--- a/test-data/Mutect2-out1.vcf	Fri Apr 10 14:10:55 2020 -0400
+++ b/test-data/Mutect2-out1.vcf	Sun May 10 17:58:00 2020 -0400
@@ -6,12 +6,14 @@
 ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation 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">
+##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">
 ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
 ##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 input.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 --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --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 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --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 --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 --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active 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 --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="4.1.4.0",Date="November 15, 2019 4:24:40 PM EST">
+##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">
+##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">
@@ -27,65 +29,65 @@
 ##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
 ##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles">
 ##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
-##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
+##INFO=<ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
 ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
 ##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors">
 ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
 ##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
 ##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
 ##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing">
-##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site">
 ##MutectVersion=2.2
 ##contig=<ID=K03455,length=9719>
 ##filtering_status=Warning: unfiltered Mutect 2 calls.  Please run FilterMutectCalls to remove false positives.
 ##source=Mutect2
 ##tumor_sample=SRR8525881
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR8525881
-K03455	4098	.	T	C	.	.	DP=1;ECNT=12;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	.	.	DP=4;ECNT=12;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	.	.	DP=14;ECNT=12;MBQ=38,38;MFRL=290,278;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=50.12	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:2,12:0.786:14:0,4:1,8:0|1:4190_A_G:4190:2,0,10,2
-K03455	4209	.	GC	AC,AA	.	.	DP=18;ECNT=12;MBQ=37,35,35;MFRL=200,295,290;MMQ=60,60,60;MPOS=10,43;POPAF=7.30,7.30;TLOD=13.72,52.71	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:1,4,13:0.263,0.632:18:1,2,4:0,2,9:1,0,15,2
-K03455	4233	.	T	C	.	.	DP=24;ECNT=12;MBQ=38,39;MFRL=252,263;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=16.13	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	1|0:19,5:0.261:24:7,2:11,3:1|0:4190_A_G:4190:16,3,5,0
-K03455	4250	.	G	A	.	.	DP=36;ECNT=12;MBQ=37,37;MFRL=273,201;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=4.14	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:33,2:0.088:35:15,2:16,0:29,4,2,0
-K03455	4259	.	T	A	.	.	DP=40;ECNT=12;MBQ=35,35;MFRL=254,276;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=134.66	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:7,32:0.784:39:3,15:4,13:0|1:4259_T_A:4259:7,0,27,5
-K03455	4262	.	A	T	.	.	DP=40;ECNT=12;MBQ=37,37;MFRL=276,254;MMQ=60,60;MPOS=48;POPAF=7.30;TLOD=23.11	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	1|0:32,7:0.216:39:16,3:13,4:1|0:4259_T_A:4259:27,5,7,0
-K03455	4268	.	G	A	.	.	DP=40;ECNT=12;MBQ=34,37;MFRL=252,273;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=47.57	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:27,13:0.368:40:11,7:13,5:22,5,13,0
-K03455	4271	.	A	G	.	.	DP=43;ECNT=12;MBQ=37,33;MFRL=250,287;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=28.52	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:34,9:0.244:43:14,7:15,2:29,5,9,0
-K03455	4277	.	C	T	.	.	DP=46;ECNT=12;MBQ=37,37;MFRL=244,276;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=148.83	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:10,36:0.767:46:3,18:4,16:0|1:4259_T_A:4259:9,1,31,5
-K03455	4279	.	GT	AC,AT	.	.	DP=47;ECNT=12;MBQ=37,35,36;MFRL=263,252,202;MMQ=60,60,60;MPOS=34,33;POPAF=7.30,7.30;TLOD=60.64,24.20	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:17,21,9:0.421,0.201:47:8,8,5:7,9,4:16,1,25,5
-K03455	4310	.	C	T	.	.	DP=39;ECNT=15;MBQ=20,18;MFRL=229,290;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=7.48	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:34,4:0.141:38:18,0:12,2:21,13,1,3
-K03455	4313	.	G	A	.	.	DP=37;ECNT=15;MBQ=20,32;MFRL=229,273;MMQ=60,60;MPOS=69;POPAF=7.30;TLOD=12.35	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:32,5:0.143:37:12,3:12,1:17,15,4,1
-K03455	4320	.	G	A	.	.	DP=38;ECNT=15;MBQ=20,20;MFRL=252,263;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=26.00	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:31,7:0.237:38:16,1:12,3:17,14,3,4
-K03455	4330	.	A	G	.	.	DP=42;ECNT=15;MBQ=20,38;MFRL=252,276;MMQ=60,60;MPOS=60;POPAF=7.30;TLOD=13.81	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:37,4:0.125:41:16,3:17,0:19,18,3,1
-K03455	4334	.	A	G	.	.	DP=43;ECNT=15;MBQ=32,36;MFRL=263,254;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=14.62	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:38,5:0.150:43:17,2:18,3:21,17,1,4
-K03455	4340	.	A	G	.	.	DP=45;ECNT=15;MBQ=37,20;MFRL=263,252;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=109.80	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:17,28:0.586:45:8,13:9,11:0|1:4340_A_G:4340:9,8,13,15
-K03455	4343	.	C	A	.	.	DP=43;ECNT=15;MBQ=33,20;MFRL=263,229;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=109.80	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:17,26:0.586:43:7,12:6,10:0|1:4340_A_G:4340:9,8,11,15
