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spades.samtools.vcf
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189 lines (189 loc) · 23.1 KB
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##fileformat=VCFv4.1
##samtoolsVersion=0.1.19-44428cd
##reference=file://../../align/spadesLinear.fasta
##contig=<ID=ordered_SL1344,length=4911359>
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=QBD,Number=1,Type=Float,Description="Quality by Depth: QUAL/#reads">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Read Position Bias">
##INFO=<ID=MDV,Number=1,Type=Integer,Description="Maximum number of high-quality nonRef reads in samples">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. Note: this version may be broken.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality non-reference bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ../../align/spades/spades_bowtie2_very_sensitive_local_k4.sorted.bam
ordered_SL1344 26 . C G 86 . DP=42;VDB=4.318433e-05;AF1=1;AC1=2;DP4=0,0,37,3;MQ=20;FQ=-147 GT:PL:DP:GQ 1/1:119,120,0:40:99
ordered_SL1344 28 . C T 95 . DP=42;VDB=8.506877e-04;AF1=1;AC1=2;DP4=0,0,39,3;MQ=20;FQ=-153 GT:PL:DP:GQ 1/1:128,126,0:42:99
ordered_SL1344 31 . T A 87 . DP=42;VDB=8.238585e-03;AF1=1;AC1=2;DP4=0,0,37,3;MQ=20;FQ=-147 GT:PL:DP:GQ 1/1:120,120,0:40:99
ordered_SL1344 66 . C A 110 . DP=47;VDB=2.766973e-01;AF1=1;AC1=2;DP4=0,0,40,6;MQ=20;FQ=-165 GT:PL:DP:GQ 1/1:143,138,0:46:99
ordered_SL1344 83 . C A 133 . DP=51;VDB=4.278987e-02;AF1=1;AC1=2;DP4=0,0,37,10;MQ=20;FQ=-168 GT:PL:DP:GQ 1/1:166,141,0:47:99
ordered_SL1344 108 . C G 140 . DP=52;VDB=3.539285e-01;AF1=1;AC1=2;DP4=0,0,37,12;MQ=20;FQ=-175 GT:PL:DP:GQ 1/1:173,148,0:49:99
ordered_SL1344 127 . C A 142 . DP=53;VDB=2.044652e-01;AF1=1;AC1=2;DP4=0,0,36,12;MQ=20;FQ=-171 GT:PL:DP:GQ 1/1:175,144,0:48:99
ordered_SL1344 145 . T C 153 . DP=55;VDB=2.857172e-01;AF1=1;AC1=2;DP4=0,0,37,17;MQ=20;FQ=-190 GT:PL:DP:GQ 1/1:186,163,0:54:99
ordered_SL1344 160 . C A 155 . DP=58;VDB=3.724667e-01;AF1=1;AC1=2;DP4=0,0,39,19;MQ=20;FQ=-202 GT:PL:DP:GQ 1/1:188,175,0:58:99
ordered_SL1344 175 . C G 159 . DP=59;VDB=3.067003e-01;AF1=1;AC1=2;DP4=0,0,38,20;MQ=20;FQ=-202 GT:PL:DP:GQ 1/1:192,175,0:58:99
ordered_SL1344 191 . T G 161 . DP=59;VDB=1.634375e-01;AF1=1;AC1=2;DP4=0,0,34,21;MQ=20;FQ=-193 GT:PL:DP:GQ 1/1:194,166,0:55:99
ordered_SL1344 217 . C G 164 . DP=61;VDB=1.322840e-02;AF1=1;AC1=2;DP4=0,0,36,23;MQ=20;FQ=-205 GT:PL:DP:GQ 1/1:197,178,0:59:99
ordered_SL1344 239 . T G 166 . DP=64;VDB=2.568838e-01;AF1=1;AC1=2;DP4=0,0,36,27;MQ=20;FQ=-217 GT:PL:DP:GQ 1/1:199,190,0:63:99
ordered_SL1344 288 . T A 172 . DP=61;VDB=3.712050e-01;AF1=1;AC1=2;DP4=0,0,30,28;MQ=20;FQ=-202 GT:PL:DP:GQ 1/1:205,175,0:58:99
