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##fileformat=VCFv4.1
##samtoolsVersion=0.1.19-44428cd
##reference=file://../../../salmonellaScaffolds/SL1344.fasta
##contig=<ID=SL1344,length=4878012>
##contig=<ID=pSLT,length=93842>
##contig=<ID=pCol1B9,length=86908>
##contig=<ID=pRSF1010,length=8688>
##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 ../../fitzy_bowtie2_very_sensitive_local_multi_rand.sorted.bam
SL1344 66308 . A G 17.1 . DP=91;VDB=1.997518e-02;RPB=-2.839391e+00;AF1=1;AC1=2;DP4=47,33,6,0;MQ=13;FQ=-161;PV4=0.078,1,1,1 GT:PL:DP:GQ 1/1:50,134,0:86:84
SL1344 66326 . C T 18.1 . DP=94;VDB=1.997518e-02;RPB=-2.658937e+00;AF1=1;AC1=2;DP4=51,32,6,0;MQ=13;FQ=-167;PV4=0.084,1,1,1 GT:PL:DP:GQ 1/1:51,140,0:89:87
SL1344 66329 . G C 17.1 . DP=93;VDB=1.997518e-02;RPB=-2.479249e+00;AF1=1;AC1=2;DP4=46,33,6,0;MQ=13;FQ=-155;PV4=0.077,1,1,1 GT:PL:DP:GQ 1/1:50,128,0:85:84
SL1344 66332 . T C 12.3 . DP=93;VDB=1.093326e-02;RPB=-2.899092e+00;AF1=1;AC1=2;DP4=49,32,6,1;MQ=13;FQ=-156;PV4=0.25,1,1,1 GT:PL:DP:GQ 1/1:45,129,0:88:69
SL1344 66335 . G A 12.3 . DP=93;VDB=1.997518e-02;RPB=-2.560761e+00;AF1=1;AC1=2;DP4=48,35,6,0;MQ=13;FQ=-162;PV4=0.077,1,1,1 GT:PL:DP:GQ 1/1:45,135,0:89:69
SL1344 66344 . C T 23 . DP=98;VDB=4.221577e-02;RPB=-3.058285e+00;AF1=1;AC1=2;DP4=49,34,7,0;MQ=14;FQ=-156;PV4=0.042,1,1,1 GT:PL:DP:GQ 1/1:56,129,0:90:99
SL1344 66560 . G A 29 . DP=94;VDB=1.603450e-01;RPB=4.330656e-01;AF1=0.5;AC1=1;DP4=33,42,8,7;MQ=25;FQ=32;PV4=0.58,0.00074,1,0.32 GT:PL:DP:GQ 0/1:59,0,147:90:62
SL1344 66563 . A G 3.54 . DP=93;VDB=1.330160e-01;RPB=-3.869623e-01;AF1=0.4998;AC1=1;DP4=31,42,7,7;MQ=24;FQ=5.47;PV4=0.77,8.2e-07,1,0.23 GT:PL:DP:GQ 0/1:31,0,149:87:30
SL1344 368931 . C T 177 . DP=100;VDB=1.952161e-01;RPB=-8.459357e-02;AF1=0.5;AC1=1;DP4=37,33,7,16;MQ=23;FQ=30;PV4=0.091,1,1,1 GT:PL:DP:GQ 0/1:207,0,57:93:60
SL1344 369013 . A G 192 . DP=98;VDB=4.560235e-02;RPB=-2.113137e-02;AF1=0.5;AC1=1;DP4=34,34,17,9;MQ=25;FQ=52;PV4=0.25,0.13,1,1 GT:PL:DP:GQ 0/1:222,0,79:94:82
SL1344 466805 . C G 3.54 . DP=86;VDB=1.801567e-01;RPB=7.113758e-01;AF1=0.4998;AC1=1;DP4=32,32,4,14;MQ=38;FQ=5.47;PV4=0.058,0.14,2e-16,0.37 GT:PL:DP:GQ 0/1:31,0,255:82:30
SL1344 635606 . T A 222 . DP=95;VDB=2.462103e-01;AF1=1;AC1=2;DP4=0,0,40,46;MQ=44;FQ=-282 GT:PL:DP:GQ 1/1:255,255,0:86:99
SL1344 1004543 . T C 7.8 . DP=98;VDB=7.629309e-02;RPB=-2.138060e-01;AF1=0.5;AC1=1;DP4=37,42,1,15;MQ=25;FQ=10.4;PV4=0.0019,0.0086,1,1 GT:PL:DP:GQ 0/1:37,0,158:95:39