-K03455	4345	.	GC	AT	.	.	DP=47;ECNT=15;MBQ=20,37;MFRL=204,254;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=44.93	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:34,13:0.302:47:12,4:14,6:16,18,6,7
-K03455	4346	.	C	T	.	.	DP=46;ECNT=15;MBQ=20,26;MFRL=197,276;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=13.91	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:31,4:0.146:35:11,2:10,0:14,17,3,1
-K03455	4358	.	T	C	.	.	DP=45;ECNT=15;MBQ=20,35;MFRL=206,254;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=17.97	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:37,7:0.171:44:13,4:19,3:16,21,2,5
-K03455	4361	.	GCT	ACT,G	.	.	DP=47;ECNT=15;MBQ=36,20,35;MFRL=237,208,247;MMQ=60,60,60;MPOS=32,32;POPAF=7.30,7.30;TLOD=101.55,49.01	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:6,28,13:0.573,0.289:47:3,9,4:2,13,7:4,2,16,25
-K03455	4364	.	A	AAG	.	.	DP=49;ECNT=15;MBQ=33,35;MFRL=208,247;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=48.10	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:34,13:0.295:47:15,4:17,7:15,19,5,8
-K03455	4370	.	A	G	.	.	DP=51;ECNT=15;MBQ=20,37;MFRL=197,291;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=64.46	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:30,20:0.466:50:10,8:13,12:13,17,7,13
-K03455	4376	.	C	T	.	.	DP=53;ECNT=15;MBQ=29,25;MFRL=231,244;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=80.90	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:28,24:0.446:52:8,10:16,12:9,19,11,13
-K03455	4397	.	T	C	.	.	DP=57;ECNT=15;MBQ=34,37;MFRL=291,247;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=66.78	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:32,19:0.381:51:9,8:17,9:15,17,9,10
-K03455	4416	.	C	T	.	.	DP=65;ECNT=21;MBQ=37,37;MFRL=270,310;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=33.57	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:54,11:0.193:65:21,4:31,4:22,32,6,5
-K03455	4418	.	A	G	.	.	DP=64;ECNT=21;MBQ=37,37;MFRL=287,229;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=6.89	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:61,3:0.066:64:24,3:35,0:26,35,1,2
-K03455	4421	.	T	C	.	.	DP=64;ECNT=21;MBQ=35,38;MFRL=259,291;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=140.93	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:28,36:0.574:64:15,13:10,21:11,17,16,20
-K03455	4424	.	T	C	.	.	DP=62;ECNT=21;MBQ=37,38;MFRL=251,291;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=104.68	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:32,29:0.498:61:14,9:12,17:12,20,14,15
-K03455	4430	.	T	C	.	.	DP=62;ECNT=21;MBQ=37,38;MFRL=284,265;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=3.90	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:60,2:0.051:62:24,2:31,0:25,35,1,1
-K03455	4439	.	A	G	.	.	DP=54;ECNT=21;MBQ=38,35;MFRL=291,241;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=18.97	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:48,6:0.115:54:21,2:24,4:21,27,2,4
-K03455	4442	.	AG	GA	.	.	DP=53;ECNT=21;MBQ=38,33;MFRL=290,209;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=18.54	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:45,7:0.159:52:18,2:23,5:19,26,3,4
-K03455	4443	.	G	A	.	.	DP=53;ECNT=21;MBQ=37,38;MFRL=282,297;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=75.44	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:26,22:0.454:48:12,9:10,10:10,16,11,11
-K03455	4448	.	C	A	.	.	DP=51;ECNT=21;MBQ=38,20;MFRL=290,126;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=9.07	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:47,3:0.062:50:18,0:25,2:20,27,1,2
-K03455	4449	.	C	T	.	.	DP=49;ECNT=21;MBQ=37,38;MFRL=209,323;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=90.60	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:25,24:0.511:49:11,10:13,13:11,14,11,13
-K03455	4460	.	T	C	.	.	DP=46;ECNT=21;MBQ=37,37;MFRL=284,329;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=18.65	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:40,6:0.159:46:15,2:22,3:20,20,2,4
-K03455	4465	.	T	TGGCC	.	.	DP=45;ECNT=21;MBQ=37,35;MFRL=310,176;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=26.99	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:35,8:0.170:43:12,6:21,1:17,18,4,4
-K03455	4466	.	A	G,AGTG	.	.	DP=44;ECNT=21;MBQ=38,38,37;MFRL=322,227,176;MMQ=60,60,60;MPOS=29,22;POPAF=7.30,7.30;TLOD=12.11,28.32	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:30,4,8:0.136,0.190:42:10,1,6:16,3,1:15,15,5,7
-K03455	4478	.	T	C	.	.	DP=33;ECNT=21;MBQ=37,33;MFRL=323,206;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=40.91	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:23,10:0.303:33:7,6:15,4:12,11,4,6
-K03455	4505	.	A	G	.	.	DP=19;ECNT=21;MBQ=39,38;MFRL=394,323;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=67.71	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:3,16:0.810:19:2,5:1,8:2,1,11,5
-K03455	4508	.	A	T	.	.	DP=17;ECNT=21;MBQ=39,35;MFRL=341,335;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=53.29	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:4,13:0.737:17:2,5:2,8:2,2,10,3
-K03455	4511	.	G	A	.	.	DP=17;ECNT=21;MBQ=37,36;MFRL=394,329;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=58.34	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:3,14:0.789:17:2,4:1,7:2,1,10,4
-K03455	4526	.	T	C	.	.	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	.	.	DP=13;ECNT=21;MBQ=38,37;MFRL=323,421;MMQ=60,60;MPOS=36;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	.	.	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	.	.	DP=13;ECNT=21;MBQ=0,33;MFRL=0,323;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=39.42	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,11:0.926:11:0,7:0,2:0,0,11,0
+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