ordered_SL1344 315 . A G 178 . DP=56;VDB=1.789161e-01;AF1=1;AC1=2;DP4=0,0,23,31;MQ=20;FQ=-190 GT:PL:DP:GQ 1/1:211,163,0:54:99
ordered_SL1344 317 . A C 180 . DP=56;VDB=2.529918e-01;AF1=1;AC1=2;DP4=0,0,22,30;MQ=20;FQ=-184 GT:PL:DP:GQ 1/1:213,157,0:52:99
ordered_SL1344 323 . A G 179 . DP=55;VDB=2.372587e-01;AF1=1;AC1=2;DP4=0,0,23,32;MQ=20;FQ=-193 GT:PL:DP:GQ 1/1:212,166,0:55:99
ordered_SL1344 329 . T A 185 . DP=54;VDB=2.036310e-01;AF1=1;AC1=2;DP4=0,0,21,32;MQ=20;FQ=-187 GT:PL:DP:GQ 1/1:218,160,0:53:99
ordered_SL1344 334 . A G 182 . DP=54;VDB=1.840742e-01;AF1=1;AC1=2;DP4=0,0,21,31;MQ=20;FQ=-184 GT:PL:DP:GQ 1/1:215,157,0:52:99
ordered_SL1344 338 . G A 185 . DP=52;VDB=1.477470e-01;AF1=1;AC1=2;DP4=0,0,20,31;MQ=20;FQ=-181 GT:PL:DP:GQ 1/1:218,154,0:51:99
ordered_SL1344 363 . G A 189 . DP=52;VDB=3.464141e-01;AF1=1;AC1=2;DP4=0,0,18,34;MQ=20;FQ=-184 GT:PL:DP:GQ 1/1:222,157,0:52:99
ordered_SL1344 370 . G C 184 . DP=52;VDB=2.762986e-01;AF1=1;AC1=2;DP4=0,0,18,34;MQ=20;FQ=-184 GT:PL:DP:GQ 1/1:217,157,0:52:99
ordered_SL1344 377 . A G 184 . DP=51;VDB=6.708689e-02;AF1=1;AC1=2;DP4=0,0,17,33;MQ=20;FQ=-178 GT:PL:DP:GQ 1/1:217,151,0:50:99
ordered_SL1344 391 . G T 185 . DP=57;VDB=6.961519e-03;AF1=1;AC1=2;DP4=0,0,15,39;MQ=20;FQ=-190 GT:PL:DP:GQ 1/1:218,163,0:54:99
ordered_SL1344 396 . G T 182 . DP=58;VDB=1.878634e-02;AF1=1;AC1=2;DP4=0,0,15,34;MQ=20;FQ=-175 GT:PL:DP:GQ 1/1:215,148,0:49:99
ordered_SL1344 400 . A G 188 . DP=58;VDB=2.757526e-03;AF1=1;AC1=2;DP4=0,0,12,42;MQ=20;FQ=-190 GT:PL:DP:GQ 1/1:221,163,0:54:99
ordered_SL1344 406 . G A 184 . DP=56;VDB=4.077749e-02;AF1=1;AC1=2;DP4=0,0,11,44;MQ=20;FQ=-193 GT:PL:DP:GQ 1/1:217,166,0:55:99
ordered_SL1344 426 . G A 168 . DP=55;VDB=3.748916e-01;AF1=1;AC1=2;DP4=0,0,8,44;MQ=20;FQ=-184 GT:PL:DP:GQ 1/1:201,157,0:52:99
ordered_SL1344 10558 . A C 17.1 . DP=3;VDB=2.063840e-02;AF1=1;AC1=2;DP4=0,0,3,0;MQ=20;FQ=-36 GT:PL:DP:GQ 1/1:49,9,0:3:15
ordered_SL1344 10561 . A T 17.1 . DP=3;VDB=2.063840e-02;AF1=1;AC1=2;DP4=0,0,3,0;MQ=20;FQ=-36 GT:PL:DP:GQ 1/1:49,9,0:3:15
ordered_SL1344 10576 . C T 27.5 . DP=4;VDB=1.496627e-02;AF1=1;AC1=2;DP4=0,0,4,0;MQ=20;FQ=-39 GT:PL:DP:GQ 1/1:60,12,0:4:21
ordered_SL1344 10577 . T C 27.5 . DP=4;VDB=1.496627e-02;AF1=1;AC1=2;DP4=0,0,4,0;MQ=20;FQ=-39 GT:PL:DP:GQ 1/1:60,12,0:4:21
ordered_SL1344 10579 . T C 27.5 . DP=4;VDB=1.496627e-02;AF1=1;AC1=2;DP4=0,0,4,0;MQ=20;FQ=-39 GT:PL:DP:GQ 1/1:60,12,0:4:21
ordered_SL1344 10596 . T C 41.1 . DP=6;VDB=3.120048e-02;AF1=1;AC1=2;DP4=0,0,6,0;MQ=20;FQ=-45 GT:PL:DP:GQ 1/1:74,18,0:6:33
ordered_SL1344 10598 . C A 35.3 . DP=6;VDB=3.008871e-02;AF1=1;AC1=2;DP4=0,0,5,0;MQ=20;FQ=-42 GT:PL:DP:GQ 1/1:68,15,0:5:27