SL1344 1066574 . T A 82 . DP=98;VDB=1.232246e-01;RPB=-1.897624e+00;AF1=0.5;AC1=1;DP4=30,42,13,9;MQ=33;FQ=85;PV4=0.22,1.8e-08,1,1 GT:PL:DP:GQ 0/1:112,0,255:94:99
SL1344 1066589 . C T 96 . DP=93;VDB=1.628777e-01;RPB=-1.266533e+00;AF1=0.5;AC1=1;DP4=28,42,11,9;MQ=32;FQ=99;PV4=0.31,0.00047,1,0.24 GT:PL:DP:GQ 0/1:126,0,255:90:99
SL1344 1066592 . A T 108 . DP=95;VDB=2.058572e-01;RPB=-1.245734e+00;AF1=0.5;AC1=1;DP4=29,43,12,10;MQ=32;FQ=111;PV4=0.33,4.8e-06,1,0.1 GT:PL:DP:GQ 0/1:138,0,255:94:99
SL1344 1066601 . G A 101 . DP=91;VDB=1.948532e-01;RPB=-1.389409e+00;AF1=0.5;AC1=1;DP4=28,42,11,10;MQ=32;FQ=104;PV4=0.33,5.1e-06,1,0.24 GT:PL:DP:GQ 0/1:131,0,255:91:99
SL1344 1066610 . T C 85 . DP=88;VDB=1.845743e-01;RPB=-1.831173e+00;AF1=0.5;AC1=1;DP4=29,39,8,10;MQ=31;FQ=88;PV4=1,3.4e-05,1,1 GT:PL:DP:GQ 0/1:115,0,255:86:99
SL1344 1066619 . T C 66 . DP=92;VDB=1.923689e-01;RPB=-1.492935e+00;AF1=0.5;AC1=1;DP4=30,41,8,11;MQ=31;FQ=69;PV4=1,6.2e-06,1,1 GT:PL:DP:GQ 0/1:96,0,255:90:99
SL1344 1066649 . T G 65 . DP=95;VDB=1.219802e-01;RPB=-1.308688e+00;AF1=0.5;AC1=1;DP4=34,41,4,15;MQ=28;FQ=68;PV4=0.069,0.0056,1,1 GT:PL:DP:GQ 0/1:95,0,235:94:98
SL1344 1066679 . C T 106 . DP=92;VDB=9.986689e-02;RPB=-4.717792e-01;AF1=0.5;AC1=1;DP4=32,35,5,18;MQ=26;FQ=109;PV4=0.048,0.031,1,1 GT:PL:DP:GQ 0/1:136,0,223:90:99
SL1344 1066725 . A G 69 . DP=94;VDB=5.957553e-02;RPB=8.967339e-01;AF1=0.5;AC1=1;DP4=40,29,2,19;MQ=24;FQ=72;PV4=0.0001,0.019,1,1 GT:PL:DP:GQ 0/1:99,0,161:90:99
SL1344 1066919 . C T 9.51 . DP=97;VDB=6.040955e-02;RPB=3.316951e+00;AF1=1;AC1=2;DP4=42,40,1,8;MQ=16;FQ=-99;PV4=0.032,1,1,0.22 GT:PL:DP:GQ 1/1:42,72,0:91:60
SL1344 1083415 . T C 34 . DP=68;VDB=4.819237e-02;RPB=5.418165e-01;AF1=0.5;AC1=1;DP4=24,28,9,3;MQ=31;FQ=37;PV4=0.11,0.023,1,0.47 GT:PL:DP:GQ 0/1:64,0,255:64:67
SL1344 1083419 . G A 34 . DP=68;VDB=1.395488e-02;RPB=-3.785282e-01;AF1=0.5;AC1=1;DP4=27,28,7,4;MQ=30;FQ=37;PV4=0.51,0.16,1,0.087 GT:PL:DP:GQ 0/1:64,0,254:66:67
SL1344 1083420 . A C 27 . DP=71;VDB=3.371720e-02;RPB=8.716719e-01;AF1=0.5;AC1=1;DP4=28,28,8,3;MQ=30;FQ=30;PV4=0.2,0.16,1,0.42 GT:PL:DP:GQ 0/1:57,0,254:67:60
SL1344 1083473 . A C 5.46 . DP=82;VDB=1.786897e-02;RPB=-1.661799e-01;AF1=0.4999;AC1=1;DP4=38,31,5,7;MQ=29;FQ=7.8;PV4=0.53,0.0074,1,1 GT:PL:DP:GQ 0/1:34,0,223:81:34
SL1344 1083483 . A C 38 . DP=77;VDB=3.175649e-02;RPB=3.795416e-01;AF1=0.5;AC1=1;DP4=34,27,5,7;MQ=29;FQ=41;PV4=0.53,0.023,1,0.48 GT:PL:DP:GQ 0/1:68,0,235:73:71
