0:0.042:21:9,0:12,0:14,7,0,0 -chr20 863873 . C T . . AS_SB_TABLE=23,11|7,3;DP=48;ECNT=2;MBQ=39,37;MFRL=353,337;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=30.15 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:21,0:0.041:21:14,0:6,0:15,6,0,0 0/1:13,10:0.440:23:8,3:5,7:8,5,7,3 -chr20 864074 . T C . . AS_SB_TABLE=19,20|8,3;DP=53;ECNT=1;MBQ=38,36;MFRL=344,355;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=31.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,11:0.465:24:7,9:5,2:5,8,8,3 0/1:26,0:0.035:26:13,0:13,0:14,12,0,0 -chr20 864199 . G A . . AS_SB_TABLE=30,18|4,9;DP=63;ECNT=1;MBQ=36,39;MFRL=343,361;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=37.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:15,13:0.470:28:7,7:7,6:13,2,4,9 0/1:33,0:0.028:33:23,0:10,0:17,16,0,0 -chr20 864301 . G T . . AS_SB_TABLE=20,17|12,6;DP=57;ECNT=1;MBQ=35,35;MFRL=344,358;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=56.37 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,18:0.594:30:9,12:3,6:6,6,12,6 0/1:25,0:0.036:25:11,0:14,0:14,11,0,0 -chr20 864455 . T C . . AS_SB_TABLE=11,17|15,17;DP=63;ECNT=2;MBQ=35,39;MFRL=343,360;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=115.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,32:0.971:32:0,16:0,16:0,0,15,17 0/1:28,0:0.033:28:19,0:8,0:11,17,0,0 -chr20 864512 . A G . . AS_SB_TABLE=17,22|11,15;DP=71;ECNT=2;MBQ=38,37;MFRL=344,364;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=88.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:14,26:0.647:40:8,12:5,14:9,5,11,15 0/1:25,0:0.035:25:12,0:12,0:8,17,0,0 -chr20 864640 . C T . . AS_SB_TABLE=16,18|14,14;DP=64;ECNT=2;MBQ=38,35;MFRL=339,354;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=94.78 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,28:0.968:28:0,11:0,17:0,0,14,14 0/1:34,0:0.028:34:22,0:12,0:16,18,0,0 -chr20 864660 . G T . . AS_SB_TABLE=16,15|11,11;DP=55;ECNT=2;MBQ=37,38;MFRL=340,358;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=69.72 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,22:0.960:22:0,8:0,12:0,0,11,11 0/1:31,0:0.030:31:17,0:13,0:16,15,0,0 -chr20 865054 . G C . . AS_SB_TABLE=10,8|6,4;DP=30;ECNT=1;MBQ=35,34;MFRL=347,347;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=30.15 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:9,10:0.524:19:7,6:2,4:6,3,6,4 0/1:9,0:0.092:9:3,0:5,0:4,5,0,0 -chr20 865366 . G T . . AS_SB_TABLE=13,13|15,11;DP=54;ECNT=1;MBQ=39,37;MFRL=343,353;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=88.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,26:0.965:26:0,14:0,10:0,0,15,11 0/1:26,0:0.035:26:10,0:16,0:13,13,0,0 -chr20 865537 . C T . . AS_SB_TABLE=17,29|6,3;DP=58;ECNT=1;MBQ=35,35;MFRL=350,358;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=24.37 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:19,9:0.333:28:10,4:9,5:8,11,6,3 0/1:27,0:0.034:27:13,0:13,0:9,18,0,0 -chr20 865664 . TC T . . AS_SB_TABLE=20,20|7,10;DP=59;ECNT=1;MBQ=35,34;MFRL=348,359;MMQ=60,60;MPOS=25;POPAF=7.30;RPA=4,3;RU=C;STR;TLOD=42.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:19,17:0.474:36:10,11:9,4:11,8,7,10 0/1:21,0:0.043:21:7,0:10,0:9,12,0,0 +chr20 862991 . C G . . AS_SB_TABLE=10,7|4,1;DP=22;ECNT=1;ECNTH=1;MBQ=39,37;MFRL=340,366;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=11.91 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:5,5:0.491:10:4,3:1,1:5,5:1,4,4,1 0/1:12,0:0.071:12:6,0:6,0:12,0:9,3,0,0 +chr20 863148 . C CTAT . . AS_SB_TABLE=19,18|4,5;DP=49;ECNT=1;ECNTH=1;MBQ=38,39;MFRL=351,362;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=1,2;RU=TAT;STR;TLOD=29.76 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:11,9:0.454:20:4,4:6,4:11,9:5,6,4,5 0/1:26,0:0.034:26:14,0:11,0:26,0:14,12,0,0 +chr20 863271 . A G . . AS_SB_TABLE=25,9|6,4;DP=45;ECNT=1;ECNTH=1;MBQ=36,37;MFRL=347,361;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=28.96 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:8,10:0.550:18:4,5:4,5:8,10:7,1,6,4 0/1:26,0:0.035:26:16,0:10,0:26,0:18,8,0,0 +chr20 863508 . A G . . AS_SB_TABLE=24,24|6,6;DP=63;ECNT=1;ECNTH=1;MBQ=39,40;MFRL=342,355;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=36.39 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:11,12:0.524:23:6,6:4,6:11,12:4,7,6,6 0/1:37,0:0.025:37:17,0:17,0:37,0:20,17,0,0 +chr20 863706 . C T . . AS_SB_TABLE=7,25|8,11;DP=52;ECNT=2;ECNTH=2;MBQ=37,39;MFRL=341,347;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=65.15 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,19:0.953:19:0,12:0,7:0,19:0,0,8,11 0/1:32,0:0.029:32:9,0:23,0:32,0:7,25,0,0 +chr20 863744 . C T . . AS_SB_TABLE=10,24|6,6;DP=48;ECNT=2;ECNTH=2;MBQ=39,38;MFRL=341,347;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=38.56 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:8,12:0.591:20:5,7:3,5:8,12:4,4,6,6 0/1:26,0:0.035:26:10,0:16,0:26,0:6,20,0,0 +chr20 863846 . C T . . AS_SB_TABLE=27,10|5,3;DP=47;ECNT=2;ECNTH=1;MBQ=40,37;MFRL=347,348;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=23.22 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:16,8:0.346:24:11,6:5,2:16,8:13,3,5,3 0/1:21,0:0.043:21:9,0:12,0:21,0:14,7,0,0 +chr20 863873 . C T . . AS_SB_TABLE=23,11|7,3;DP=47;ECNT=2;ECNTH=1;MBQ=39,37;MFRL=353,337;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=30.16 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:21,0:0.042:21:14,0:6,0:21,0:15,6,0,0 0/1:13,10:0.440:23:8,3:5,7:13,10:8,5,7,3 +chr20 864074 . T C . . AS_SB_TABLE=19,21|8,3;DP=54;ECNT=1;ECNTH=1;MBQ=38,36;MFRL=345,355;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=31.87 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:14,11:0.447:25:7,9:6,2:14,11:5,9,8,3 0/1:26,0:0.035:26:13,0:13,0:26,0:14,12,0,0 +chr20 864199 . G A . . AS_SB_TABLE=30,18|4,9;DP=63;ECNT=1;ECNTH=1;MBQ=36,39;MFRL=343,361;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=37.97 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:15,13:0.470:28:7,7:7,6:15,13:13,2,4,9 0/1:33,0:0.028:33:23,0:10,0:33,0:17,16,0,0 +chr20 864301 . G T . . AS_SB_TABLE=20,17|12,6;DP=57;ECNT=1;ECNTH=1;MBQ=35,35;MFRL=344,358;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=56.37 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:12,18:0.594:30:9,12:3,6:12,18:6,6,12,6 0/1:25,0:0.036:25:11,0:14,0:25,0:14,11,0,0 +chr20 864455 . T C . . AS_SB_TABLE=11,17|15,17;DP=63;ECNT=2;ECNTH=2;MBQ=35,39;MFRL=343,360;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=115.14 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,32:0.971:32:0,16:0,16:0,32:0,0,15,17 0/1:28,0:0.033:28:19,0:8,0:28,0:11,17,0,0 +chr20 864512 . A G . . AS_SB_TABLE=17,22|11,15;DP=71;ECNT=2;ECNTH=2;MBQ=38,37;MFRL=344,364;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=88.07 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:14,26:0.647:40:8,12:5,14:14,26:9,5,11,15 0/1:25,0:0.035:25:12,0:12,0:25,0:8,17,0,0 +chr20 864640 . C T . . AS_SB_TABLE=17,18|14,14;DP=65;ECNT=2;ECNTH=2;MBQ=37,35;MFRL=339,354;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=94.52 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,28:0.968:28:0,11:0,17:0,28:0,0,14,14 0/1:35,0:0.027:35:23,0:12,0:35,0:17,18,0,0 +chr20 864660 . G T . . AS_SB_TABLE=15,15|11,11;DP=54;ECNT=2;ECNTH=2;MBQ=37,38;MFRL=341,358;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=69.93 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,22:0.960:22:0,8:0,12:0,22:0,0,11,11 0/1:30,0:0.031:30:17,0:13,0:30,0:15,15,0,0 +chr20 865054 . G C . . AS_SB_TABLE=10,9|6,4;DP=31;ECNT=1;ECNTH=1;MBQ=35,34;MFRL=347,347;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=29.95 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:10,10:0.500:20:8,6:2,4:10,10:6,4,6,4 0/1:9,0:0.092:9:3,0:5,0:9,0:4,5,0,0 +chr20 865366 . G T . . AS_SB_TABLE=13,13|15,11;DP=54;ECNT=1;ECNTH=1;MBQ=39,37;MFRL=343,353;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=88.44 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:0,26:0.965:26:0,14:0,10:0,26:0,0,15,11 0/1:26,0:0.035:26:10,0:16,0:26,0:13,13,0,0 +chr20 865537 . C T . . AS_SB_TABLE=17,30|6,5;DP=61;ECNT=1;ECNTH=1;MBQ=35,35;MFRL=350,358;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=28.19 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:20,11:0.358:31:10,5:10,5:20,11:8,12,6,5 0/1:27,0:0.034:27:13,0:13,0:27,0:9,18,0,0 +chr20 865664 . TC T . . AS_SB_TABLE=20,21|9,11;DP=63;ECNT=1;ECNTH=1;MBQ=35,35;MFRL=347,359;MMQ=60,60;MPOS=23;POPAF=7.30;RPA=4,3;RU=C;STR;TLOD=51.28 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:19,20:0.512:39:10,12:9,5:19,20:11,8,9,11 0/1:22,0:0.042:22:7,0:10,0:22,0:9,13,0,0
--- a/test-data/all_fasta.loc Wed Aug 24 17:58:18 2022 +0000 +++ b/test-data/all_fasta.loc Tue Feb 03 18:50:29 2026 +0000 @@ -1,1 +1,2 @@ hg38 hg38 Human hg38 ${__HERE__}/cached_locally/cached_reference.fa +test_ref test_ref Test Reference ${__HERE__}/test_ref.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bqsr_expected.table Tue Feb 03 18:50:29 2026 +0000 @@ -0,0 +1,1949 @@ +#:GATKReport.v1.1:5 +#:GATKTable:2:17:%s:%s:; +#:GATKTable:Arguments:Recalibration argument collection values used in this run +Argument Value +binary_tag_name null +covariate ReadGroupCovariate,QualityScoreCovariate,ContextCovariate,CycleCovariate +default_platform null +deletions_default_quality 45 +force_platform null +indels_context_size 3 +insertions_default_quality 45 +low_quality_tail 2 +maximum_cycle_value 500 +mismatches_context_size 2 +mismatches_default_quality -1 +no_standard_covs false +quantizing_levels 16 +recalibration_report null +run_without_dbsnp false +solid_nocall_strategy THROW_EXCEPTION +solid_recal_mode SET_Q_ZERO + +#:GATKTable:3:94:%d:%d:%d:; +#:GATKTable:Quantized:Quality quantization map +QualityScore Count QuantizedScore + 0 0 93 + 1 0 93 + 2 0 93 + 3 0 93 + 4 0 93 + 5 0 93 + 6 0 93 + 7 0 93 + 8 4 8 + 9 0 93 + 10 0 93 + 11 0 93 + 12 129 12 + 13 0 93 + 14 0 93 + 15 0 93 + 16 0 93 + 17 0 93 + 18 0 93 + 19 0 93 + 20 0 93 + 21 0 93 + 22 154 22 + 23 0 93 + 24 0 93 + 25 0 93 + 26 0 93 + 27 224 27 + 28 0 93 + 29 0 93 + 30 0 93 + 31 0 93 + 32 582 32 + 33 0 93 + 34 0 93 + 35 0 93 + 36 11567 36 + 37 37 37 + 38 0 93 + 39 0 93 + 40 555 40 + 41 0 93 + 42 0 93 + 43 0 93 + 44 0 93 + 45 0 93 + 46 0 93 + 47 0 93 + 48 0 93 + 49 0 93 + 50 0 93 + 51 0 93 + 52 0 93 + 53 0 93 + 54 0 93 + 55 0 93 + 56 0 93 + 57 0 93 + 58 0 93 + 59 0 93 + 60 0 93 + 61 0 93 + 62 0 93 + 63 0 93 + 64 0 93 + 65 0 93 + 66 0 93 + 67 0 93 + 68 0 93 + 69 0 93 + 70 0 93 + 71 0 93 + 72 0 93 + 73 0 93 + 74 0 93 + 75 0 93 + 76 0 93 + 77 0 93 + 78 0 93 + 79 0 93 + 80 0 93 + 81 0 93 + 82 0 93 + 83 0 93 + 84 0 93 + 85 0 93 + 86 0 93 + 87 0 93 + 88 0 93 + 89 0 93 + 90 0 93 + 91 0 93 + 92 0 93 + 93 0 93 + +#:GATKTable:6:4:%s:%s:%.4f:%.4f:%d:%.2f:; +#:GATKTable:RecalTable0: +ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors +GM12878-1C981705 M 25.0000 30.5769 12611 127.00 +GM12878-3294E832 M 19.0000 20.4664 66 20.00 +GM12878-7025832C M 40.0000 41.0000 144 8.00 +GM12878-766FF01A M 38.0000 39.8681 431 12.00 + +#:GATKTable:6:17:%s:%d:%s:%.4f:%d:%.2f:; +#:GATKTable:RecalTable1: +ReadGroup QualityScore EventType EmpiricalQuality Observations Errors +GM12878-1C981705 8 M 8.0000 4 0.00 +GM12878-1C981705 12 M 12.0000 120 5.00 +GM12878-1C981705 22 M 22.0000 154 4.00 +GM12878-1C981705 27 M 27.0000 221 1.00 +GM12878-1C981705 32 M 32.0000 545 3.00 +GM12878-1C981705 37 M 36.0000 1345 19.00 +GM12878-1C981705 41 M 36.0000 10222 95.00 +GM12878-3294E832 12 M 12.0000 9 1.00 +GM12878-3294E832 27 M 27.0000 2 0.00 +GM12878-3294E832 32 M 32.0000 27 4.00 +GM12878-3294E832 37 M 37.0000 14 7.00 +GM12878-3294E832 41 M 40.0000 14 8.00 +GM12878-7025832C 41 M 40.0000 144 8.00 +GM12878-766FF01A 27 M 27.0000 1 0.00 +GM12878-766FF01A 32 M 32.0000 10 1.00 +GM12878-766FF01A 37 M 37.0000 23 0.00 +GM12878-766FF01A 41 M 40.0000 397 11.00 + +#:GATKTable:8:1796:%s:%d:%s:%s:%s:%.4f:%d:%.2f:; +#:GATKTable:RecalTable2: +ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors +GM12878-1C981705 8 -5 Cycle M 8.0000 1 0.00 +GM12878-1C981705 8 -65 Cycle M 8.0000 1 0.00 +GM12878-1C981705 8 133 Cycle M 8.0000 1 0.00 +GM12878-1C981705 8 136 Cycle M 8.0000 1 0.00 +GM12878-1C981705 8 CA Context M 8.0000 1 0.00 +GM12878-1C981705 8 CT Context M 8.0000 1 0.00 +GM12878-1C981705 8 GG Context M 8.0000 1 0.00 +GM12878-1C981705 8 TG Context M 8.0000 1 0.00 +GM12878-1C981705 12 -1 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -10 Cycle M 12.0000 1 1.00 +GM12878-1C981705 12 -101 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 -102 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -103 Cycle M 12.0000 1 1.00 +GM12878-1C981705 12 -105 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -11 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -118 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -120 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 -127 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -128 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -129 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -13 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 -131 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -134 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -137 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -14 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -17 Cycle M 12.0000 1 1.00 +GM12878-1C981705 12 -18 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -2 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -21 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 -24 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -26 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -27 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -28 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 -3 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -31 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -33 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -34 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -35 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -38 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 -39 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -4 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -41 Cycle M 12.0000 1 1.00 +GM12878-1C981705 12 -43 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 -48 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -49 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -5 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -50 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -51 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -52 Cycle M 12.0000 3 0.00 +GM12878-1C981705 12 -53 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -54 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -57 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -58 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -59 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -6 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -60 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -61 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 -62 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 -63 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -64 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -65 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 -67 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -68 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -69 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -71 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -76 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -77 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -78 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -79 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 -8 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -80 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -84 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -92 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -93 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -96 Cycle M 12.0000 2 1.00 +GM12878-1C981705 12 -97 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 -99 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 100 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 105 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 111 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 120 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 125 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 135 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 141 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 142 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 143 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 144 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 16 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 2 Cycle M 12.0000 4 0.00 +GM12878-1C981705 12 31 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 35 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 41 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 45 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 5 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 51 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 52 Cycle M 12.0000 2 0.00 +GM12878-1C981705 12 53 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 56 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 69 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 70 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 71 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 83 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 86 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 89 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 9 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 97 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 98 Cycle M 12.0000 1 0.00 +GM12878-1C981705 12 AA Context M 12.0000 8 1.00 +GM12878-1C981705 12 AC Context M 12.0000 8 0.00 +GM12878-1C981705 12 AG Context M 12.0000 4 0.00 +GM12878-1C981705 12 AT Context M 12.0000 9 0.00 +GM12878-1C981705 12 CA Context M 12.0000 7 0.00 +GM12878-1C981705 12 CC Context M 12.0000 7 1.00 +GM12878-1C981705 12 CT Context M 12.0000 13 1.00 +GM12878-1C981705 12 GA Context M 12.0000 6 0.00 +GM12878-1C981705 12 GC Context M 12.0000 5 0.00 +GM12878-1C981705 12 GG Context M 12.0000 6 1.00 +GM12878-1C981705 12 GT Context M 12.0000 5 0.00 +GM12878-1C981705 12 TA Context M 12.0000 5 0.00 +GM12878-1C981705 12 TC Context M 12.0000 12 0.00 +GM12878-1C981705 12 TG Context M 12.0000 14 0.00 +GM12878-1C981705 12 TT Context M 12.0000 10 1.00 +GM12878-1C981705 22 -104 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -105 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -107 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -108 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -109 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 -110 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -111 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -116 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -118 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -119 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -12 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 -121 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 -123 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -124 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 -125 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -129 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -130 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -131 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -132 Cycle M 22.0000 3 0.00 +GM12878-1C981705 22 -133 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 -134 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 -135 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -136 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -137 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 -138 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -14 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -15 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -18 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -2 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -25 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -29 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -3 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 -32 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -34 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -35 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -38 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -4 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 -40 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -42 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -44 Cycle M 22.0000 2 0.00 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1 1.00 +GM12878-1C981705 22 -91 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 -92 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -96 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 -98 Cycle M 22.0000 2 1.00 +GM12878-1C981705 22 -99 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 101 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 102 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 109 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 112 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 115 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 127 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 131 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 132 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 137 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 139 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 144 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 147 Cycle M 22.0000 2 0.00 +GM12878-1C981705 22 148 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 31 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 35 Cycle M 22.0000 1 0.00 +GM12878-1C981705 22 39 Cycle M 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41.0000 52 2.00 +GM12878-1C981705 41 72 Cycle M 41.0000 54 0.00 +GM12878-1C981705 41 73 Cycle M 41.0000 52 0.00 +GM12878-1C981705 41 74 Cycle M 41.0000 51 0.00 +GM12878-1C981705 41 75 Cycle M 41.0000 45 0.00 +GM12878-1C981705 41 76 Cycle M 41.0000 47 1.00 +GM12878-1C981705 41 77 Cycle M 41.0000 40 0.00 +GM12878-1C981705 41 78 