ordered_SL1344 10605 . A C 53 . DP=9;VDB=4.289230e-02;AF1=1;AC1=2;DP4=0,0,9,0;MQ=20;FQ=-54 GT:PL:DP:GQ 1/1:86,27,0:9:51
ordered_SL1344 10611 . A C 59 . DP=13;VDB=2.632038e-02;AF1=1;AC1=2;DP4=0,0,13,0;MQ=20;FQ=-66 GT:PL:DP:GQ 1/1:92,39,0:13:75
ordered_SL1344 10620 . G C 59 . DP=13;VDB=3.020320e-02;AF1=1;AC1=2;DP4=0,0,13,0;MQ=20;FQ=-66 GT:PL:DP:GQ 1/1:92,39,0:13:75
ordered_SL1344 10627 . A T 58 . DP=13;VDB=2.063488e-02;AF1=1;AC1=2;DP4=0,0,12,0;MQ=20;FQ=-63 GT:PL:DP:GQ 1/1:91,36,0:12:69
ordered_SL1344 10628 . A G 59 . DP=13;VDB=2.994939e-02;AF1=1;AC1=2;DP4=0,0,13,0;MQ=20;FQ=-66 GT:PL:DP:GQ 1/1:92,39,0:13:75
ordered_SL1344 10641 . G T 58 . DP=13;VDB=3.898929e-02;AF1=1;AC1=2;DP4=0,0,12,0;MQ=20;FQ=-63 GT:PL:DP:GQ 1/1:91,36,0:12:69
ordered_SL1344 10656 . T A 59 . DP=13;VDB=3.228742e-02;AF1=1;AC1=2;DP4=0,0,13,0;MQ=20;FQ=-66 GT:PL:DP:GQ 1/1:92,39,0:13:75
ordered_SL1344 10658 . G T 58 . DP=13;VDB=4.040973e-02;AF1=1;AC1=2;DP4=0,0,12,0;MQ=20;FQ=-63 GT:PL:DP:GQ 1/1:91,36,0:12:69
ordered_SL1344 10662 . A C 58 . DP=13;VDB=4.186227e-02;AF1=1;AC1=2;DP4=0,0,12,0;MQ=20;FQ=-63 GT:PL:DP:GQ 1/1:91,36,0:12:69
ordered_SL1344 10666 . A G 57 . DP=13;VDB=2.887760e-02;AF1=1;AC1=2;DP4=0,0,11,0;MQ=20;FQ=-60 GT:PL:DP:GQ 1/1:90,33,0:11:63
ordered_SL1344 10669 . G T 46.1 . DP=13;VDB=4.334669e-02;RPB=-6.681531e-01;AF1=1;AC1=2;DP4=1,0,12,0;MQ=20;FQ=-46;PV4=1,1,1,1 GT:PL:DP:GQ 1/1:79,19,0:13:35
ordered_SL1344 10670 . A G 58 . DP=13;VDB=4.040973e-02;AF1=1;AC1=2;DP4=0,0,12,0;MQ=20;FQ=-63 GT:PL:DP:GQ 1/1:91,36,0:12:69
ordered_SL1344 10674 . T G 58 . DP=12;VDB=4.186227e-02;AF1=1;AC1=2;DP4=0,0,12,0;MQ=20;FQ=-63 GT:PL:DP:GQ 1/1:91,36,0:12:69
ordered_SL1344 10677 . A G 58 . DP=13;VDB=4.186227e-02;AF1=1;AC1=2;DP4=0,0,12,0;MQ=20;FQ=-63 GT:PL:DP:GQ 1/1:91,36,0:12:69
ordered_SL1344 10680 . T A 58 . DP=13;VDB=4.186227e-02;AF1=1;AC1=2;DP4=0,0,12,0;MQ=20;FQ=-63 GT:PL:DP:GQ 1/1:91,36,0:12:69
ordered_SL1344 10682 . T C 58 . DP=13;VDB=4.334669e-02;AF1=1;AC1=2;DP4=0,0,12,0;MQ=20;FQ=-63 GT:PL:DP:GQ 1/1:91,36,0:12:69
ordered_SL1344 10683 . T C 58 . DP=13;VDB=4.186227e-02;AF1=1;AC1=2;DP4=0,0,12,0;MQ=20;FQ=-63 GT:PL:DP:GQ 1/1:91,36,0:12:69
ordered_SL1344 10685 . T C 58 . DP=13;VDB=3.419002e-02;AF1=1;AC1=2;DP4=0,0,13,0;MQ=20;FQ=-66 GT:PL:DP:GQ 1/1:91,39,0:13:75
ordered_SL1344 10699 . T A 58 . DP=21;VDB=2.971712e-02;AF1=1;AC1=2;DP4=0,0,21,0;MQ=20;FQ=-90 GT:PL:DP:GQ 1/1:91,63,0:21:99
ordered_SL1344 10702 . A C 58 . DP=21;VDB=3.376025e-02;AF1=1;AC1=2;DP4=0,0,21,0;MQ=20;FQ=-90 GT:PL:DP:GQ 1/1:91,63,0:21:99
ordered_SL1344 10706 . T C 59 . DP=21;VDB=7.131505e-02;AF1=1;AC1=2;DP4=0,0,20,0;MQ=20;FQ=-87 GT:PL:DP:GQ 1/1:92,60,0:20:99
ordered_SL1344 10717 . A C 58 . DP=21;VDB=1.112405e-01;AF1=1;AC1=2;DP4=0,0,21,0;MQ=20;FQ=-90 GT:PL:DP:GQ 1/1:91,63,0:21:99
ordered_SL1344 10719 . G T 58 . DP=21;VDB=1.262897e-01;AF1=1;AC1=2;DP4=0,0,21,0;MQ=20;FQ=-90 GT:PL:DP:GQ 1/1:91,63,0:21:99
ordered_SL1344 10724 . G C 58 . DP=21;VDB=1.612522e-01;AF1=1;AC1=2;DP4=0,0,21,0;MQ=20;FQ=-90 GT:PL:DP:GQ 1/1:91,63,0:21:99
ordered_SL1344 10725 . A G 58 . DP=21;VDB=1.679314e-01;AF1=1;AC1=2;DP4=0,0,21,0;MQ=20;FQ=-90 GT:PL:DP:GQ 1/1:91,63,0:21:99
ordered_SL1344 10727 . A G 59 . DP=21;VDB=1.870599e-01;AF1=1;AC1=2;DP4=0,0,20,0;MQ=20;FQ=-87 GT:PL:DP:GQ 1/1:92,60,0:20:99
ordered_SL1344 10732 . T A 58 . DP=23;VDB=1.126467e-01;AF1=1;AC1=2;DP4=0,0,22,0;MQ=20;FQ=-93 GT:PL:DP:GQ 1/1:91,66,0:22:99
ordered_SL1344 10735 . C A 58 . DP=23;VDB=1.371208e-01;AF1=1;AC1=2;DP4=0,0,22,0;MQ=20;FQ=-93 GT:PL:DP:GQ 1/1:91,66,0:22:99
ordered_SL1344 10768 . A T 57 . DP=26;VDB=9.575839e-02;AF1=1;AC1=2;DP4=0,0,25,0;MQ=20;FQ=-102 GT:PL:DP:GQ 1/1:90,75,0:25:99
ordered_SL1344 10779 . T G 56 . DP=26;VDB=3.222537e-02;AF1=1;AC1=2;DP4=0,0,26,0;MQ=20;FQ=-105 GT:PL:DP:GQ 1/1:89,78,0:26:99
ordered_SL1344 10792 . C T 70 . DP=27;VDB=1.348121e-01;AF1=1;AC1=2;DP4=0,0,25,1;MQ=20;FQ=-105 GT:PL:DP:GQ 1/1:103,78,0:26:99
ordered_SL1344 10798 . C A 70 . DP=27;VDB=1.305868e-01;AF1=1;AC1=2;DP4=0,0,25,1;MQ=20;FQ=-105 GT:PL:DP:GQ 1/1:103,78,0:26:99
ordered_SL1344 10819 . C T 70 . DP=27;VDB=1.012524e-01;AF1=1;AC1=2;DP4=0,0,25,1;MQ=20;FQ=-105 GT:PL:DP:GQ 1/1:103,78,0:26:99
ordered_SL1344 10826 . C A 83 . DP=28;VDB=2.164841e-01;AF1=1;AC1=2;DP4=0,0,24,2;MQ=20;FQ=-105 GT:PL:DP:GQ 1/1:116,78,0:26:99
ordered_SL1344 10832 . C T 94 . DP=29;VDB=1.477170e-01;AF1=1;AC1=2;DP4=0,0,25,3;MQ=20;FQ=-111 GT:PL:DP:GQ 1/1:127,84,0:28:99
ordered_SL1344 10845 . T G 108 . DP=29;VDB=2.048035e-01;AF1=1;AC1=2;DP4=0,0,24,4;MQ=20;FQ=-111 GT:PL:DP:GQ 1/1:141,84,0:28:99
ordered_SL1344 10856 . C G 108 . DP=27;VDB=9.272622e-02;AF1=1;AC1=2;DP4=0,0,21,4;MQ=20;FQ=-102 GT:PL:DP:GQ 1/1:141,75,0:25:99
ordered_SL1344 10871 . T G 117 . DP=26;VDB=1.547776e-01;AF1=1;AC1=2;DP4=0,0,21,5;MQ=20;FQ=-105 GT:PL:DP:GQ 1/1:150,78,0:26:99
ordered_SL1344 10880 . C T 137 . DP=29;VDB=2.709214e-01;AF1=1;AC1=2;DP4=0,0,21,8;MQ=20;FQ=-114 GT:PL:DP:GQ 1/1:170,87,0:29:99
ordered_SL1344 10923 . C A 155 . DP=28;VDB=2.166228e-01;AF1=1;AC1=2;DP4=0,0,11,14;MQ=20;FQ=-102 GT:PL:DP:GQ 1/1:188,75,0:25:99
ordered_SL1344 10931 . C A 158 . DP=28;VDB=1.674801e-01;AF1=1;AC1=2;DP4=0,0,9,17;MQ=20;FQ=-105 GT:PL:DP:GQ 1/1:191,78,0:26:99
ordered_SL1344 10932 . A C 147 . DP=29;VDB=9.218029e-02;RPB=1.600000e+00;AF1=1;AC1=2;DP4=0,1,8,17;MQ=20;FQ=-86;PV4=1,1,1,1 GT:PL:DP:GQ 1/1:180,59,0:26:99