Cycle M 41.0000 46 1.00 +GM12878-1C981705 41 79 Cycle M 41.0000 48 0.00 +GM12878-1C981705 41 8 Cycle M 41.0000 64 0.00 +GM12878-1C981705 41 80 Cycle M 41.0000 47 0.00 +GM12878-1C981705 41 81 Cycle M 41.0000 44 0.00 +GM12878-1C981705 41 82 Cycle M 41.0000 47 0.00 +GM12878-1C981705 41 83 Cycle M 41.0000 46 0.00 +GM12878-1C981705 41 84 Cycle M 41.0000 46 0.00 +GM12878-1C981705 41 85 Cycle M 41.0000 41 1.00 +GM12878-1C981705 41 86 Cycle M 41.0000 29 0.00 +GM12878-1C981705 41 87 Cycle M 41.0000 43 0.00 +GM12878-1C981705 41 88 Cycle M 41.0000 42 0.00 +GM12878-1C981705 41 89 Cycle M 41.0000 36 0.00 +GM12878-1C981705 41 9 Cycle M 41.0000 63 1.00 +GM12878-1C981705 41 90 Cycle M 41.0000 32 1.00 +GM12878-1C981705 41 91 Cycle M 41.0000 43 0.00 +GM12878-1C981705 41 92 Cycle M 41.0000 36 1.00 +GM12878-1C981705 41 93 Cycle M 41.0000 33 0.00 +GM12878-1C981705 41 94 Cycle M 41.0000 30 0.00 +GM12878-1C981705 41 95 Cycle M 41.0000 36 0.00 +GM12878-1C981705 41 96 Cycle M 41.0000 34 1.00 +GM12878-1C981705 41 97 Cycle M 41.0000 37 0.00 +GM12878-1C981705 41 98 Cycle M 41.0000 36 0.00 +GM12878-1C981705 41 99 Cycle M 41.0000 25 2.00 +GM12878-1C981705 41 AA Context M 41.0000 1242 1.00 +GM12878-1C981705 41 AC Context M 40.0000 425 24.00 +GM12878-1C981705 41 AG Context M 39.0000 596 34.00 +GM12878-1C981705 41 AT Context M 41.0000 916 3.00 +GM12878-1C981705 41 CA Context M 41.0000 747 0.00 +GM12878-1C981705 41 CC Context M 41.0000 402 6.00 +GM12878-1C981705 41 CG Context M 41.0000 63 7.00 +GM12878-1C981705 41 CT Context M 41.0000 675 0.00 +GM12878-1C981705 41 GA Context M 41.0000 499 3.00 +GM12878-1C981705 41 GC Context M 41.0000 458 0.00 +GM12878-1C981705 41 GG Context M 41.0000 322 0.00 +GM12878-1C981705 41 GT Context M 41.0000 441 0.00 +GM12878-1C981705 41 TA Context M 41.0000 620 5.00 +GM12878-1C981705 41 TC Context M 41.0000 618 5.00 +GM12878-1C981705 41 TG Context M 41.0000 752 3.00 +GM12878-1C981705 41 TT Context M 41.0000 1393 3.00 +GM12878-3294E832 12 -1 Cycle M 12.0000 1 0.00 +GM12878-3294E832 12 -2 Cycle M 12.0000 3 0.00 +GM12878-3294E832 12 -3 Cycle M 12.0000 1 0.00 +GM12878-3294E832 12 -6 Cycle M 12.0000 3 0.00 +GM12878-3294E832 12 -9 Cycle M 12.0000 1 1.00 +GM12878-3294E832 12 AT Context M 12.0000 4 0.00 +GM12878-3294E832 12 GG Context M 12.0000 1 0.00 +GM12878-3294E832 12 TA Context M 12.0000 1 0.00 +GM12878-3294E832 12 TC Context M 12.0000 1 1.00 +GM12878-3294E832 12 TT Context M 12.0000 1 0.00 +GM12878-3294E832 27 -3 Cycle M 27.0000 1 0.00 +GM12878-3294E832 27 -4 Cycle M 27.0000 1 0.00 +GM12878-3294E832 27 TA Context M 27.0000 1 0.00 +GM12878-3294E832 27 TG Context M 27.0000 1 0.00 +GM12878-3294E832 32 -1 Cycle M 32.0000 1 0.00 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1 0.00 +GM12878-3294E832 37 -12 Cycle M 37.0000 1 1.00 +GM12878-3294E832 37 -5 Cycle M 37.0000 1 0.00 +GM12878-3294E832 37 -6 Cycle M 37.0000 2 0.00 +GM12878-3294E832 37 -7 Cycle M 37.0000 3 3.00 +GM12878-3294E832 37 -8 Cycle M 37.0000 1 1.00 +GM12878-3294E832 37 AA Context M 37.0000 1 0.00 +GM12878-3294E832 37 AG Context M 37.0000 1 1.00 +GM12878-3294E832 37 AT Context M 37.0000 2 0.00 +GM12878-3294E832 37 CG Context M 37.0000 2 2.00 +GM12878-3294E832 37 CT Context M 37.0000 2 1.00 +GM12878-3294E832 37 GA Context M 37.0000 1 0.00 +GM12878-3294E832 37 TC Context M 37.0000 3 3.00 +GM12878-3294E832 41 -1 Cycle M 41.0000 2 0.00 +GM12878-3294E832 41 -10 Cycle M 41.0000 2 2.00 +GM12878-3294E832 41 -2 Cycle M 41.0000 1 0.00 +GM12878-3294E832 41 -3 Cycle M 41.0000 1 0.00 +GM12878-3294E832 41 -4 Cycle M 41.0000 1 0.00 +GM12878-3294E832 41 -5 Cycle M 41.0000 1 0.00 +GM12878-3294E832 41 -8 Cycle M 41.0000 3 3.00 +GM12878-3294E832 41 -9 Cycle M 41.0000 3 3.00 +GM12878-3294E832 41 AG Context M 41.0000 1 0.00 +GM12878-3294E832 41 CG Context M 41.0000 2 2.00 +GM12878-3294E832 41 CT Context M 41.0000 4 3.00 +GM12878-3294E832 41 GG Context M 41.0000 1 0.00 +GM12878-3294E832 41 TA Context M 41.0000 1 0.00 +GM12878-3294E832 41 TC Context M 41.0000 3 3.00 +GM12878-7025832C 41 -1 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -10 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -11 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -12 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -13 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -14 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -15 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -16 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -17 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -18 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -19 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -20 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -21 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 -22 Cycle M 41.0000 1 1.00 +GM12878-7025832C 41 -23 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 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0.00 +GM12878-7025832C 41 16 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 17 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 18 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 19 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 2 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 20 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 21 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 22 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 23 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 24 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 25 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 26 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 28 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 29 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 3 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 30 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 31 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 32 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 33 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 34 Cycle M 41.0000 1 0.00 +GM12878-7025832C 41 35 Cycle M 41.0000 1 0.00 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+GM12878-766FF01A 37 -19 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -2 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -41 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -47 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -55 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -56 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -59 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -7 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -8 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -81 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -82 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -86 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 -9 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 107 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 2 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 3 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 4 Cycle M 37.0000 2 0.00 +GM12878-766FF01A 37 5 Cycle M 37.0000 1 0.00 +GM12878-766FF01A 37 AC Context M 37.0000 2 0.00 +GM12878-766FF01A 37 AT Context M 37.0000 1 0.00 +GM12878-766FF01A 37 CT Context M 37.0000 3 0.00 +GM12878-766FF01A 37 GA Context M 37.0000 3 0.00 +GM12878-766FF01A 37 GC Context M 37.0000 2 0.00 +GM12878-766FF01A 37 GG Context M 37.0000 1 0.00 +GM12878-766FF01A 37 GT Context M 37.0000 2 0.00 +GM12878-766FF01A 37 TA Context M 37.0000 2 0.00 +GM12878-766FF01A 37 TC Context M 37.0000 1 0.00 +GM12878-766FF01A 37 TG Context M 37.0000 1 0.00 +GM12878-766FF01A 37 TT Context M 37.0000 4 0.00 +GM12878-766FF01A 41 -10 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -100 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -101 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -103 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -105 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -106 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -107 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -108 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -109 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -110 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -112 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -113 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -114 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -115 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -116 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -117 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -118 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -119 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -12 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -120 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -121 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -122 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -123 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -126 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -127 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -128 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -129 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -13 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -130 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -131 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -132 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -133 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -134 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -135 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -136 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -137 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -138 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -139 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -14 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -140 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -141 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -142 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -143 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -144 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -15 Cycle M 41.0000 1 1.00 +GM12878-766FF01A 41 -16 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -17 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -18 Cycle M 41.0000 1 1.00 +GM12878-766FF01A 41 -20 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -21 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -22 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -23 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -24 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -25 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -26 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -27 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -28 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -29 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -30 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -32 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -33 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -34 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -35 