ordered_SL1344 10971 . C A 154 . DP=27;VDB=3.972358e-03;AF1=1;AC1=2;DP4=0,0,5,21;MQ=20;FQ=-105 GT:PL:DP:GQ 1/1:187,78,0:26:99
ordered_SL1344 11023 . C A 126 . DP=29;VDB=6.495744e-07;AF1=1;AC1=2;DP4=0,0,3,26;MQ=20;FQ=-114 GT:PL:DP:GQ 1/1:159,87,0:29:99
ordered_SL1344 11033 . G T 131 . DP=29;VDB=6.760591e-13;AF1=1;AC1=2;DP4=0,0,3,25;MQ=20;FQ=-111 GT:PL:DP:GQ 1/1:164,84,0:28:99
ordered_SL1344 331762 . C T 8.64 . DP=100;VDB=1.952161e-01;RPB=-8.459357e-02;AF1=0.5;AC1=1;DP4=37,33,7,16;MQ=15;FQ=11.3;PV4=0.091,1,1,1 GT:PL:DP:GQ 0/1:38,0,57:93:40
ordered_SL1344 331844 . A G 20 . DP=98;VDB=4.560235e-02;RPB=-2.113137e-02;AF1=0.5;AC1=1;DP4=34,34,17,9;MQ=15;FQ=16.9;PV4=0.25,0.13,1,1 GT:PL:DP:GQ 0/1:50,0,45:94:47
ordered_SL1344 1030051 . T G 53 . DP=71;VDB=2.819538e-24;RPB=3.701679e+00;AF1=1;AC1=2;DP4=0,8,6,55;MQ=12;FQ=-123;PV4=1,1,0.023,1 GT:PL:DP:GQ 1/1:86,96,0:69:99
ordered_SL1344 1581385 . G A 36 . DP=100;VDB=2.752249e-01;RPB=1.171129e+00;AF1=0.5;AC1=1;DP4=28,34,21,8;MQ=29;FQ=39;PV4=0.023,0.00019,2.2e-10,1 GT:PL:DP:GQ 0/1:66,0,255:91:69
ordered_SL1344 1581394 . C G 25 . DP=100;VDB=2.589062e-01;RPB=8.606900e-01;AF1=0.5;AC1=1;DP4=34,33,18,9;MQ=29;FQ=28;PV4=0.18,0.086,1.9e-09,1 GT:PL:DP:GQ 0/1:55,0,255:94:58
ordered_SL1344 1581395 . A G 19.1 . DP=100;VDB=1.877230e-01;RPB=1.261163e+00;AF1=0.5;AC1=1;DP4=32,33,17,8;MQ=29;FQ=22;PV4=0.16,0.002,2.1e-09,1 GT:PL:DP:GQ 0/1:49,0,255:90:52
ordered_SL1344 1781792 . G A 3.01 . DP=100;VDB=1.605872e-01;RPB=-4.688577e-01;AF1=0.4997;AC1=1;DP4=32,36,2,27;MQ=25;FQ=4.77;PV4=0.00013,0.0076,0.00044,1 GT:PL:DP:GQ 0/1:30,0,253:97:28
ordered_SL1344 1885592 . T C 16.1 . DP=91;VDB=2.987750e-01;RPB=-2.779699e+00;AF1=1;AC1=2;DP4=6,11,37,34;MQ=12;FQ=-83;PV4=0.28,0.12,1,1 GT:PL:DP:GQ 1/1:49,56,0:88:69
ordered_SL1344 2310282 . C T 18.1 . DP=90;VDB=1.729541e-01;RPB=-3.346501e+00;AF1=0.5;AC1=1;DP4=18,45,8,15;MQ=21;FQ=21;PV4=0.6,0.0061,1,0.31 GT:PL:DP:GQ 0/1:48,0,185:86:51
ordered_SL1344 2310284 . G A 25 . DP=90;VDB=1.872664e-01;RPB=-3.031881e+00;AF1=0.5;AC1=1;DP4=18,44,9,14;MQ=21;FQ=28;PV4=0.44,0.029,0.49,0.42 GT:PL:DP:GQ 0/1:55,0,187:85:58
ordered_SL1344 2310336 . T C 40 . DP=80;VDB=1.702749e-01;RPB=-4.157775e+00;AF1=0.5;AC1=1;DP4=13,38,5,18;MQ=20;FQ=43;PV4=1,0.1,1,1 GT:PL:DP:GQ 0/1:70,0,165:74:73
ordered_SL1344 2310338 . A G 43 . DP=80;VDB=1.541612e-01;RPB=-3.900868e+00;AF1=0.5;AC1=1;DP4=12,38,5,18;MQ=20;FQ=46;PV4=1,0.15,1,1 GT:PL:DP:GQ 0/1:73,0,165:73:76
ordered_SL1344 2700503 . G T 56 . DP=94;VDB=4.446144e-01;RPB=3.534105e+00;AF1=1;AC1=2;DP4=6,4,39,42;MQ=10;FQ=-170;PV4=0.52,0.13,1,1 GT:PL:DP:GQ 1/1:89,143,0:91:99
ordered_SL1344 2766741 . T G 50 . DP=60;VDB=2.685056e-15;AF1=1;AC1=2;DP4=0,0,54,0;MQ=18;FQ=-190 GT:PL:DP:GQ 1/1:83,163,0:54:99
ordered_SL1344 2766746 . G T 50 . DP=59;VDB=1.454132e-11;AF1=1;AC1=2;DP4=0,0,57,0;MQ=18;FQ=-199 GT:PL:DP:GQ 1/1:83,172,0:57:99
ordered_SL1344 2766749 . C A 74 . DP=61;VDB=2.018795e-11;AF1=1;AC1=2;DP4=0,0,58,1;MQ=19;FQ=-205 GT:PL:DP:GQ 1/1:107,178,0:59:99
ordered_SL1344 2766772 . A G 60 . DP=63;VDB=3.153931e-09;AF1=1;AC1=2;DP4=0,0,54,1;MQ=18;FQ=-193 GT:PL:DP:GQ 1/1:93,166,0:55:99
ordered_SL1344 2766817 . A G 60 . DP=61;VDB=1.164759e-02;AF1=1;AC1=2;DP4=0,0,52,1;MQ=19;FQ=-187 GT:PL:DP:GQ 1/1:93,160,0:53:99
ordered_SL1344 2766821 . A T,G 58 . DP=61;VDB=2.715204e-02;AF1=1;AC1=2;DP4=0,0,55,2;MQ=18;FQ=-196 GT:PL:DP:GQ 1/1:91,169,0,93,152,90:57:99
ordered_SL1344 2766822 . A T 70 . DP=61;VDB=1.470443e-01;AF1=1;AC1=2;DP4=0,0,55,2;MQ=18;FQ=-199 GT:PL:DP:GQ 1/1:103,172,0:57:99
ordered_SL1344 2766829 . G T 59 . DP=61;VDB=3.182051e-02;AF1=1;AC1=2;DP4=0,0,53,1;MQ=18;FQ=-190 GT:PL:DP:GQ 1/1:92,163,0:54:99
ordered_SL1344 2766834 . C T 73 . DP=62;VDB=2.048759e-01;AF1=1;AC1=2;DP4=0,0,58,2;MQ=18;FQ=-208 GT:PL:DP:GQ 1/1:106,181,0:60:99
ordered_SL1344 2766839 . G C 80 . DP=61;VDB=6.477678e-02;AF1=1;AC1=2;DP4=0,0,54,3;MQ=18;FQ=-199 GT:PL:DP:GQ 1/1:113,172,0:57:99
ordered_SL1344 2766862 . T G 106 . DP=65;VDB=3.663402e-02;AF1=1;AC1=2;DP4=0,0,50,9;MQ=17;FQ=-205 GT:PL:DP:GQ 1/1:139,178,0:59:99
ordered_SL1344 2766869 . C T 112 . DP=65;VDB=9.649980e-04;AF1=1;AC1=2;DP4=0,0,51,10;MQ=17;FQ=-211 GT:PL:DP:GQ 1/1:145,184,0:61:99
ordered_SL1344 2766875 . T A 111 . DP=66;VDB=1.827077e-04;AF1=1;AC1=2;DP4=0,0,45,13;MQ=16;FQ=-202 GT:PL:DP:GQ 1/1:144,175,0:58:99
ordered_SL1344 2766879 . C T,G 110 . DP=66;VDB=1.206593e-05;AF1=1;AC1=2;DP4=0,0,47,13;MQ=16;FQ=-205 GT:PL:DP:GQ 1/1:143,178,0,145,163,142:60:99
ordered_SL1344 2766885 . A G 108 . DP=65;VDB=2.673657e-07;AF1=1;AC1=2;DP4=0,0,41,14;MQ=16;FQ=-193 GT:PL:DP:GQ 1/1:141,166,0:55:99
ordered_SL1344 2766887 . T A 112 . DP=65;VDB=1.458898e-07;AF1=1;AC1=2;DP4=0,0,39,16;MQ=16;FQ=-193 GT:PL:DP:GQ 1/1:145,166,0:55:99
ordered_SL1344 2766911 . A G 68 . DP=68;VDB=2.609006e-02;RPB=6.952218e-01;AF1=0.5;AC1=1;DP4=15,15,14,13;MQ=16;FQ=69.3;PV4=1,0.053,1,0.26 GT:PL:DP:GQ 0/1:98,0,101:57:99
ordered_SL1344 2766912 . A T 74 . DP=68;VDB=1.122564e-02;RPB=8.015189e-01;AF1=0.5;AC1=1;DP4=17,15,16,13;MQ=16;FQ=73.5;PV4=1,0.12,1,0.28 GT:PL:DP:GQ 0/1:104,0,103:61:99
ordered_SL1344 2766933 . C A 146 . DP=59;VDB=1.613905e-02;AF1=1;AC1=2;DP4=0,0,16,35;MQ=17;FQ=-181 GT:PL:DP:GQ 1/1:179,154,0:51:99
ordered_SL1344 2766935 . C A 139 . DP=57;VDB=1.275435e-02;AF1=1;AC1=2;DP4=0,0,15,36;MQ=17;FQ=-181 GT:PL:DP:GQ 1/1:172,154,0:51:99