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -36 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -37 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -38 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -39 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -40 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -42 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -43 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -44 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -45 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -46 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -48 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -49 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -50 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -51 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -52 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -53 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -54 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -57 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -58 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -60 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -61 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -62 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -63 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -64 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -65 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -66 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -67 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -68 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -69 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -70 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -71 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -72 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -73 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -74 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -75 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -76 Cycle M 41.0000 1 1.00 +GM12878-766FF01A 41 -77 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -78 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -79 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -80 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -83 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -84 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -85 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -87 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -88 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -89 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -90 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -91 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -92 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -93 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -94 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -96 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -97 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -98 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 -99 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 10 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 100 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 101 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 102 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 103 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 104 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 105 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 106 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 107 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 108 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 109 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 11 Cycle M 41.0000 2 1.00 +GM12878-766FF01A 41 110 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 111 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 112 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 113 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 114 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 115 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 116 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 117 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 118 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 119 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 12 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 120 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 121 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 122 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 123 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 124 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 125 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 126 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 127 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 128 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 129 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 13 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 130 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 131 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 132 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 133 Cycle M 41.0000 1 1.00 +GM12878-766FF01A 41 134 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 135 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 136 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 137 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 138 Cycle M 41.0000 1 1.00 +GM12878-766FF01A 41 139 Cycle M 41.0000 2 1.00 +GM12878-766FF01A 41 14 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 140 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 141 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 142 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 143 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 144 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 145 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 146 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 147 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 148 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 149 Cycle M 41.0000 2 1.00 +GM12878-766FF01A 41 15 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 150 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 151 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 16 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 17 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 18 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 19 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 20 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 21 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 22 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 23 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 24 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 25 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 26 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 27 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 28 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 29 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 30 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 31 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 32 Cycle M 41.0000 2 1.00 +GM12878-766FF01A 41 33 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 34 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 35 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 36 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 37 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 38 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 39 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 40 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 41 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 42 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 43 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 44 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 45 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 46 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 47 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 48 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 49 Cycle M 41.0000 2 1.00 +GM12878-766FF01A 41 5 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 50 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 51 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 52 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 53 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 54 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 55 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 56 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 57 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 58 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 59 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 6 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 60 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 61 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 62 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 63 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 64 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 65 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 66 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 67 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 68 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 69 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 7 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 70 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 71 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 72 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 73 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 74 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 75 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 76 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 77 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 78 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 79 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 8 Cycle M 41.0000 2 1.00 +GM12878-766FF01A 41 80 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 81 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 82 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 83 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 84 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 85 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 86 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 87 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 88 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 89 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 9 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 90 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 91 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 92 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 93 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 94 Cycle M 41.0000 1 0.00 +GM12878-766FF01A 41 95 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 