ordered_SL1344 2766947 . C G 126 . DP=53;VDB=1.223404e-03;AF1=1;AC1=2;DP4=0,0,12,34;MQ=16;FQ=-165 GT:PL:DP:GQ 1/1:159,138,0:46:99
ordered_SL1344 2766969 . T C 58 . DP=58;VDB=8.426448e-03;RPB=6.827567e-01;AF1=0.5;AC1=1;DP4=6,23,5,21;MQ=17;FQ=47.8;PV4=1,0.41,1,1 GT:PL:DP:GQ 0/1:88,0,75:55:78
ordered_SL1344 2766984 . T G 140 . DP=59;VDB=5.412042e-03;AF1=1;AC1=2;DP4=0,0,12,46;MQ=17;FQ=-202 GT:PL:DP:GQ 1/1:173,175,0:58:99
ordered_SL1344 2767027 . C A 138 . DP=67;VDB=2.110505e-01;AF1=1;AC1=2;DP4=0,0,13,53;MQ=17;FQ=-226 GT:PL:DP:GQ 1/1:171,199,0:66:99
ordered_SL1344 2767038 . C A 126 . DP=67;VDB=1.528772e-04;AF1=1;AC1=2;DP4=0,0,9,54;MQ=17;FQ=-217 GT:PL:DP:GQ 1/1:159,190,0:63:99
ordered_SL1344 2767047 . A T 37 . DP=66;VDB=7.148092e-02;RPB=-1.137527e+00;AF1=0.5;AC1=1;DP4=5,16,3,16;MQ=16;FQ=38.3;PV4=0.7,0.087,1,1 GT:PL:DP:GQ 0/1:67,0,70:40:68
ordered_SL1344 2767048 . T C 114 . DP=41;VDB=2.385829e-05;AF1=1;AC1=2;DP4=0,0,8,30;MQ=16;FQ=-141 GT:PL:DP:GQ 1/1:147,114,0:38:99
ordered_SL1344 2767050 . T A 115 . DP=65;VDB=2.413513e-05;AF1=1;AC1=2;DP4=0,0,9,30;MQ=16;FQ=-144 GT:PL:DP:GQ 1/1:148,117,0:39:99
ordered_SL1344 2767057 . A G 32 . DP=66;VDB=1.365349e-01;RPB=-1.420094e+00;AF1=0.5;AC1=1;DP4=6,16,3,19;MQ=17;FQ=34.4;PV4=0.46,0.34,1,1 GT:PL:DP:GQ 0/1:62,0,70:44:64
ordered_SL1344 2767062 . C G 119 . DP=68;VDB=4.893656e-03;AF1=1;AC1=2;DP4=0,0,9,36;MQ=17;FQ=-162 GT:PL:DP:GQ 1/1:152,135,0:45:99
ordered_SL1344 2767070 . C A 127 . DP=69;VDB=6.473737e-05;AF1=1;AC1=2;DP4=0,0,9,58;MQ=17;FQ=-229 GT:PL:DP:GQ 1/1:160,202,0:67:99
ordered_SL1344 2767076 . T A 126 . DP=69;VDB=6.820261e-06;AF1=1;AC1=2;DP4=0,0,9,55;MQ=17;FQ=-220 GT:PL:DP:GQ 1/1:159,193,0:64:99
ordered_SL1344 2767085 . T C 124 . DP=71;VDB=4.645075e-05;AF1=1;AC1=2;DP4=0,0,8,58;MQ=18;FQ=-226 GT:PL:DP:GQ 1/1:157,199,0:66:99
ordered_SL1344 2767097 . C G 125 . DP=71;VDB=2.071120e-04;AF1=1;AC1=2;DP4=0,0,8,59;MQ=18;FQ=-229 GT:PL:DP:GQ 1/1:158,202,0:67:99
ordered_SL1344 2767102 . C T 128 . DP=71;VDB=3.212713e-03;AF1=1;AC1=2;DP4=0,0,9,59;MQ=17;FQ=-232 GT:PL:DP:GQ 1/1:161,205,0:68:99
ordered_SL1344 2767120 . T G 126 . DP=69;VDB=1.733848e-02;AF1=1;AC1=2;DP4=0,0,7,59;MQ=18;FQ=-226 GT:PL:DP:GQ 1/1:159,199,0:66:99
ordered_SL1344 2767124 . T G 124 . DP=69;VDB=1.158917e-02;AF1=1;AC1=2;DP4=0,0,7,59;MQ=18;FQ=-226 GT:PL:DP:GQ 1/1:157,199,0:66:99
ordered_SL1344 2767128 . A C 114 . DP=64;VDB=7.511536e-04;RPB=1.457306e+00;AF1=1;AC1=2;DP4=0,1,6,56;MQ=18;FQ=-198;PV4=1,1,0.29,0.4 GT:PL:DP:GQ 1/1:147,171,0:63:99
ordered_SL1344 2767129 . C A 119 . DP=63;VDB=5.384455e-04;AF1=1;AC1=2;DP4=0,0,6,55;MQ=18;FQ=-211 GT:PL:DP:GQ 1/1:152,184,0:61:99