96 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 97 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 98 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 99 Cycle M 41.0000 2 0.00 +GM12878-766FF01A 41 AA Context M 41.0000 42 0.00 +GM12878-766FF01A 41 AC Context M 41.0000 18 2.00 +GM12878-766FF01A 41 AG Context M 41.0000 29 0.00 +GM12878-766FF01A 41 AT Context M 41.0000 38 0.00 +GM12878-766FF01A 41 CA Context M 41.0000 27 1.00 +GM12878-766FF01A 41 CC Context M 41.0000 16 1.00 +GM12878-766FF01A 41 CG Context M 41.0000 1 0.00 +GM12878-766FF01A 41 CT Context M 41.0000 20 1.00 +GM12878-766FF01A 41 GA Context M 41.0000 19 0.00 +GM12878-766FF01A 41 GC Context M 41.0000 16 0.00 +GM12878-766FF01A 41 GG Context M 41.0000 23 2.00 +GM12878-766FF01A 41 GT Context M 41.0000 17 0.00 +GM12878-766FF01A 41 TA Context M 41.0000 39 1.00 +GM12878-766FF01A 41 TC Context M 41.0000 12 1.00 +GM12878-766FF01A 41 TG Context M 41.0000 27 1.00 +GM12878-766FF01A 41 TT Context M 41.0000 53 1.00 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bqsr_interval.interval_list Tue Feb 03 18:50:29 2026 +0000 @@ -0,0 +1,22 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr22 LN:40001 M5:1922b52e1af6977302717072ebaca0a1 UR:file:/sfs/7/workspace/ws/iizha01-dsl2_testdata_human-0/tmp/nxf.DB5Cm4sZ5K/chr22_region.fasta +chr22 1 124 + . +chr22 682 727 + . +chr22 1018 1186 + . +chr22 1396 1501 + . +chr22 2440 2611 + . +chr22 3337 6047 + . +chr22 8785 9261 + . +chr22 9051 9261 + . +chr22 10481 10576 + . +chr22 10481 10681 + . +chr22 18725 20784 + . +chr22 20869 20949 + . +chr22 23063 23459 + . +chr22 27394 28084 + . +chr22 29861 30189 + . +chr22 29885 30189 + . +chr22 29885 30189 + . +chr22 29922 30189 + . +chr22 30018 30189 + . +chr22 30024 30189 + .
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hc_interval.interval_list Tue Feb 03 18:50:29 2026 +0000 @@ -0,0 +1,4 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr22 LN:40001 M5:1922b52e1af6977302717072ebaca0a1 UR:file:/sfs/7/workspace/ws/iizha01-dsl2_testdata_human-0/tmp/nxf.DB5Cm4sZ5K/chr22_region.fasta +@PG ID:1 CL:IntervalListTools --INPUT genome.interval_list --OUTPUT genome_split --UNIQUE true --SORT true --SCATTER_COUNT 25 --SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW --TMP_DIR . --PADDING 0 --DONT_MERGE_ABUTTING false --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr22 3337 6047 + .
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_interval.interval_list Tue Feb 03 18:50:29 2026 +0000 @@ -0,0 +1,6 @@ +@HD VN:1.6 SO:coordinate +@SQ SN:chr22 LN:40001 M5:1922b52e1af6977302717072ebaca0a1 UR:file:/sfs/7/workspace/ws/iizha01-dsl2_testdata_human-0/tmp/nxf.DB5Cm4sZ5K/chr22_region.fasta +@PG ID:1 CL:IntervalListTools --INPUT genome.interval_list --OUTPUT genome_split --UNIQUE true --SORT true --SCATTER_COUNT 25 --SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW --TMP_DIR . --PADDING 0 --DONT_MERGE_ABUTTING false --ACTION CONCAT --INCLUDE_FILTERED false --BREAK_BANDS_AT_MULTIPLES_OF 0 --INVERT false --OUTPUT_VALUE NONE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:IntervalListTools +chr22 18725 20784 + . +chr22 20869 20949 + . +chr22 23063 23459 + .
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_ref.fasta Tue Feb 03 18:50:29 2026 +0000 @@ -0,0 +1,668 @@ +>chr22 +ACTCAAGATAATGATGAGTAAAGAATATATTTCTAACAACAAAAAGGAAATTTGATAGTA +TTTCTAAAGACAAAAAGGAAATTTGTATTCACATTCAGTTAGTCATTCCACCAGAATGAC +TTCATCACACAATATTTTGTGACAAGAACCTGAACAGCCTCATGTTTTACAATATTCTTT +TCATCTTTTATTATATGCACCAAAATTTTCTTTTTTAAATTTTCTTGAACCTCTAAATCT +ACTTTAAAAATTTACCTGATACACTTTTTAAATGGACAAATGCTGAAGGTAGCTGTGTAT +ACAAATGTGACTAGAAGGAAAAAGATGATGTAGAAATACAATAACTCCTTGAGTTGATCA +TTCTGATTGGCATTTATAGAGTAGAAATGTTTTGTAATTACAGAGGAAAAAAGATGGCCT +TTCCTTCAACAGTTATGAGCCGTCAGAATTTTCAAAAATATTGCATTTTGACAATGTAGT +TTCTAGTTTGACAATGATATATTTATCTTCAAAACCAGGAAAATGTAGATAAGGATTTGG +TTTTATAATATTTAAATTCTTATTAAAATGTATAATAAAATTGTTTTCCCCATCACTTTA +TTCTTCTGTAAGTTATTTTACGTTTAAAATGTAAACAAATAAAAATAAGTAAATAAACAG +TAGCAGCTTCTTTTCCTGGTGAATCGAGGATTGAGTATGTATTATATCTTTCCTGGACTA +TTGGAATAACCTCTCCCTCCTTCCACAGAGAAGCCATAATAATCTTTATGAAATACAAAT +CAAATCATGGTATTCATTCTTTAAATAGTTATCAATAAAAATAAAATCCCAACTTTATAC +CCTGTTCTGCAAATTTTAACGTGGTCTGAATTCAGCTTACATTTCTTCTTTCCCTTGTCT +ATTGCCCATCAGGCTCACTGGCCTTATTCCTTCACACCAAACTAGTTATTTCCGGGGTGG +GAGGAAGGCTTGCAGTGTTTTCTCCATCTGCAATAGTCTTTCCCAAATCTTAGTGTGGAT +AAAGTTTCCTTCTTGTTACTTGAATCACAAATACTATGTTCTTAGTCATTCTCTGTTACA +TCATCCAGAGTACATTATATCAATTTTCCAATATTTTTATTTATTTGATTTCCCACTATA +ACAGAGGCTCTGTTAGTGCAGGGTCTTTTACTCTTTTGTAATCCCAACAGCAAGAACAAA +ACAAGGTACATAGTACATATTTAATAAATACCTGTTGAACAAATATGTGCCAGTAATATT +TCTTCATGCTGCTGAATAAGTTAACAGCATATAAACACATACAAACCAAGTGGCATGGAT +GTCTGCTTTGATTTTTAGCCATTTAAAAATATACGTAACCCATCCTAAGGGGTTTATATT +TGTTTTGCATAATACATTAATATGTACTCATTATTCATTACACAGTTAATATATCTATAT +TTGCAGGGAATATACATTGCTTGGAATTATACAAAAAAATATTATTTTTCGTTTTCTAAT +ATTCAGGATACAGTGTTTTAATGGGGGTGTTTCTTCATTCTTTTTTTCTTACTGGTTTTT +ACTTTTTAAATTTGAAAGCCTTGCAGTGATCATAAGGATCTGTTCAGGCAAAGAACATGA +AAGAGTTTAAATTTTTATCATTTTAGTGTTTCTTATTCTCTATATCAAAAACATTCACAG +GTAAGTTAACAAGATCCTCATCAGGAGGAAAAGTAAATTGTTCACTACCATCCTCTAGTA +TCCTAATCTGGTCTTGTTGTTGGCTAACTTCAGCAGTTACTATTCTGTGATTGGTGTAAT +ATTAACCAAATAAATTACTGGATTTGTTCCACAAATATTATATCTTAGATTGGTTCTTTC +CTGTCTCTGAAAATAAAGTCTTGCAATGAGAATAAATTATTTTACAACAGTTAATTAGCA +ATGTAAAGTTTATTGAAAATGTATTTGCTTTTTTTGTAAATCATCTGTGAATCCAGAGGG +GAAAAATATGACAAAGAAAGCTATATAAGATATTATTTTATTTTACAGAGTAACAGACTA +GCTAGAGACAATGAATTAAGGGAAAATGACAAAGAACAGCTCAAAGCAATTTCTACACGA +GATCCTCTCTCTGAAATCACTGCGCAGGAGAAAGATTTTCTATGGACCACAGGTAAGTGC +TAAAATGGAGATTCTCTGTTTCTTTTTCTTTATTACAGAAAAAATAACTGACTTTGGCTG +ATCTCAGCATGTTTTTACCATACCTATTAGAATAAATGAAGCAGAATTTACATGATTTTT +AAACTATAAACATTGCCTTTTTAAAAACAATGGCTGTAAATTGATATTTGTAGAAAATCA +TACTACATTTGTAGTTGGCACATTAAATGCTTTTTCTTACTCTGAATTCCTGATATGACT +TTCTTTAGGATTGTTTAAAATATTCTAGTAGTTTTAGGTCAATTTAGATGTGATTTAGTT +GCTCTAGATATTATAATTTTTAGGGGTTCCCTTTCATTTTTTTCTTACGTTTCTTCAAAT +AGTATAATGCCTTATTTTCATTTATGAAGAAATTACCCTGCTGTTGGTGATACGGGTATA +TTTAAATAAACCAGTTGCAGTGCATTTTTGCAGAAAGTCCATTAAGACATAAATTTTGTC +CAGTAACCACAGTAGAAGTGGTGACTCTATGATTCATTCATGTTGCATAAGTAGGTGAAA +AATATGAGCTATATTCTGTCTGTTAAATGGAATTCTAGAGATGAAGTAGCCCAGGTAAAT +GTATGTTTGAGATTACTAGATAACTGTTGTACAAATTGGTATGTCACTTAAATTGTTTTC +TCTCAGAAAGTCCACATAAATAAATGAAATAGACTAATAATAGTAATATGGTGTAGAAAA +AACTCCCTTAACATTATTTCCATAGATAAAACTAATTAGAACTGTAAATTCTAAGGAGAT +TATTTATCTAAACTAATTTTAAAATCAGAAGTTAAGGCAGTGTTTTAGATGGCTCATTCA +CAACTATCTTTCCCCTTTAAATATGATTTATTGTCTTTCTCATACACAGATGTATTGCTT +GGTAAAAGATTGGCCTCCAATCAAACCTGAACAGGCTATGGAACTTCTGGACTGTAATTA +CCCAGATCCTATGGTTCGAAGTTTTGCTGTTCAGTGCTTGGAAAAATATTTAACAGATAA +CAAACTTTCTCAGTATTTAATTCAGCTAGTACAGGTAAAATAATGTAAAATAGTGAATAA +TGTTTAATTACAATAATAATTTATTTTAGATCCATACAACTTCCTTTTAAAAAACCTACT +GCACTAACTAGTTTTATGCTTAAAAAAAATTATTACCAGTAATATCCACTTTCTTTCTGA +AAAAATTTTCTTTAGATCGGCCATGCAGAAACTGAACCTGATTTGTTTTTTTTGAATCAC +CTAGGTCCTAAAATATGAACAATATTTGGATAACTTGCTTGTGAGATTTTTACTGAAGAA +AGCATTGACTAATCAAAGGATTGGGCACTTTTTCTTTTGGCATTTAAAGTAAGTCTAATT +ATTTTCCCATTAAATTCTTAAGGTACATATTACTTGCTTTCTTAATAGATTTATAAATAT +GTATTACTTATATACTTTTGTTTATGTTTGGCTGGAAGAGTTTTCCATACTAAAACTATT +TTGTACCAGTGATGAGCTTCTCAACTTTTGCTCTTTGAAATTTAAAAAGTAATAAATTCA +AAACTAAATTTCAGTCATGAATGAGAGCTTAAATATTTTTAAAGATTTTTGTTCTACTTA +AGTAAAATTTTCTAGGTCCAGATGAATATTGCTGTAGGTTTCACTGTGTGTATGGATTAA +AATATCCCCAAAAAAAGAAAAAAAATGTTTTACCTTGAGATTCAGAACAATAATGTCAAA +CTCCCGTGGTTCTTACTGAAAAACAAGCTAATTAAGAATAAAAAATGTTTTGTAGAATGT +GATATATGCAGTACTCAAAAGTTACAGGTCATAAACCATATAACTTTTCATAAATTTAGA +AACAGATTTATATCTAATATGATATTTTAAGTGTTAAAATTTAAAAATGGAACCCAGAAG +TTAAGTTGAAAACAAGAAGCGTAGACGTGTGTCAGAAGAGTCAAACAGCATTCACTGAGC +GCTTTGTTCCCTCCCTCTTCATTTGATTATTTTTGTGCTCAATTTCCTTTTTTCATGCTT +TTATATCTTGTACTGAGATTAGTCAATGAAAACTAGTTGAAATAAACCTAAAAACTAGAT +GTTTATTTAATCACATATTCAGGAACTACCTGAAACTCATGGTGGTTTTGCTTCTAAATT +ACAGGTTTTGAATAATGTTATTATTAGTATGATTGTAACATTTATTGGATTTCAAAAATG +AGTGTTTAAATTGTTTAGCAAAGATTATTTGTATACTGATTTAAGACTATATATATATTT +TTCTAATTTTGCATGATTCTTTTAGATCTGAGATGCACAATAAAACACTTAGCCAGAGGT +TTGGCCTGCTTTTGGAGTCCTATTGTCGTGCATGTGGGATGTATTTGAAGCACCTGAATA +GGCAAGTCGAGGCAATGGAAAAGCTCATTAACTTAACTGACATTGTCAAACAGGAGAAGA +AGGATGAAACACAAAAGTTGTGTGACTCTAGTCTGTGTTTGAGACTCTTTTCACTGCAGT +GGGGCAGAGTTGTTTAGAAGCCCAGTGTATATACAGATCATGGTCCTTGGAATCAAGCAG +ATTAGGATTTGGAACCAAGTTCCACTGCCTCTCATCTGTGTAGTGTTAGACACGTTATGC +AGGCTCTCAAGACTCATTTTCTTTGTCTGTAAAATGGGAATAATACCTGCTTCGTAAGGC +CATTGTGAGAATTAAATTACATGAGATATGCAAAGAACCTATCACAATCCTTGGAACACA +GAAGGTGCCCAATAAATGTTAGATCCCTTTACTTTCCCTTCCTTTCTCTTATTCAGGTCC +CTAAGTATTTACAGTGATTATTTCCTTATTCTGTCATTTATTATCTCTCAGTAATGACCC +TGAAAATGAGTGGAAAGAAGTTAGTTTTTACATTTCCAAGTTTAAAATGGATTTCGAGTC +ACTCAGTAAATATATCACACCCTCTAGTCATCTGCTGTCTAGCTTAGTGTAACTAAGAGT +AGGAAATACAATGTAAACTTTTTTTTTTGAGACAGGGTCTGGCTCTTTTGCCCGGCCTGG +AATGCAGTGGTGCAATTTCGGCTCACTGCAGCCTTGACCTCCTGGGTTCAAGCCATCCTC +CCACCTCAGCCTCCTGAGTAGCTAGGACTATAGGAGCATGCCACCACTCCCAGCTAATTT +TTGTATTTTTAGTAGAGACAGTGTTCTATTCTGCTTTATATTAAAAGCCCCTTAGAAAAT +GGGAACCTGGTGAATATATAATGAATTGTAAAATATTTTAATGTGTAACTTTTTCAACTG +TGAAACTGACTACTGATTTTTTGATGAAAACAGCTGCTGATAAAGTATTTTGTGTAAAGT +GTAGTTCTTATTAATCAGGAAAATGATGACTTGATTAGACTGTATATGCCCTCTTGGATT +TTATTTTAAATGGATTGGTGACTTTCACATAGGTAAAACACAGTCCATCTGTATTCTTTT +TTCCATCAAAAAGCGAGTGATTTAGAATTATAAAAAAATTTGTGAGCAGCCTATTTGAAA +GGCATCATGGAAATTTCACAGCACAATAACATGGATTTGTTTTTTTCTTAATGATGTAAA +TCCGTTTAATTCATATTTTGATCAATAGCCCATGCTTGCCAACTCTGAAGAAATTTAATT +TCCAGCAGTATTTTAAAGCTAGCCTGTTAACTTTTTCTGAATATTTAAAGTTCCTCTTTT +TTCTATGTCTGCACAAACTGCAGACCTGGGCTGGACCCACATACTCAAGAGTCCACCTTA +AGAAATTATTTTGATGTCCAAGACATCACTAAAATATTTCAGTTTAAAGATAACATGTGG +TGTTAATAGATTGTGGTGCTTTTACTATTTAAAGACAACTTTCATACTTCAGATGTTTTT +GAGAAGAGGGGAATGTGAGGGGAGGGGGCAGAACAGGGAGGAGTTTGAATGAATTACATT +CTTTATATCCATCCTGCTCATTTGGGGCATGTCTTTAAGAGAAGGCTGAAAGTTGTGAGA +GTATATTGTATACCGTAAGAGAATCAACTCTTCATCATGGATGGGATTGTGAAGGCTGAA +CTGTAAAAGTCAGCATTGACAGCATCCTCAATTAATAATTCTTGGTGACAGAATAATACA +GCTGGGCTGTTTTATAAATATAAACAATACCATTTTTAATTATTACATTAAAAATTTTAA +ATATATCTATGTGCCATGGCCTGGGAAGCCTGTTTTCTATTTTCATAAAAATTATTTTTA +CTGTATGAAAAGATTATGGGGTTTAGCTCAAAATATCTGTGGTCCTGATAAAATTGGATT +GGTAACTCTACCTCAGAAGGAAAATGGGAAAAAAAAATAGATGAGTCACAATTCAATACT +TCAAGCTCAGAAACTGTGCAGATCACTGAATTTTAGATTTATAAAGTCAGAGTTGGCATG +CGTTGTTTTTAATGATATGGAAGACCTTAAGAAAAAAACTTGGCTGAAGTTTAATCGTTG +GTCCAGCCATTTGAAAAAGGCAATAGTTCGAGGAGGTTTCCGAATTCGGCATTTGAAATT +CATTTTGTTCTCTCTTCTTCATTATTAGTGCATTTGGTGTGTGTATACTTGCACACAATT +CTGTTTGTGTACACACTGCTTGCTAAGCCCTAGTCAAGAGGCATCTTTTATAAAAGGTGT +AAAGAAATATCAAGGTTCTAAAATTCGGAAGAGTTTAGAATTTATTAGGAGTTTCCCAAG +TTGGGATGTTAGTCTTTAAATAAACTTCATGCACCTATTCCACTTAAGGTTTTGCACCTC +CTTTTTATTAGTGCAGTGCCATTTCTTCTGCTTGATTTTAGGTATGTTAATATTCCAGCC +TTGCTAGTTAGCATAAAGTGACAGGTGTGAGCCATGAGGAAATTTTCTGACTTAATTTTT +ATACAACTACATATGAGTTTTAGTGGAGAAAAAAAATTAGTCCCTTGTGCATATATAGTA +GTTAGGTAAATGATTTTTCTACCAACAGTGTACTCCATTCCTCATGTAGGTAAGTACAGA +AAAGGTTTTTAAATGTATTTTGTTAGCCAGTTAAAGTCTATGAATCTATCTGCAACCTTA +TTTAATCTGTCACTACAATAATTTTGTGGTTATGCTAAGAACCATGTATACTTTTAGGTA +TTCTTATTTTTGTCAATTTTTCTAGGTTAGCAAGGAGGCAGAAAAGCTTCACTGTTTCAT +ATTAAAATATAATTAGACTAAACTTAATTCTAGTATGAATTTCCAAAATCATTATCTATT +TATTTCATTTTTATTTAATTTTGTTTTTAGTTCATTTTTAAAAGTCCCTTGTTCAATTTA +ATTTATGTTCCTAAGAGTGGTTGGAGAACTTGGCCTTCATCTGATTTCAAAAACATTTTG +AGTTTCAAATGAAGTTAATGGTTTCAGTGTGATTCAGTCCTCAGACCTAATTGGGTTGAA +TAAAATCTAAAAGAATATACCCTTTTGGAGCATAACATTTTAATACCTTGAGGAATGTGG +CACTACCAAAAGAAGACTACTAACACGTCAGATGTTCACCTGGAAGCTTTAACAAGAAAT +TCGAACCACCCTTTTGGCCCCATTAATTGTAGCAAGTTTATTTCTCTATATTTTGTCATT +CAGTGAATTGAAGTCCTGTGGTATACTGCATTCATTAGAAGAAAAACGTTTTTAATGTCC +TTTTAATGATGGCCCAGAAAGCATTTGACACAGCAAGATGCATGTATTATTATATTGAGA +ATACAGAATAATAACAGTATCACTAAATTTAAGACCTCTTCCCAGTCTTGCTGTTCCTAG +CAAGAAGTTTGGCCCGTGACTGCACTTACTGTTTATGCTCATCAGAAACTGTCAATGTCT +GCTTTTCTTTAACTCTGCAGTCTGTAACATCATGCTGTTTATTAAAAAAAAAGAAAAATT +ACTTTGACTTGTGTCCAAACAATCCTTAGTGTACTACATAAGCAAAAAACTGTGATAATT +CTCTTTTGCCATTCCTTTTGAAAAGCAAGCCAGTGTTGCTAAAATCAAAATTTAGCTGAA +TTTGAGTTCTTTTCAGTAATGACTAAGAATACTTGATTGAAAATCTGAAACTATTATACC +TTAAAAGCCAATTTTTCTGCCCCAGTAAAGTGATGAATATTAAAGAAATGTATGTTTAAA +TATTTACTTCCTTTAAGCATAAAGAATTATATGCTTGTATTTTAAGAAATATATGTATGT +ATACATACATATGAATGTATGTATATGCAATAGGTAAGTGGACTTTTTTCCAAGTCATTT +GAAGATCAGAACCTAGAAATGAAGTTAGGCTACAAGCAAACTGGTTTTGCTTTCAGTTCT +CATAAACATTGCAAAAGGTAAGTGTGGGCTTTTCTTTGACCATTAATGCACATAGGCATT +AACAACTTAGTATTTCTGAGCAATTAAGCAAATAATTACTTACATTTTATTTATTTGCCA +AATGGTTTAAATAATTTTGAATTGACTTTGCTCTCCAGGGATAATATCTCTCTTTGCTGG +AATGATTCAGGTAGCTCCTATCTAAATGGAAAACTGTGGTAATTGAAACACACACTTTAC +ATTTTAAATTAGCAGTTTTGAATTTGTTAGGGAAAAAAATCCCAGCAATTGCATATTGTT +AGGTAGAAGTCAAATTTACAAAGAAACGGAATAGAGATGTGCCCTTGAGAAAAGTGTAGA +ATCTCAATGTGCAGATGATTTAAAATGTGCGTGCATATAAAATGTTCATGTGTACTTACA +TACTTTATTACAGAGAAGTCTTTGGTATACAAAATAGTTTACCACAACCTTTTAAACAGC +AGGTTCTGGGCCTTAAATGCGTATCACATTTAGCCAAGAGAACTCGGGTAGGGGCATGGA +AAATGAACTGCAGCTCCCTATCCCTAGCCTCTATACCAGCTGTTCAATGAAAAGTACCAA +GGCTCACTGAATGTTATAACCTAGCAGATTGTTACATAAATGATCTAACATTTTTGAGCA +CCGCTACTGGATGCTAGAAGCTAAGCTAAAGTGTTTCACATGCCCTACTTTGCTTATTCT +ATAAAATAACTGCGTGAAAGAACAGGTTATCCCCATTTTATAGATGAGAAAAGAAAGGTT +TACACAGGTTAGCTTATTTGCCCAAAGTTGTGATTATGGCCTACAAAGTCAAATAAATCC +TACTCTGAGACACATGTTCTTTCCACCATTGCACACTAGAAAGGAAAACACCAAGATTAT +TCATTACTGATCAAGTCAATATTGCTGTATTCAGCTAATTTAGTAATATGTGTCTTGAAA +TTAATTGCTAAAAGGGATTAAACTGACTTAGAATCAGTTTTTTGTTTGATTACATCTACA +TACAAAAGTAGCTTCAAATGTCTCATTCTACTGTCCATAATTTAAGATTTTTGAGTATAA +TACAATTTTAAAGATACTTTGAGGCACTTTGGAAAATCAGACCAAAATCTCTTTTCCACT +CACAGATTCGGCTTAATCAATCTGGAAAGCATTTGTTGAGAGCCTTATGACATCATTTAA +TAACCACGGTTGATTCATTAATTAAAGTACAGACAATTGTTGACTATCCATGTGGGACTT +TTCTATTAGGTTGACGCAAAAATAATTGCGGTTTTTCGCCATTAAAGGTTAACAGCGAAA +ACTGGAATTACTTTTGCACCAGCCTAATACGATGTGGATCATCTGAGATGAATGTTGAAA +TCCAGTATAGCTTCTTCATATTTCTGGCCCATTTTTCCCACCAGAAAGTGCACAAAGTGA +AATGAGCTTATGAAAAGCTTAATTAACTAGAAAAATGTTACTGAAAGAAAAATTACATGG +TACATGACAAGGCTAAATACTAGTAACTCTAAACTTAGTGAATTTTCTAGGCAGCAGCTT +TCCTCTGCTGTCTAGACTGGTAAAGAACAAACTAAGGCCAGGCGCAGTGGCTCATGCCTG +TAATCCCAGCACTTTGGGAGGCTGAGGCGGCCAAATCACCTGAGGTCAGGAGTTCAAGAC +CAGCCTGATCAACATGGTGAAACCCTGTCTACACTAAAAATATAAAAATTAGCTGGGCGT +GGTGGTGCACACCTGTAATCCCAGCTACTTAGGAAGCTGAAGCAGGAGAATTGCTTGAAC +CCAGGAGGCAGAGGTTGCAGTGAGCCAAGATCACGCCACTGTGCTCCAGCCTGGGCTACA +AGAGCAAAACTCCATCTCAAAAAGGAAAAAAAAGAAAAAAACTATAATAAATATGTTAGG +TCCATGTTTTCTTAAGTTTTCTACCGGATTTTTATCTTCGTATAGTGAACGAACTGTTAA +GAACTTTTTTATGAGAAATATTTTAGTATGACTATATTGCATAGAGTTAGGCTGATGGTT +CAGTGTTCAGTAGGTTAGATACCCTCATTGTTTATTTCCATATTGACTGGTTCTAGCTAG +AGCTGAAATTAGGCAAAGAATATCTTGAACTCATTTTGCTATACAGGAAAAAAGTGCTTC +CTTAGCTCATTTGGAAAGAGATTGAGATTAGAAAAGATGGTTAATTTGTATGTATTTATA +GAAATAAATAGAATACAAAATGAGGCTTTTAAATTTTTTCCCACATGAAAATATGATACT +TTAATCATTACGTTTTACATTGTTAGTTTGCAGACAGGCATAATTAGGTCCTCAGTTGCA +GAAATCACAGACATCTGAAGGCCAGCCCTTTAATTTGGCCACCGTCTTAAGATTTCTCTG +CTCCTTCCTTTGCTCCTCCTCCTACTGCACAGTTTGAACTGATGCTGTTCTATATAAGGT +ACTTTTCCACCTACCTCATCTCTGACTACAGTGCTATATTTTTCACACAGTAAGGACAGG +TGTTGTGTTAATCTCACCATGCCAACAATCAGGGCACCACCTAGCAGAGTCAGTGAAGGC +CAAAATAAACAGTGGAAGATAGCCATTTGGTCATACTTTTTTATAAGAATGACATCTTCA +GATTGGCTGGCTGGACTGTAGAAGCATGAAAAGGGGGTTCCATTTTTGTGATCGAAGAAT +TCTTTTATGTCCAGAGCACTGTTGAGCAAATCATTTCTATCTTGGTGGCACTTAGGTGTG +TAAAAGCACTAGGAATATGGAAGAGGGAAAAAGATAAAGGCACTGTCACCAATACCAAAT +ACTTAACAGTTTCTAATTATGAAATAGCTTCAGGCTGAAGTTATTAGTGGGCAGTTTCAA +TCTTAGAAGGTGGTAAAATATTACATAGCTCATGGGAAAGGGTTGATTGGAGGGCCACAG +TGAAATGGCCATTTCCAGTCATTAAGCAAGGATGTGGAAGAGAATTCTTAGTTTATATGA +CATTGCAGGAGAGTCAGTGACCAATTTCATAAGGAATATGACTCCTCCCTACATGCAGGT +TCTTGGACTCTTGGACAGTATGAATCCGTTTGTCCATTGAACAAAAATGTATTGAGCCTT +ACTATGAGCTTTCAACACCTAGTAATGCCTCTGTGGTCTCTGTCTTGATCTCCTGTAGCA +AAATATTACCCTGAAGAAAAGCACGTTGAGGCTTTTGCTCTAGACTCACAGACAGGGAGC +CCCACCTGGACTTTGGTTCCTGGGAGACAGAACCAGTGGAGAAGGGAGCTCTGTCAGCTG +GTGACTTTTTTCAAAAAAGCTTGAGGTTTATTACCATATCCATTAGGTACTTGAGGTACT +GTGCTAAAGGCCTACAAACTGTTTGAAATCTTAAAAATCATTGCATCCAAAATAGAAAAC +AAAAGTCATCAGATTGAAATTGATGCTTAAAGACAATAAAGTGTAACATGTCAACTAATC +TAACACAACTCAACTTTTATAGTTAGGTATAAATATAAATTTTAAATCATATGAAAGACT +ATACTTTCAGGGATCATTTCTATAATTCGTTAAATCATATGAACCCATTGTGTAACTTAT +TAAAATAAAAATAATCTTTACATTTATTTGATAAGAAAAAATTACTCGCTTGATTCAAGG +GAGACTGTGGTACACTGTAGCATATGTTATATGGCGCGGAGTGGAATCTCCAAAAGAAAG +ACTCCCCACAAATGACTACTCATTGGCTCAGCCTATAAATTCCAGACACCAAGTTGTGAA +ATTGGAATAATTTCTCTCCTTTCTATATACCCCATTTCTCCACCAAGAAGAAAGCTTCAT +TTATCCTGATTTGATCACTATAAAAATGTTCACTCCAAAAAAATAGATTTATCCCTAAAG +ACAGCCCTGGGTTATTTATGTACCCTGCTAGGGACAGTCTGGCAGGGAAAGGTTGCTGTC +ATAAGAACTCTTTAAACTTTACAATACCTTGGGATTTATCTGGACAGCCTCTTCATTATA +ATGTAGGAGAGCTTTCTGAGCTGAATGGGTGAGGTTCACAAACACCCGAAGACACGAGTA +CTTCCCGTGACCACGGCAGTGCACACCACAGGTGAAGGCACAGTCCAGCCAGTCGTCCAT +GATATCTGTGTGGATGGCAGTGCAGGTTGATTCTTCTCTCCGAATGCTTCAATTTGAAAA +AAAAAAAAATGTTCTTCACTTACTAGAAAATTTCGTTCTACATTTTGGTGCGGTTATGAG +CTTATGTACACAATTAGCTGGGATTACAGGCGCTCAGCTGCCATGTCCAGCTAATTTTTG +TATTTTTAGTAGAGACAGGGTGTTGGCCAGGCTCGTCTCCAACTCCTGACCTCAAGTGAT +CCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCACCTGGCCC +AAATACTATGTTTTATCAATTCTAAAGTGCACTTTAGTATTTACATTTTAATATAACTAA +AATCAATATGTATTTTGCAATCAATGGCATCTTGCTATTATTTGAAAACATTTCTTTAAT +AGTCTGTAAAATAATGGAACATGCCCAGATGCAGTGGCTTATGCCTGTAATCCCAGCACT +TTGAAGGGTCAAGATAGGAGGATCGCTTGAGCCCAGGAGCTGGAGACCAGCCTGGCCAAT +ATAGTGACAGAATAAATAAATAAGTAAATAAAATAATGGAAAATCTCACAAATGGTGATG +TTTTAGGTTCGACAAAATACATTAACTAGCCCATTTAGTTTTCTGAAATTATTTTGATGT +TATTGCTTACAATATTTGTTCTGTGGTACACAACCATAGGATTAATAATATTGATGAAAA +TAATAAAAGAATAATAAGCATGTATTGAGCTCTTCCTGTGTGAAGTTCTGGACAAATCCT +CATAAAGCCTTAAAAGGCAGATACTAGGCTGGGCACGGTGGCTCATGCCTGTAATCCCAG +CACTTTGGGAGGCCGAGGCAGGCAGATCACGCGGTCAGGAGATTGAGACCATCCTGGCTA +ACATGATGAAACACGGTCTCTACTAAAAATACAAAAAATTAGCCAGGCATGGTGGCACGT +GCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAAAATCGCTTGAACCTGGGAGGCT +GAGGTTGCAGTGAGCCAAGATCGCACCACTGCTCTCCAGCCTGGGCGACAGAGCAAGACT +CTGTCTTAAAAAAAAAAAAAAAAAAAAGAAAGAAACAGGCAGATACTAGCCCAGGCACGG +TGGCTCATGCCTGTAATCCCACACCTTCGAAGGCCCAGGCGGGTGGATTATCTGAGGTCA +GGAGTTTGAGACCAGCCTGACCAACATTGTGAAACCCTGTCTCTACTAAAAATACAAAAA +TATTAGCCAGGTGTGGTGACAGGTGCCTGTAATTCCAGCTACTCAGGAGGCTAAGGCAGG +AGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCTGAGATTGTGCCACTTTACTC +CAGCCTAGGTGACAGAGGAAGACTCTGTCTCAAAAAAAACAAACAAACAACAACAACAAC +ATCAAAAAGAAACCTATAGTAATAAAATTGAAATAGAAGGAGGTTTGCAATCAAAATGAC +TGACTAGGAATGAAATAGGAAACATAATATTTTGCATCTGCATAGGGAAGTCTGAGATTG +GCTGATCTTGTTCTCTTCTGTAGGGGAAATACTAGTCCAGAACTTGGGGTGCCTGCCAAG +AGGGGAGCAGCCACAGTAGGAAAGGGGGACTCTGGAATGCTAGGGTTCTGGGGTCTGTGG +ACACAGGAGGCAGAGGACATGTGTTAAGATGTTTTAAGAAATGAATGTTGAACTGGATAT +GAAAATATTTTTCAGCCGGGCGCAGTGGCTCACGTCTGTAATCCCAGTACTTTGGGAGGC +TGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACC +CCGTCCGTCTCTACTGAAAATACAAAAAGTTAGCCAGGCGTGGTGGCGGAGGCCTGTAAT +CCCAGTTACTCTGGCGGCTGAAGCAGGAGAATGGCGTGAACCTGGGAGACGGAGCTTGCA +GTGAGCCGAGATTGCACCAGTGCACTCTAGCCTGGGCGACAGAGGGAGACTCCATCTAAA +AAAAAAAAAAAAAGAAAGAAAATATTTTTCACTATAGAGAGGCATATGTCCCCTGAACTT +GCCGGGATCCACCTTTCCTGCTGGTGCATTCTGTGAGTTAGAAGAAAACTTCCAAAGAGC +CATTTTTTCCACCCTGTCTACTGTATAAAATTGCTTCTCAAACATGTGCTGCATTGCAGA +GGATTACCATTGTTTTGCTAACCAGCGTCTGGTCTTTCTTATGTGGCGCTGCAATTACTA +GTGTCAAACCCTGTTGGTAATACCCAGAGGACGGTGTCTGAAGTCTTTACTCAATATTCA +CATTTGGCCGGGTGTGGTGGCTCACACCTGTAATCCCAGCACTTTCGGAAGCAGAGGCAG +GCGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCATCT +CTACTAAAAATACAAAAATTAGCCGGGTATGGTGGCGGGTGCCTGTAATCTCAGCTACTA +GGGAGGCTGAGACAGGAGAATCACTTGAACCCAGGAGGTGGAGGTTACAGTGAGCCAAGA +TTGTGCCACTGTACTCCAGCCTGGGGGAAAATTCACATTTGTAGAGAGTTTAAATTCTTT +TTTGATACGGAGTCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCAGGGTCTTGACTCA +CTACAACCTCTGCCTCCCAGGCTCAAGGGATTCTCCTGCTTTAGCCTCCTGAGTAGTTGG +GATTACAGGCACCCACCAAAACACCTGGGCAATTTTTGTATTTTTATTAGAGACAGGGTT +TCACCATGTTGTCCAGGCTGATCTGAAACTCCTGACCTCAGGTGATCTGCCTGCCCTGGC +CTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCACGCCCGGCCGAGAGTTTAAATTCT +TAAGTCCTACACTCCAATGTGTGGGAAGTATTCGTGCTATGCTTTTATAACTAAATCATC +TCAGTATTTCTATTTCTAGCCCCCTTTTTCTGCCTGATGGTAAGATACTTAATCTAGTCA +ATTCCAGGTAAACTTTGGCCTTTTATGATTTTTCCTGATCAGGCCAAACCTCAACCAAGT +CCCTTCTTGATCTTCTCCTTCACCTCCTTCTCTCATTCACCCGACAATTAGCCTCCAGTC +CACGGGCTGATGCAGCATCTTGGTGTCCTGTGGTCTGAGGTCATTTTCTGTCTTTCTCAA +GCCTCAGCTAAAGTTTACAATCCTACCTTTTCTCATGACCTTGAAATGCCCTAAGGTTCA +GGGGCTTCATGGTTGCTGCTTCATGGGGGAACCTGGCTGTTCTCTGAGGCTGCTCGGCCG +CGAACACCCCATCAACTACCCGGGGCCCATCTACGCCCGAGGCCTCAGCCATTCCTGCTC +TACAGCTCTGCTGTCCCATTGGCACAGGGAACTTCTTGGGGCCCCAGGGTTCCAGATTGG +AAGCAGAGAATCTCCTCTGTTCTCAGACCCCCAAACTTTGTTGTGGATTCTAATTGTCCT +TTCCCCCATCTCACTCCTTGGAACCCACTGGGAGGTGAGTAGAATCCCTGTCAGAGATTC +TACCACCATCTCCCTCATTCTTACCCTAACTTTCTTCCTCTTCCTCCCTAGTTAGGAAAG +AGGATCTTTAGCCTGCGGCGGGGGGGTGGGGGTGGGGATGCTTGATGTTTCAGGGGAAAA +GGTGACTCAGCTACTTTTGGAATATCTGTCATACCTGTCTACTGGTGCAATGAGCTGGGA +TCACACCACTACACTCCAGCCTGGGTGACAGAGCAAGATTCCATCTCAAAAATAAATAAA +TAAATAAATAAAGACTCTGGAGAAACAACTCAATACACATGAGAAGAGGCTGGCCCATGT +AGGGAAAGGACTGGCAAACTATGACAACTCTTTTCTGTTGTTTTGTTTTCAATAGTCTCT +TCACAGTTCTTTTCACAGTTTGGAATTGATACCTTTTTCTCTTCATCAGAACTCCAATGT +TTTTGTAGATTGAAGTCTTTTTTTTTTTTTTTCTTGAGAAAGGGTCTCACTTTGTCACCC +AGGCTGGAGTGCAGTGGACCAATCACTGCTCACTGCAGCCTCGACTTCCTGGGCTCAAGA +AATCCTTCCACCTCAGCCCCCCAGTAGCTAGGACTACAGGTGTTCACCACCATGCCCAGT +TAATTTTTATTTTTTAATGTATTATTATTATTATTATTATTATTATTATTATTATTATTA +TTATTTTGAGATGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGCGGCACCATCTCGG +CTCACTGCAACCTCTGCCTCCTGGGTTCAAGAGATTCTCTTGCCTCAGCCTTCCAAGTAA +GTGGGACTACAGGTGCATGCCCCCACACCTGGGTAATTTATTTTTTTGTAGAAAAGGGGT +ATCAGTGTGCTGTCCAGGCTGGTCTCAAACTCCTAACCTCGAGTGATCTGCCTGCCTTGG +CCTTCCAAACTACTGGGATTAGAGGTAATGAGTCACCATGACTGGCCTACGTATAGCCCA +AATGGATGAGCAGTTCCCAAGGCTCATTCCCAGCCTCCACTATCCAAGTCAGCCTCTCAT +CTCCTTCATTTCCCAGGACTTAGTTCTCATTTTCCTCCCCTGTTTTCTCCGGATTGTGGC +TATTGTTCCCTGGTTGCTAGATCAACCTGGAGCACAGTAAAGCAGTGTCACAAAGCTGGA +AGGGGTCTGGGATGAGTCCACCAGCTACAAGTTCTTATAGAAAACGTACTCCGGGGATGG +CCGGGCCCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATC +CCCTGAGGTTGGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCCGTCTCTACTAA +AAATACAAAATTAGCTGGGTGTGGTGGCACATGCCTGTAATCCCAGCTACTAGGGAGGCT +GAGGCAGGGGAATCGCTTGAACCTGGGAGGCGGAGGTTGCGGTGAGCCAAGATTATGCCA +TTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAAAAAAGA +AAATGTACTCCAGGAATTGTCATTTCTGAAATTCAACAGCTTCTGGAATTGAAGCAAACA +GCTCATCTTGGAAGAGAAATATGTAGCCAACTCCAAAGCCAAAGCCTTTGAGTATTGAGA +CCTAGCATGCTAGGAGACCTTGATCCTGTAACCTCAGAAGAAGAATCTGGATCTGGCCAA +ATTGAGGTCAAATTCTGCTCAACTTCTCCATAGTCAGTAGGAGAAAAAAACCAACTTGAT +GTTTGAGTCATATGTTTTGACAACTAAAGAGGACACTTATGCTGGGGTCGGTGGTTCATG +CCTGTAATCCCAGCACTTTGGGAGGTCGAGGCGGGTGAATCATTTGAGGTCAGGGGTTCG +AGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACAAAAAATTCAAAAAAATTGGCT +GGGGGCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGAGATGGGTGGATCAC +GAGGTCAGGAGTTCAAGACCAGCCTGGCCATTATGGTGAGACCCTGTCTCTACTAAAAAT +ACAAAAATGATCCGGGCATGGTGGCGCACGCCTGTGGTCCCAGCTACTCAGGAGGCTGAG +ACAGAAGAATCTCTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACGCCACTG +CACTCCAGGCTGGGTGACAGAGTGAGATGTCATCTCAAAAAATAAATAAATAAATAAATA +AAATTAGTCTGACTTAGTGGCGGGCCCCTGTAATCCCAGCTACTGGGAGGCTGAGGCAGG +AGAATCACTTGAACCCGGGAGGTGGATGCAGTGAGCCAAGATCATGCCACTGCACTCTAG +CCTGGGCGAGTGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAGACACTTAAAGATG +ACATTAAAGAGGATACTTAGATTCTAGACAAAATCAAGATATAGCAAATTGGGGTGGGAC +ACACCTGTAATCTCAGCATTTGGGGAGGCCGAGGCAGGTGGATCACCTGAGGTCCAAAGT +TTGAGACCACCCTGACCAACATGGCGAAACCCCGTCTCTACTAAAAATACAAAAATTAGC +CAGGCATGGTGGTGGACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCA +TTTGAGCCCAGGAGGCAGAGGTTGCAGTGAGCTGAGACTGCACTGCTGCACTGGTGCCTG +GGCCACACCAGTCACTATGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAATAAATAAAT +AAATAAATAAAATTTTGTTTTGCTGTGTTGCGGCTAATATGCGTGCTATAAGACAATGGT +TTCTTGAGTCTCATTCTCTCTGCATATGCCTAAAGCTTTTTTATTTTTATGATTCTAAAA +GATTGTACCTTCTCATCTCCTAGATTCTGTCCCATAGGTTCTGATTTTTCCTAGAGTAAC +TTGGAAGTTAAAAAAGTGGAAAAAGCTTTGCGTATTAGGTGCCAAACCCACTCAGCTCTG +CTCAAACCCCTTCTTTAATGCCCAAGGTTGTCCAATCCTAGCCCTTCCCCCTACCCTCAG +CTTTCTCCTCACCTACACAGCAACCTTAGTATAGTCCTAAAGTATGTGTTCTTATCTTCT +GTTATCTATGCCAAGGATGTTTGCTGGTTTTGTTTTGTTTTGTTGAGACAGGGTCTTGCT +CTGTCTCTTAGGCTGGAGTGCAGTGGCACAATCACAGCTCACTGCAACCTCGATCTCCTG +GGCTTAAGTGATCCCCCCACTCAGCCTCCTGAGTAGCTGGGACTACAGGTATGCATCACC +ACGCCTGGCTAATTTTTTTTTTTTTTTTTTTTTTTGAGGCAGAGTTTTGCTCTTGTTGCC +CAGGCTGGGGTACAATAGTGTCATCTCAGCTCACCACAACCTCTGCCTCCCAGGTTCAAG +CAATTCTCCTGCCTCAGCCTCTCAAATAGCTGGGATTACAGGCATGTGCCATCACATCCG +GCTACTGTTTTGTATTTTTAGTAGAGATGGGGTTTCTCCACGTTGGCCAGGCTGGTCTTG +AACTCCTGACCTCAGCTGATCCACCCACCTTGGGCTCCCAAAGTGCTGGGATTAAAGGCT +TGAGCCACCATGCCCGGCCCATGCCTGGCTAATTTTTTTTAATTTTTATTTTTGTAGAGA +TAGGGTCTCACTATGTTGTCCAGGCTAGTCTTGAACTCCTGGACTCAAGCGATCTTCCTG +TCTCAGCCTCCCAAAGTGCAGGAATTATAGGCATGAGCCACTTTGCCAGGCAAGGATTTT +TTTCTTTTTAAGTTACATTTCTGCCTGCCACCACAGCAGCTCTTTCTCCTGCTCTCTCTC +TCTCTCTGTGCTTTAAGATGATAGTCCCTTCTTTTTTTTCAAATAACCACAACAGGAAGG +ACTGACCACTCTTGTAAGCTGCAACTGATGTTTTCAGACTCCTAAAGTGACATCTAGACA +TAAGTCCATATATGTCAGAATATCATGCAGGGAATGCTCAAATAGTTGGGAAGAGATTGC +TGCACTGTGTTTTGCACGCCCAAAGCCCACATAGGTACTCAGTTTAAAAATCTTAATAGA +ATTGAATCCTGCTCTTATCATAGGAAAGGAAGAGCATCTGATAGAAACACAAAATGAAAA +GGTCAAGAACTGGCTGGGCACAGTGGCTCTCGCCTGTAATCCCAGCACTTTGGGAGGCTG +AGGCGGGAGGATCATGAGGTCAGGAGTTCGAGACCAGCCTGGTCAATATGGTGAAACCCC +GTCTCTACTAAAAATACAAAAAATAGCTGGGCGTGGTGGCGCGCACCTGTAGTCCCAGCT +ATTCAGGAGGCTGAGGCAGGAAAATCGCTTGAACCTGGGAGGCGGAGGTTGCAGTGAGCC +AAGATCACGCCACTGCACACCAGCCTGGGCAACAGAGCAAGACTCCGTCTCTCAAAAAAA +AAAAACAAAAAAAGTCGAGAACTGGAAAGGAACTAAGCGCATGAAAAGAAATTTTATGTT +CCTTCATGTTTTTATTTAAAGAAAGTGAATCAAGTACCAAACACGGAATAAAGGCAAACA +TTCATTTTTGGGGTGATTGTTCCCTTCTTGGCAATCCCTGTTTTATTGAGGGTATCACTA +GTTATTCAATCCAAGGATTTTTTTTGTTTCCACAGGAGGTGGGTGTTTCTTTGTCTTCTT +AGAGTCAGGATTCCAGATCTCCTGATGTGTGGGACTTTTCTTGGCCACTACGATTTCATC +TACAGTCACGAGCTGTAGCACCACCTCAGCCACTGCTCGAAATCCTTGGGCTTTGACTAT +TAGGGTGTCCCACACCCCTTCCTGGGCCACATTTATTATCCCTTCAGTTCCCACACCCAT +TAGGAGGTTCCCACCTTGGTGCACTCCACTCATTTCTGCCATCACGTCTGAGACAGCTAA +GCCTGCATTCTCTGCCAAAGTTTTAGGAAGATACTTCAGGGCCCAGGCAAATGCTAGGAA +TGCAGGCCCACTGGGCCCTTCCAATCTGCTTCCTTTATCAGAAAGCATTTTTGCCAAAGC +CATTTCTGTGGCCCCAGCTCCTGGAATCAGTCTGGGATCTTGACATAGCTGGAAATAGGC +ATCAATGCCGTGGTAGACGGCCTGCTCTGCACTCCGCAGCCCCTGGGTGGTGGCTCCCCT +GAGAACCACAGTGAGGGCAGGTGTGCCTGTACATTCCCATTCAAATACCACAGCCAAACC +ATCTCCCAGCTCCTGCCTGTAAACCCTCTGGCACTTGCCTGGCCTCTGGGGAGGGAGCAG +ACGAGGCAGCAGAGGTGTGTCCAACACCTCACTCAGGTAAATGATCTCCATCCAAGACCT +AGCTTGAATCACCACGATGCCATACTTGTCCGCCAGTGTGAGGGTCTCCTCGTCGACCTC +CCCCAACACCACTGCCACATTAATTCCTGCAGCTGCTAGCTGGCCTACTTGCTTTTCTAG +TAATTGATCGCTTCCTTTACTAAATTGAGCTAGATCAGCAGGACTAGAAAGACGGGCCGT +TGCTGGTGCATTTGGATGGGCAGGACCAAAGGGGCAAGCAAAGAGAGCCACCCTGGCACC +ACTTAACACTGTGGCCATTTGCCCACAGAGCTTCCCAGATATTGCTAACCCCGGGAGGAG +GCAGGAATCCTCCAGTGTCCCCCCGGGCAGCGCGCACACCCCAACACGCTCAGGCTTGAA +GCTGCCGTCTAGTTCCTTGATAGCCCAGCAGGCGTGGGCCACCAGCTTGGTCAAGTGGTC +CATGGGGGACAGGGTGTGGGTATTCATCACAGAATGGAGGGCCCAGGATGGATCTTCCAA +AGGCCCCAGAGATTGGATGGCCAGGGAGGGCAGTGTGGCCAGGACCTCTGCAGTGGCCGT +GGCGTAGGCCTCCCGGAGCTGCGGGCGAGGCAGGCCAGCCTTCAGCAGCTGCTCTGCCTG +TTCCAGCAAGGCTTCCGTCAGCAGAACCACGAAGGCTGTGCCGTCCCCACTATTCTCTGC +CTGGGTTTGTCCTGCTTCCCGGAGGAGCCATGCTGCTGGGTGCTCCAGCTCCAGGGCCCT +GAGGATGGCAGTGGCACACCCCGTGCACACTGTTTCTCCTTTCATGGTCACCAGGAACTT +CTGCCGGCCGTGGGGGCCATAGCAAGGCCGGATGACACTGGCCAGGGTCTGGACTGCAGC +CAAGCTGCTCAGCAGGTGGGGCTCCTCCTCTTCTGGACTCCTCGGGCTCTCCCTTGGGTT +CAGTGCCAGCCGCTGGGGCAGCTCCAGGGCTGAAGGGACTGTGCTGTCCATGGCCCGCAG +AGAGAGGAGAGGCCACCGTGGGTTGCAGAGATGCTCTAGAAACAGCAGCTGGGGCACTCC +TGACACCGATCGTTGAAAGTACTCAAGAGGTCAGTGGAAGCAAGGAGCCAAATGCCCATT +GATTGGTATCTGAAGACATCAGCACGGACCAGCACTCCACTGTGGGTCCAAGGATGAGCT +CCAAAGAGCCCAGTCCTAAAGCCACCCCAGGGTTGATTCTGTAAAGGAACTGGGTCTTGG +GGCCTCTCAACCTTGGTGGCTGAAATGGGATCTTTAACTGATGAAGTCACAAAGTGGAAA +ATGGAACCAGGATAGAGAATGAGGTCACAGAAGGCTGGTTAGAACTGAGGAGGCCCTACC +AGCAGGCAAAAGTCAGGCCTTGTCCAGCAATGGAGGTACATGCACCTCTGCACCAGGTTT +GAGACTTGTTTAAACGTAAGAGACAATGAGGAGGAGATCAAGTGAAAAACTACCCATTTC +ACCCTATCTGGAGTGCAGGGGCATAACCATGGTTCACTGCAGGCCCAGCTCCCTGGTCTC +AAGCAGTCCTCCTGCTCAGGTTCCCAAGTACCTGGGACTACAGGCACACACCACCACACC +TAGCTAGTTTTTTTATTTTTTGTAGAGACAGTGTTTCTGTCTGTTGTCCAGGCAGGTCTC +GAATTCCTAGCCTCAAGAGAGCCTTCCACCTTGGCCTCCCAAAGTGCTAGGACTACAGGT +GTGAGCCACCACCTCACCCACCCTTTTTTTTTTTTTTTTTTTGAGACAGAGTCACACTCT +GTTGCCCAGGCTGGAGTGCAGTGGTACAATCTTAGCTCACTGCAACCTCCACCTCCCAGG +TTCAAGCAGTTCTCCTGCCTCAGCCTCTCAGTAGCTGGGATTACAGGTGCCAGCCACCAC +GCCCGGCTAATTTTTTATATTTTTAGTAGAGATAGGGGGATTTCACCATGTTGGCCATGG +TTGGCCAGGTTAGTCTCAAACTCCTGGCCTCAAGTGATCCGCCCACCTCGGCCTCCAAAA +GTGCTGGGATTACAGGTGTGAGCCACTGCACCTGGCCTTTTTTTTTTATTTGAGAAGGAA +CTGAGAGATGATGTCTGTGTTTTGTTTTGTTTTGGTGTTACTTTCTCTTGCAGTACTGTG +TAATATTAGCCATGTTTTGCTGTCTGCCTTTGACTTTTTGGGTATCTTATCAGTTTGTGC +TTGTGTATCAGGTTTCTTAGGGTGTCTGTTGGTCTTTCAGGGTGCAGGTGTGGGAGGCTG +CACAGCGTGCATGCCTGTGCCACGACTCCCAACTCTGCCTCCCTGGCAGAGGCAGGGCAA +GACAAGTGGGGAAGGATGCTGACAGCTCACAGACAAATAGAAGTGAACCCAGAGGGGTGA +AAAGCAACCAGCCTCCCAGCGGTCAGGGAGGTAGAAGCCTAAATGGGGTCCTGAGATTTA +AATGCGAATCGCCTTCCCATCCTAACCTTCAATGCTTACAATTTAAGTCTCTTTTTTTCA +TTCTCTCTCCTTTCCTCACTTGTCTCCTCTTTCCTCCTATAGAGCCTACTCGGGTAATGA +TGCTTCTGCTTTAGTTTAACACATATTTAGTCTGGGCGTGGTGGCTCATGCATGTAATCC +CTGCACGTTGGGAGGCTGAGGCGGGAGGATTGCTTAAGCTCAGGAGGTTGAGGCTTCAGT +GAGCCATGATTGCACCACTGCATTCCAGCTAGGGCAACAGAGTGAGACTTGTCTCAAAAA +AAATAGGGGAAAGGTCATTTGGAATCCTAGTCCAGAGATAACCATTGTTTACAACTTGAT +GAACATTACTACTTTGCACATATTATATGCATACATAATTATAGATTTACACCATTTTAC +ATAAGATTATGATACATATATGCTATTCTGTGATCATTTCCCCCTCAACATTATCTTGGC +TCAGAGAAATGTTTCTTTTTTTGTTTGGACATGGAGTTTCGGAGTTTCGCTCTTGTCGCC +CAGGCTGGAGTACAATGGCGCAATCTCGGCTCACCCTCGGCTCACCACAGCCTCTGCCTC +CCGGGTTCAAGCAATTCTCTTGCCTCAGCCTCCTGAGTAGCTGGGACTGAGTAGCCATGT +GCCACCATGCCCGGCTAATTTTGTGTTTTTAGTAGAGACAGGGTTTCTCCATGTTAGTCA +GGCTGGTCTCAAACTCCTGACCTCAGGGGATCCACCCGCCTCGGCCTCCCAAAAGTGCTG +GGATTACAGGCGTGTGCCACTGTGCCTGGTCTGTGAGCCACTGTGCCCGGCCTGAGAAAT +GTTTCTTTTTTTCTTTCTTTTTTTTTTTTTAAGCAGAAACACATTCATTTATTAACCAAA +GGGATGATCCTAATGAATCCAACACACTTTGAAATAGCTGCATGTAAAATGTTTGTGATA +AAGATAATTGAACACAGTAATGAAAAAAAAAAAAGAAAGAAAGAAACGGTATGGAGATTT +GCTCATTGAACTGAGCTTGGTCATTCTCTTAGTTAACTCCTGTCCAAAGTGATGATGGAA +TCTTTATTGTACTTTTTCATAGATCCGAGTACAGGCGACATGGTTCATGACACAGTCCAC +CACTAATTTCCCATCTTTCAATGTTCTTGTTATTGTGCTTTCCTTCCCATCCCACTCCTG +ATGCTGAACCAATGCACCATCTGTAAAGTTGCACACAGTCTGAGTTTTTCTGCCATCAGC +TGTGGTTTCTTCAAACTTCTCTCCCAGGGTACAAGAAAACTGTGTTGTTTTCAAAGTGCT +CTCAGTTTTTATGGTGAGGTTTTTGCCATCACAAGTGATGATACAATCTGGCTTGGCCAT +TGCGCCCATTTTTTGCAAAGCTATTTCCTCCTAGCTCCTTCATGTATTCATCAAAGCCTT +CGCTGTCCACCAGGCGCCATCTTCCTTCCAGCTGCTGAACTGTGGCCATGGTGGGTGCAG +GGGGGCTGGTGTGCAGAGCAGGGTCTGCGTCGGCGTGGCAGCGTGCTGTCGAGAAATGTT +TCTAAGGAGATCTTATTTGGTCTGAGAACCATGAATGATTATTTTGAGCACTTTTGATTC +TGGAGACTCCATTTGGATCAGGCATGGTCCTCCAAATTCAGGCTTCTGAAAGCCTGTACC +TCAGAGTAGGCTTGATGTTCCATAAAAGATGTGGTTATGAGTGCAAAGATGACTTGCCTG +TATTGTTATACAAATGTAAAATGTAACAATCAACAAAAATGTAGCAAAGTATGCATGTAT +ACATTTTCTCTAAAGATACAGTTTCTTTTTTGAAAAAATAAACACATTAGGCAGGTGTGA +TGGCGGGTGCCTGTTATCCCAGCTACTCCGGAGGCTAAGGCACGAGAATCTCTTGAACCT +GGGAGGTGGACAAATTGCAGTGAGCCAAGATTGCGCCACTATACTCCAGCCTGGGCAATA +GAGCGAGACTCAGTCTCAAAAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAA +TAAACACTACCGGCCAGTGGCCATGGCTCGAGCCTATAATCCCAGCACTTTGGGAGGCCT +GAGCCAGGTGGAGTTCAGGCATTCAAGACCAGCTTGGGCAATATGACAAGACCCCTGTCT +CTACTAAAAATACAAAACAATAGCCGGCCGTGGTGGTGTGTGCCTGTAGTCAGCTGCTTG +GGAGGCTGAGGTGGGAGGATTGCTTGAGCCCTGAAGGTGGAAGTTGCAGTGAGCTGAGAT +AGTGCCATTGCACTCCAGCCTGGGTGACAGAGTGAGACCCTGTCTCAAAAAATAAAATAA +AATAAACACTCCTATAAAGGATCCTCTTAGCTCTTTTTCTAACACCTAATCTACATTTTC +ATATTCATTTCAGTTACCCTACAACTGTTCACTGAGCTGCTGTTGAATAGGGGAAATAAG +GCAGATAACTACTGCCATCTCCGCTGGAGGGACGATACAGACATTAATCTGGGCACTTTG +ATTACAGGCAATGAGAGCTGTGAGTGGGGAAAGCACAAGGTTGGCAGAAGCATTTAGGGG +GACACAGCCATTCTCACGGAGGGCAGAGGTCTAAAGCAAGAGCTGAATAAAAAGTAGGAA +CTGGCCTCGTGGAAAGGGGAAGGGTGATGGGACAGCCTGGTGGTTTGTAGCCCACTGGAA +GGAGTTCTGAAAACTGGTGGTCAGGTGAGAAGGAAAGCTGGGGAAGAGATGAGCACGTTC +GCCAGAGGGTAGCAGGGGCTCTCCGGACCTAGTGAGTCAAGCCAAGGAATTAAGGCTTCA +GCCTGCAGGGTGATGAATAGGGCTGTCTATTCCATTTCTTCCTTCTTTCTTTCTTTTCTT +TCTTTTTTTGAGACAGCGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGGCACGATCCT +GGCTCACTGCAACCTCTGCCTCCCTGATTCAAGCAATTCTCCTGCTTCAGCCTCCAGAAT +AGCCGGGATTACGGGTGCCTGCTACCACGCCTGGCTAATTTTGTATTTTTAGTAGAGGCG +AGGTTTCACCATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCAAGTGATCTGCCTACC +TCGGCCTCCCAAAGTGCTGGGATTACAGGTGTAAACCACCGTGCCTGGCCTGAAAATTTC +TAGTTTATGATACTTGCCAGCAGAATGTGTTCTGTCACCCTCTTCTGAATAGATATGGTT +GTCTGCTATGACTTCTCCCACTGCTGCCCTTCCCCCTGAATCCACAGATGCATTTCTTTT +AAAACTATGATCTTGTACACAATGGATGTAAATATTTAATCTTTCTATTTGTATGTTTTT +CCATGTTTCTTTTCTTTCTTTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTGGAGGTGGTG +TCTGCCTCTATTGCCCACAGGCTGGAGTGCACTGGTACAATCTCGGCTCACTGCACCCTC +CGCCTCCTAGGTTCAAGGGATTCTGCTGCCTGAGCCTCCTGAGTAGCTGGGACTACAGGT +GTGCACCACCACGCCCGGCTAGTTTTTATATTTTTAACAGAGACAGGGTTTCACCATATT +GGCCAGGCTGGTCTCGAACTCCTGACCTCGTGATCCTCTCACCTCGTCCTCCCAAAGTGC +TGGGATTACAGGCATGAGCCACCGTGCCCGGCCTCCATGTTTATTTTCTAGTTGCTTACT +TGTCCTTTTGTGTTTATCCTTGTTAACTACTACTGCCAGGCTTAAAGTATAGACCCCTAG +AGGGCAAGATTTGTATCTATATAAAATGTACTGCAAAACATCTACTTAAGCCTCACATTC +TTAAACACAAATTACTTTTGAAGATGACTGTTCTGTTTGTTTCCTTCCTGGTTTCTTCCT +TTAACTTTTCCACCAAACAGGTACATGATATACTTTACTGAAATAACTTATATAGCAATA +TGAATTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGCCCAGGCTAGAGTGCAATGGCGT +GATCTTGGCTCACTGCAACCTCCGCCTCCTGGGTTCAAACAATTCTCCTGTCTCAGCCTC +CAGAATAGCGGGGATTACAGGCGCACACCACCATGCCAGGCTAATTTTTGTATTTTTAGT +AGAGACGGGGGTTCACCATGTTGGCCACGCTGGTCTCGAACTCCTGACCTCAGGTGATCC +GCCTGCCTTGGCCTCCCAAAGTGCTGGGACTACAGGCATGAGCCACCGTGCCCGGCAAAT +TTGAGGTGGAGGTTGCAGTGAGCTGAGATCGCATCACTGCACTCTAGCCTAGGTGACAGA +GCAAGACTGTCTCCCACTTCAGCCTCCCAAGTAGCTGGGACTACAAGCATGTGCCACCAG +ACCTGGTTAATTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCCATCACCCAGGCT +GGAGTGCAGTGGCGCGATCTCAGCTCACTGCAAGCTCCCCCTCCCGGGTACACGCCACTC +TCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCACCTGCCAGCACGCCCGGCTAAC +TTTTTGCATTTTTAGTAGAGACAGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCC +TGACCTCATGATCCACCTGCCTTGGCCTCTCAAAGTGCTGGGATTATAGGCGTGAGCCAC +CGCGCCCAGCCAGGCCTGGTTAATTTTCTTTGGTATTTTTTTGTAGAGACGGAGGTCTCA +CTATGTTGCCCAGGCTGGTCTCGAACTCCTGAGCTCAAGTGATCCACCTGCCTTGGCCTT +CCAAAGTGCTAGGATTACAGGCATGAGCCACGGTGCCCAGCCTACAGTGCAACTTTAATA +ATAACAATATGAACACAAAAATTCTAAGATCTAAAATTTAAGCTTTCAGTAGTCCTTCTA +TAACTGTGAAAGTTTGGTTCCTAAAAAGCCCTGAGGAATTTATGGGAAAACAAGAGAGAC +AACATTTAGTAGTGAACCTGTGCATTCTAAATAAAGACAATATCAATGACGTGTTATAGG +TCTTCAATTAGTAAGAATGAATATTGGACTATGAATTTTTATTCACTGTCACTTGTTTGC +TAGATGCTTTGAGAATCTTCCTTGCCTATATTTTCCTGAGATGTTGGTTTTTCTTTGTCA +CAGATAACAATGCTCATTCCCTCCCCATTAAAAACTAAATATATATATATATATATATAT +GATTAAACGATTACTACATGTGCTTTGAAATATTCAAATATTTTAGACAGTAAAAGTCCC +TTGTAATTCAACCCTTTGCAGATGATTGGTTAACAGGTTAGTACACATCTACCTAAATTT +AAAATCCCATATTTAACATGTATACTTATTAGAAAGTACACATTCTAATATTTTTCTATT +GTATTTGGTACTATTTTCAGATGCTCCTGCCTTTTTCTTTCGTAATTTTGAAGGACCTCA +GCTCCCTGCCTCCTAGATTTTTGCTACTATGGTCTCAGAGCTGTGTAATTTGGATGACTG +AGATGGAAAAACCTCTGGAAAACCTTTATTTATGTTGAATAAGTATTCCTTGAATCCTTC +CTCAGCATCCTGGGTTATATTTGATTTGCTCTGCTCATGATAACTTCATGCCAAGGAGAC +TGCTATCAGTTCTCTTAAAACAGATCCCAACTCCCTGCTCATAGTGGCCAAAGGAATGGA +GATTTCAGGCTGAGTTTACTTACGTGCATCATCTTCATCTATCCAGAAGCATCCCTGCAC +AAAACCTCTGTTTCTACCCTTCCATTCACTCGGCTCACTTTTCTGCTCTTAGTACCCTTT +GTTTCTTGTGAACTCTCCAGCAGGAGTGACTTGCAATTTGTATCCACTGACACTTAAGTT +CTCGGAAGTGCTGGAGAAGTGTATGGAAGTAAATTATCCTGATGTATAATTTTGTGCATG +TGAAACTCACCGTGGAAGTGCCTATCTAATTTCAGTATGGAACACAGCTAAACATTTGGA +TCAATAATCCAGTTTTGAAACCACACTTCATTTAAAGTACAATGTGCTGAAAAAAATGAA +AAAAGGGTGCTTTCAAATTTGTACTTAGTAAACTTTCACTAGATCACATCATATGTTTAT +CACTAGTCATGTTGTATTTCTATGTGTAATCGCCAGGCACTTTTAATTTCTAGTTTGCAT +TTACCATGCCAGCCTCCTCCTCAATCCCAAATTTCCTTTGGTTATAAATTTAGTAAATTT +GAAAGAGCCAGCAGGGATTAAACCCTGAAGGTATTCAAATGACTATCTGACGTTATTCCT +CATTTCAGCCATTTCGAAAAATTATGCTTTCATTTAGAATAGGCTCTGGGAATCAAAGTG +TGTGTATTTTGCCCAAGTAGAAGACACAGTTTAAAGTTAACATCCTAGCTACTAGAAGGG +AAAGCAAACAACATCGCTGCAAAAGGAGCCTATTTTTTTTTTACCTTACACTAAAACTAC +ATTGTGAAGATCAAACGAAATCAAGATGAGAGTGTGCCTCTTAACGCCAGGTCCAAAGTA +GATGCTTATTAAATGATAGTTTACCCCAATCCTTCACAAATGGTTGATAGGTCTTACTAT +TTCCCCCCTATTCAAATCTAGAATTTTTTCACTCCCATATACTAATCGATAGTTAATGGA +AAGCACAGAATAGATCATCGTCCAAGTGTTAGGTATTAGCCTGAGGAATCCGGAATCCCA +TATTTGTAACTGTCCTTCTTGAGAAAGTGCATTTTTCAGGCGGATTCTAGCCCCATTTTT +CCTTTTACCATTTTTACATGTTATGAGAGGTGGCTTAGAAATACTTCGATTTTTGCCTCT +TCATCACAACACACTGAACGTTAAAATCAAGTGGTTGGGTTTTTATTGGCTTATTTTGTC +TCTAACCGTTTTATTTCTCGAGCTGTCATCGTTCTTTTCGTCTTACATCCTTATGAACCT +TTTCTGGATTAAAAAAATGACGTTATAATAAGGAAACTGTAACTGGCGTTGGATTAGAAC +GAAGTTGACTCCATTCCTTTTCCTCCCCGTAGTGTGGGCGATACGAGGAAAGACCTCGGC +AAGAACCAGCGAAGCCCCGGCTGCCCTCGCCCTGCGGGCGCACACTTGCTCCTCGCGCCG +GGCTGCGCCGGGCGCCCGCGCCGCCTCGGCGTGTGTCCGCGGCTCCCTCCCGCCCTCGCC +CGCAGTCCCCCGATCCCGATCCCGGATCTCTGGGTCCACAGCTTGGCTCCCTCCCGAGCC +GGAGCCGGAGCCGGAGCCGAAGTCGCGGCTGGGCCCGGCCGCCCCGTCACAGGGGGAGGG +AACCCATGGGGAGGGGGAGGGGCGGTGAGGTCAGCGGCGGCGGCGCGTCCGCGGGCGGCG +GGAGCTTCGCATGCGCGGAGCGAGGCCCGTGAGTGGCAGCGGCGGCGCGCGGGGGGCGGG +CGAGGGGCCGAGAGTGGGGGAGCGGGCGGGGGCCGTCGAGGAGGCGTTGTGTGGGCGCGA +CGGCTGCGAGTTGGGGAGGTCTGTGGTGCGGGTCGCCCCGGGGGATCCCCGGCGCGGGCC +TCGCGCGACGGCCACGGTCGCGCGGCGTGTGTGGGGGGTCCACGCACACCCGCAAAACTT +CCTCCTCCCCTGCTCCGGGAGAGCGAGCGAGCGTGTGTGAGAGCGAGTGTGAGGAGCGAG +CCGCGGCCCGACGCCCAGCGCCGCCGCTGGAGCAGCTGTCAAAACTTCGCCGCCGCCCGG +GCCCCGCGGCCCGCCCTCCCCGCGCCGGGCCCCTTTCTCTTCCTGCTGCGGGCGGCCCGG +GGGAGGGGCCGCGGGCGGAGACCCCGGAGGCCGGCGCCCCTCACGCCGCCCGCCCGCCCG +CTCCCCGCCCGGCCCCTGCGCGCGTGCGTGTCCTGCTCGCTCCATGTTGCCGCCTCTCCC +GGTACCTGCTGCTGCTCCCGGGGCTTCGGGAAATGCGAGAGTCTGAGCCGGGGAGGAGGA +ACCCGAGCAGCGGCGGCGGCGGCCGCGGCGGCGGGAGCCCCCCAAGAGGAGGACCGGGAT +CCATGTGTCTTTCCTGGTGACTAGGATGTCGTCGGAGGAGAACAAGTGCGTGGAGCAGCC +GCAGCCACCACCCCCCGAGGAGCCTGGAGCCCCGGCCCCGAGCCCCCCAGCCGCAGACAA +AAGACCTCGGGGCCGGCCTCGCAAGGCGCTTCCCCTTTCCAGAGAGCCAGAAAGAAGTAA +GTTGAGTGCGAGGGAGCCAGGCCGGGAGCCAGCGGCGGCGCCGGGCCGGAGCTGCCACCG +GGCGCCCGCCCCGCGGCCTCCACGCCTTGGCGCCCCCCGGCGGGATGGGGGCGGGGCGGG +CCCGCGGGCGGCGGCAGCTCCCGGCCCCGGCCCCACGCCCCTCGGTAGCCGCCCGCGCCC +GGCCTCCCCCGCTCCGCGCCGCCCGCCCGGGCTCCCGTCGGCGCCCGGCTTCGCACACTT +TACTTTTCAGTCGGGCCTTTTCAGTGGGTCTTCTCCGCGACTCTTCTTTTGGAGAAATTT +CTCGTAGCCGCGTCTTGGCCTAGCTGGATCATTGAGAAAACAAGCCCGGAGCGCGCGCAG +GTAGTCCCCGGACGGACTCCGAGCGAACCGCCGAGCCGTGGGCGCTCGGGAAACTCGGAG +CTGTCAAAACGCCCGGGCCAGGTGGTCTCGGGGCGCGGGCTGGGGGCGAGAAGAAAGCGG +CCGGGCGAGTGCAGCTTTTGTTTGTCAGCGACTCGTTCGTGGAACTTTTCCTGGTCCCAA +ACCTGTGTTTTCTTCTTTTGATGATATATTAGGAAGCCATTTGGCTTCTTCCTTCCCCCT +CCCCCAACACCCAGCACCGCACTCCCGGGCTCCGAAAGCACAAGTCCTGTGGGAACCCCC +AGCTTCGGGGAACGGCCTGCCTAAGTTTTGGAGACGTAGCCAGCGTCCCCTCGTAAGGCA +GAATACCAAGAGCACTTATTCAGAGAGAGTGCAGATGTAAATGTCGTTTCCCTCGTAAGT +CTTAGCTGTAAGGGGCTTGGGAATAGGGTCGCCTGCCTTTGACCGACCGTACTGTAGGGC +TGGACACCGGCTTATTAGAGGACCAGAAATGTCTTCTTACAGAACGGTTATTTGACGGCT +TTGCTTGTAAATTAAGACACCGTTTTAGTGCCAGCGAGCTGCTCGGCTTCTGTGGCTCTC +GCGTGTGCCGTGGAAGAACTGTGAATGTCTTTCGAAGTTGTAGAATGGCGTGTGTGCTTA +CTCATTTCATGAGATGATATTCTCATTGAACTGTCGGGAGTGGAAGGGTGCGCTGGGACG +TGAAGGAAGCCAGCACGTTTATGGATAGGCTGTTTCTTTGGTTCGGGTGCATTCACTTAG +TAATAGTGTTGTTTGGTGATTTGTAGTAAAAATAGTAGCGTGAACTGAGGCATAGCAGAG +CTGGGTTGTGGGAACCCATTAAGCTCTTGACTTGAATGTGCTCTTTTCTTGCCCCGCTGT +CCTTTTACTATGAAAATGATTCAGGGCCTTCAACTTGCCTCCATATTTTATTGCCAGCTC +TTACCTAGCTATGATAATCGTGAGGGAGGCAAGTACAGGATGTGTGTACGTTATTACATT +AGCTTCTTCGTGATACAAAGTTAGGACTTACTTATGCCACTTGCGTTGTAATACAATGGC +AAATATAAAATGCCCTTATTCTATATTAACTGAAATTTGGAGAAGGAAGTGGAGGTTTAA +GTAATTTTTAGACGTCTAAGCCACTTTTTTGCATCCTTTAAAGCAACTCAGGACAAGCCA +TATTGGGGGTTTTACCTTGATTGCCTCCCATTTCACTATTTGCAAAGCATTTCTTCATCT +CTTACTGAACATTAATTTGCAATTTTTTTTTTTAATTTGCATTTGAATTCTTACTCCAGA +AAGATTAGATCTGTGTTGTCACACCCCACACCCCATACTCCTGTAAGGGCGTGCTTGTGC +ACGCGCACACGCTCACACGCACGCGCACACTCGCACACACCCTACTTTTGAAATGAGCTC +ATTTGTATTAGTGCAGCTCCTGAGTGCACTGGACGATTAGGGTATTGCCACTTTATTATT +TTAATTCTTAATCTCATATTATGAAGAAATAGGTAGCCTTTGGAGAAGATAAAAAATTTC +TGCTGAATAACAGTATAATCTAACTATGAAACATCAAAACTTTTGGAAATATTTAGAACA +AATGTAAGTCTGTAGAGAGCTTTTTCTTTTAGATTTGAAAACTAGTACTGCTTTCTTTAT +AGGAAAGTAAAGTCTACTGGTAAATTTCACGGGTCTAAACTTTTTAGAGCTTTTTTTTGA +AATTGTGTCTTTTGAAGGGAGTGGAATCTCCAGTTGTTTTTAGAAACATGTAAATGGAAA +CTAACATATGAATTGGAAAGCAAAGAGAAAGTTTTTCAATTGTGTATCTCTATACTGTAT +AAGAATCCATGCAGAAAAGACCCTGTAGTTGGATAGTAAAGACCCTGAAGGTGAAACTTA +TGTGTAACCAGTGTAAATTAGGTTTGTAACCAGTGAAATTATGTGAAATTGCAAATAATT +CACCTGAGAAATGAAAATTAATCTTCTTTGCTAAATGCCATAGAGATATTTTAAGTTGCT +AATGTTACTTAGATGTTCATTAACTTAGTGAGTTACATTAAGTAGAGAAGATGCCTTTTT +TTTTTTTCTGTACGAAGTCTTGCTCTGTAGCCCAGTGTAGTGGTATGATCTCGGCTCACC +ACAACCTCCGCCTCCTGTATTCAAGCGACTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGA +TTACAGGTGTGCACCATCGCACCTAGCTAATTTTTTGTATTTTTAGCAGAGACAGCATTT +CACCATGTTGGCCAGGCTGTTCTTGAACCCCCGACCTCAGGTAATCCACCCTCCTTAGCC +TCCCAAAGTGCCAGGATTACAGGCGTGAGCCACTGCACCCTGCTGAGAAGATGCCTTTTG +ACAATGAAGTGGATTTGTATATTTATCTTTGGCTTAAAAAAACATGCACCACCAATTACA +CTTTCCTCAAGTTTAAATTTTTAATAATTAGGAAAATAAAGCATTTTCTTGTCTTATAGT +GTTAGCTAGATTGTTTTTGTGTATTTTGTCATGAATAAAAAGCATAGCTATATAGTTACT +GCTTTTACATTAACTATAAATATCTTAAAATTTTACTACCTAAAATCAGGAAACTTGAAC +TGAAGCTACTAATCTTAGAGTTGGAAAAGTAAATACATAGAGGTTTCCTGTTGTACAAAT +GTCAAGTGGCACAGTGAAATTTACATTCATTTGAAAGTTTTCCTTAACTGTAAAAAGTAT +CAAATTACTTGATACTTTGGAGTAGTTCATCATCTTTATCAGAGGCACAGGTCTTAACCA +TTGGCAAGCCTCTGTCAGAATATGCACATATTAAAGATCTGATTATTTTTGTGTTAATGT +TAAAAAATTTTTCTGAAGCTTTTATCTTATTTTTTCCATCCTTACACCGTAAATTCACAT +TACCAAGTTGGGAAGCCAAAGAAACATTCTACTCTACTATGTTTCTTACCAGTTCATGAA +AGTTGATGTTAGAAATGGGTGTGGGTGTGGGGGATGGGGGTGGTTGTACAGAAGCAGCAG +GTGGTAGGGATAGGATTTCTGAAGCACTATCCTTGGCCTTTTTTGAGTAAACTCTTTATA +CCCTGAGCCACTTTCTTTTCAGAGGGCAATTGCTATTATTAGAGAGCCACCTTAAGCATT +ATTGTTGTAGAAAAATTAGGCACAACCAGTGATTGTCATTACAAGGACCAGCAAAAATGG +CTAGGTTGCTACTCTGTATTTGTAACGCCCTTCCCCCAACAAAATTTCTCCTTTTCATAT +CTGTGAATTAGAAATAAGTGATAGAAAACTGTACTGCATTACAATATATACCATTTAATA +AAACAAGTTTATAGTTGAGAGCACTATTCATGCTTTTTGAGATAATGCAAATTTGTAATT +TTTATGATAGCAATTCTTAATAATTTATTGTCCAAGAGATTTGATAAAATTTTTGATAGT +TATTGGTCTCTGGGACTCAATAGGCACTGAAATGTTTTAATTCAGTTGAAAAGTTGGTTC +AGGATTGCTACCCTCTCTTACCTGTTAGGAGGTTGTTGTTTAACCTGACCTGAAATTCCC +ATGAATAAGAACCTGTTTTTTTTTTTTTTTTCTTTGACAGAGTCTTGCTCTGTCGCCCAG +GCTGCAGTGCAGTGGTGCGATCTTGGCTCGCTGCAAGTTCCGCCTCCCAGGTTCAAGCGA +TTCTCCTGTCTCAGCCTCCCAAGTAGCTGGAGTAGCTGGGACTGCAGGCACGTACCACCA +TGCCTGACTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG +TCGCAATCTCTTGACCTCATGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAG +GTGTGAGCCACCGCACCTGGCCCAGGGAATTTCTAATATTTGAGAAGATGTTATTTTTAG +TCTATTATACAAATTTATATATTGTTTACTAATATATAAATTTACATATTGGTTACTAAT +ATGTAAACACCAATTTACATATTGGTTACTAATATGTAAACTTGATAAACATGGATTTCC +ATGGAAATTTAAAAGTATCACAACAATTTGTTTTCCCATTCTGAAACTTGTGATTTATTA +CATTTTCCTACTATTTCAGTTAATTCCATAATGCCAGATTTGTTGTCAATTTGCCGAGTG +ACAAGCCACACTGCTTCCTCTCATTCCTCTATTCCGCAAAACTGCAAAGTTTCCCAGACC +ACAGTCAGGTTTCTCTGGGTTGTCCAACTCTGTAAACTTACAGAGTGGTTGTCCAACTCT +GTAAACTTACAGAGTGGTTGTCCAACTCTGTAAACTTACAGAGTGGTTGTCCAACTCTGT +AAACTTAAGTCACTTTAAGTTTATGACGGAGGGGCTTCGTGAAACTTCATTGACCTTCCA +AGGTGAAAATTGGTCAGTTTTCAGTTATAAAGGACATTAAGGATGGGTGTGGTGGCTGAT +ACATGTAATCCCAGCACTTTCGGGAGACTGAGTCAGGAGGATCACTTAATCCTCATTTAA +AAGGAGTTTGAGACCAGCCTGGGCAACAAAGTGAGGCCTTGTCTCTACAAAAAAATTAGC +TGGGTGTGGTGGTAGGCACTTGTAATCCCAACTACTCTGGAGACTGAGCTGAGAGAAGAT +TGTGTGAGGCTTGGAGGTTGAGGCTGCAGTGAACGGACATCACACCACTACACTCTAGTC +AGGTGACAGAGCAAGACTCTAAATAAATAGGAACATTAGATGGTCTCTCTGCACTCTTGC +CTGGTGGGGACGTGTTAGATACCCTCGTTAGGTTGTGATTTAGTTTTTAATCTGTGAGAT +GTTTGGGTCAAACAATTTTTAGCTGCCATGGAATAAACTTTCCAGTCAGCGTGTGAGTTT +GTGTTTGCCTTTACTTTTTTTTTTCTATATTGTTTTGGTCTATTTTTATCTTTTAATTTC +AGAAAGCTGATTAATCTCTTCCTTTTCTCTTTAAAAATTTTCTTTATCATGTTTGTGCTA +CAGTGGTTATTTTGAGAACTTGTTGGCAGGATAAGTTGCAAAAGTTATGAAGTAGAATAG +GGATGATTTCTGTTTTTGTTTTTTTTTTTTTCAGACAGAGTCTCACTCTCTTGCCTAGGC +TGGAGTGCAGTGGCGTGATCCTGGCTCACTGCAGCCGCCGCCCTCCGGATTCAAGTGATT +TGCCTGGCTCAGCCTCCCAAAAAGCTGGGATTACAGGTGCATGCCACCACACCCAGCTAA +TTTTTGTGTTTTTAGTAGAGATGGGTGTTCACCATGTTGGCCAGGCTGGTCTCAAACTCC +TGACCTCAGGTGATCTGCCTGCCTCCGCACTCCCAAAGTGCTGGGATTACAGACGTGAGC +CACCATGCCTGGCTGAGATTATTTCTTTTTTTATTATAGCCATTGCTTGTAGATATATGC +TGGTGGTTATCTGTAAAAATGTAATAGAAAGGCCGGGCACGGTGGCTCACACCGGTAATC +CCAGCACTTTGGGAGGCTGAGGTGGGCGGATCACAAGGTCAGGAGTGGGAGACCAGCCTG +GCCAATATGGTGAAACCCCGTCTCTACCAAAAATACAAAAATTAGCTGGGCATAGTGGCG +GGCACCTATAGTCCCAGTGACTCGGGAAGCTGAGGCAGGACAATCGCTTGAACCCAGGAG +GCAGAGGTTGCAGTGAGCTGAGATCGTGCTATTATTGCACACCAGCCTGGGCGACAGAGT +GAGACTCCGTCTCAAAAAGAAAAAAGTAATAGACCAATCTTGAATTTATAATTGGAAGTG +TTGATCCCTTTATTTGCAGAATTTATTTATTTGTGACGCAGCTGTTGCTACCTCGCCTTT +TCTTTTGTTGAGCTTAATCTCATGTCAAGTCATTCAACCAACTCAAAAGCGATGAAGACA +TTATTGAATCAACCTGAACTAAATCAGACCTAGGCTTCTTAAAATATACAGCTTAATGCT +TCCAAATGATTTAGAAAACTAAAAAACCTAGCTACGCTGTAGGACACACAGTGGCCAATA +ATACAGGACCCCCAAACTGGCCAGTGGACCACTGCAACCACTATTTACTTCCTCCGTGTT +TAGGAATGTTCAACGCTCCAAGCCCCATAGGCTGATTCAAGAAGATAAAGTGAGACTCAA +GGAATTTCGAAGTGGAACAATACACCAAAGCCTTAAACCTGAAATGACTCTCCTTTTCTG +GGGGGTGAGGGGGAAAGAAAAAGAAAAAGTTTCTAGGGCTCTCGGGGTGGCCTGGATGCC +AGGGTCCCAGAAGTGGCCTTTTCTAGCTCCTGTAACTAAACCTGGCGGAAAACTCCCCGC +CTGCTCACTCCACCCCCACCCGCCCAAGAATGCGTCTTCCCGTCTTCGGTGGCCCTACCC +AGAATCCCAAAATGTGGGTTCCAACCCGGGCCCTGAATGTCTTCTCAAATCCCCGGGACC +CAGGTTCCGGTGCGTGCCTTGCGTGCCGGGTCTTGCCCCTCGGGCGGTACCACCCAGGCA +GCCCTAAATCCAGCCTCCCGGGCCCCCAGCAGCGCCCTCCGCCCCTCCACTATCCGGTCC +GGCTCGAAGTCGGGGCCAAATCCAGAGACAAGAGGGCTGTGCCTGAAACTGAGCAGTTTC +ACCACTCGGCACTCCTGGCGGAAACTTCCCTTTAAAAAAAAGAAAAGAAAAGAAAAGCAA +CAGCACTTTTGGGCTAGCATTTCAATCCTTCCTGCCCTTTAGAGTTCCCAGTTCTGCTTC +CAGCTGGCTTTGGGTGTTCCACTAGAATTGAGTTGTAAAGATATTCTTTAAGTGTTTATA +GAACATTAAGACTTAAAAAAAATCTTTAAAATTAGAGGAGGGAAAAAGCCACCTTATCGC +ACACATCCAGGAAATGCAGCCCCGTGCATCCCTGCTCAGGGATGAGCAGGCGCCCCAGGA +CTCCCGGAGACAGATTTTTGGGCACCCGAGGGAGTCACCGGGCGCGTGTCGGGGTCCGCG +GTGAGGCCCAGCCCCTCCGGCGGTCCCTTAGACGCGCCCTCTGCCCGGCCGGTGTGGACC +GTCCCGGCCATTGTTTACGGGGGATGCCCGTCCAGACGCATTGTTTTGGCCGTTTCCAAC +TTGCCCCGGCCCTTTCCGGGGCATCGCGGGGGACCCTACACCGACGTCCCCCCTCCGCCC +GCGCCCCAAGGGCTGACTGGGCAAATTGGCAGATCCGCCCCGCGGGGCGACCCAACTTTT +CGGAACAGCCCCCCACCGCCCACCCCTGCAGATCCCCGGACCCCCGCTCCCGGCGGAGAT +TCAGGGAACCCCGCATCCCAAGCCCTTCTAAATCGTGCGGCCTGAGTGTGACGGCCAAGA +GCGGATGCAGCCCGGGATCGCCCGCACCTTCCCGTGGGCGG