ordered_SL1344 2767131 . C A 109 . DP=64;VDB=7.408168e-04;AF1=1;AC1=2;DP4=0,0,4,56;MQ=18;FQ=-208 GT:PL:DP:GQ 1/1:142,181,0:60:99
ordered_SL1344 2767140 . T G 116 . DP=69;VDB=8.843391e-06;AF1=1;AC1=2;DP4=0,0,6,62;MQ=17;FQ=-232 GT:PL:DP:GQ 1/1:149,205,0:68:99
ordered_SL1344 2767142 . T G 111 . DP=69;VDB=1.585240e-05;AF1=1;AC1=2;DP4=0,0,5,63;MQ=17;FQ=-232 GT:PL:DP:GQ 1/1:144,205,0:68:99
ordered_SL1344 2767151 . C T 93 . DP=45;VDB=2.550717e-06;AF1=1;AC1=2;DP4=0,0,4,35;MQ=16;FQ=-144 GT:PL:DP:GQ 1/1:126,117,0:39:99
ordered_SL1344 2767178 . C A 86 . DP=40;VDB=2.329167e-01;AF1=1;AC1=2;DP4=0,0,3,34;MQ=17;FQ=-138 GT:PL:DP:GQ 1/1:119,111,0:37:99
ordered_SL1344 2767185 . C A 25 . DP=12;VDB=1.104589e-01;AF1=1;AC1=2;DP4=0,0,2,9;MQ=10;FQ=-60 GT:PL:DP:GQ 1/1:58,33,0:11:54
ordered_SL1344 2767187 . T G 21 . DP=12;VDB=8.354620e-02;AF1=1;AC1=2;DP4=0,0,2,8;MQ=10;FQ=-57 GT:PL:DP:GQ 1/1:54,30,0:10:47
ordered_SL1344 2767188 . C G 30 . DP=12;VDB=1.252190e-01;AF1=1;AC1=2;DP4=0,0,1,10;MQ=12;FQ=-60 GT:PL:DP:GQ 1/1:63,33,0:11:58
ordered_SL1344 2767190 . C A 27 . DP=12;VDB=1.342001e-01;AF1=1;AC1=2;DP4=0,0,1,9;MQ=12;FQ=-57 GT:PL:DP:GQ 1/1:60,30,0:10:52
ordered_SL1344 2767192 . T G 31 . DP=12;VDB=1.051503e-01;AF1=1;AC1=2;DP4=0,0,2,9;MQ=11;FQ=-60 GT:PL:DP:GQ 1/1:64,33,0:11:59
ordered_SL1344 2767194 . C G 27 . DP=12;VDB=1.363825e-01;AF1=1;AC1=2;DP4=0,0,1,9;MQ=12;FQ=-57 GT:PL:DP:GQ 1/1:60,30,0:10:52
ordered_SL1344 2767206 . T C 21 . DP=11;VDB=1.302440e-02;AF1=1;AC1=2;DP4=0,0,1,9;MQ=10;FQ=-57 GT:PL:DP:GQ 1/1:54,30,0:10:47
ordered_SL1344 2767207 . C A 21 . DP=11;VDB=1.206574e-02;AF1=1;AC1=2;DP4=0,0,1,9;MQ=10;FQ=-57 GT:PL:DP:GQ 1/1:54,30,0:10:47
ordered_SL1344 2767214 . T C 20 . DP=10;VDB=3.852326e-03;AF1=1;AC1=2;DP4=0,0,1,9;MQ=10;FQ=-57 GT:PL:DP:GQ 1/1:53,30,0:10:47
ordered_SL1344 2767215 . C A 21 . DP=10;VDB=3.188557e-03;AF1=1;AC1=2;DP4=0,0,1,9;MQ=10;FQ=-57 GT:PL:DP:GQ 1/1:54,30,0:10:47
ordered_SL1344 2767217 . T G 17.1 . DP=10;VDB=2.475551e-03;AF1=1;AC1=2;DP4=0,0,1,9;MQ=10;FQ=-57 GT:PL:DP:GQ 1/1:50,30,0:10:44
ordered_SL1344 3509635 . G C 44 . DP=87;VDB=2.010525e-01;RPB=-7.706536e-01;AF1=1;AC1=2;DP4=5,5,34,41;MQ=11;FQ=-156;PV4=1,0.45,1,1 GT:PL:DP:GQ 1/1:77,129,0:85:99
ordered_SL1344 4386925 . T C 21 . DP=20;VDB=4.041064e-02;RPB=7.024394e-01;AF1=0.5;AC1=1;DP4=8,4,4,2;MQ=17;FQ=23.9;PV4=1,0.0022,1,0.095 GT:PL:DP:GQ 0/1:51,0,67:18:54
ordered_SL1344 4387047 . G A 15.2 . DP=13;VDB=4.374793e-02;RPB=3.171491e-01;AF1=0.505;AC1=1;DP4=1,4,0,6;MQ=16;FQ=-10.4;PV4=0.45,0.32,1,1 GT:PL:DP:GQ 0/1:45,0,17:11:20
ordered_SL1344 4387064 . C A 9.82 . DP=11;VDB=7.269818e-02;RPB=0.000000e+00;AF1=0.543;AC1=1;DP4=0,3,0,4;MQ=17;FQ=-19;PV4=1,0.023,1,1 GT:PL:DP:GQ 0/1:39,0,8:7:12