SL1344 1083484 . A G 30 . DP=77;VDB=3.794517e-02;RPB=-5.205973e-01;AF1=0.5;AC1=1;DP4=34,28,4,8;MQ=30;FQ=33;PV4=0.22,0.012,1,1 GT:PL:DP:GQ 0/1:60,0,232:74:63
SL1344 1458612 . A T 73 . DP=93;VDB=2.268170e-06;RPB=-3.044047e+00;AF1=0.5;AC1=1;DP4=31,32,18,5;MQ=34;FQ=76;PV4=0.026,1,0.0025,1 GT:PL:DP:GQ 0/1:103,0,255:86:99
SL1344 1530959 . G A 34 . DP=96;VDB=1.082305e-01;RPB=-3.501499e-01;AF1=0.5;AC1=1;DP4=35,43,7,5;MQ=23;FQ=37;PV4=0.54,1,1,1 GT:PL:DP:GQ 0/1:64,0,107:90:67
SL1344 1531064 . T G 6.2 . DP=95;VDB=4.661049e-02;RPB=-6.467773e-01;AF1=0.4999;AC1=1;DP4=37,41,12,2;MQ=25;FQ=8.65;PV4=0.0091,0.31,1,1 GT:PL:DP:GQ 0/1:35,0,175:92:36
SL1344 1618370 . G A 56 . DP=100;VDB=2.752249e-01;RPB=1.171129e+00;AF1=0.5;AC1=1;DP4=28,34,21,8;MQ=35;FQ=59;PV4=0.023,0.00019,3e-36,1 GT:PL:DP:GQ 0/1:86,0,255:91:89
SL1344 1618379 . C G 46 . DP=100;VDB=2.589062e-01;RPB=8.606900e-01;AF1=0.5;AC1=1;DP4=34,33,18,9;MQ=36;FQ=49;PV4=0.18,0.086,2.2e-36,1 GT:PL:DP:GQ 0/1:76,0,255:94:79
SL1344 1618380 . A G 40 . DP=100;VDB=1.877230e-01;RPB=1.261163e+00;AF1=0.5;AC1=1;DP4=32,33,17,8;MQ=36;FQ=43;PV4=0.16,0.002,3.8e-34,1 GT:PL:DP:GQ 0/1:70,0,255:90:73
SL1344 1621894 . C T 21 . DP=98;VDB=1.958408e-01;RPB=-1.606686e+00;AF1=0.5;AC1=1;DP4=34,39,9,12;MQ=33;FQ=24;PV4=0.81,0.046,1.9e-11,1 GT:PL:DP:GQ 0/1:51,0,255:94:54
SL1344 1621927 . A C 5.46 . DP=100;VDB=4.882539e-02;RPB=1.849425e-01;AF1=0.4999;AC1=1;DP4=34,42,7,13;MQ=34;FQ=7.8;PV4=0.46,0.047,1.5e-12,1 GT:PL:DP:GQ 0/1:34,0,255:96:34
SL1344 1621937 . T A 5.46 . DP=100;VDB=4.185181e-02;RPB=3.788414e-01;AF1=0.4999;AC1=1;DP4=34,41,7,13;MQ=34;FQ=7.8;PV4=0.46,0.072,5.9e-12,1 GT:PL:DP:GQ 0/1:34,0,255:95:34
SL1344 1815932 . A T 14.2 . DP=100;VDB=2.292903e-01;RPB=5.542098e-01;AF1=0.5;AC1=1;DP4=36,36,17,7;MQ=35;FQ=17.1;PV4=0.098,0.0046,9.7e-41,0.41 GT:PL:DP:GQ 0/1:44,0,255:96:47
SL1344 1816838 . G A 11.3 . DP=100;VDB=1.605872e-01;RPB=-4.688577e-01;AF1=0.5;AC1=1;DP4=32,36,2,27;MQ=37;FQ=14.2;PV4=0.00013,0.0076,5.2e-62,1 GT:PL:DP:GQ 0/1:41,0,255:97:43
SL1344 1921476 . G T 13.2 . DP=99;VDB=1.581505e-02;RPB=3.104761e+00;AF1=0.5;AC1=1;DP4=37,34,9,15;MQ=30;FQ=16.1;PV4=0.24,0.0056,1.6e-09,1 GT:PL:DP:GQ 0/1:43,0,255:95:46
SL1344 1921520 . G A 36 . DP=97;VDB=6.015507e-05;RPB=-5.674664e+00;AF1=0.5;AC1=1;DP4=40,31,15,6;MQ=29;FQ=39;PV4=0.31,0.17,0.00098,1 GT:PL:DP:GQ 0/1:66,0,255:92:69
SL1344 3257857 . A G 3.01 . DP=100;VDB=5.750374e-02;RPB=2.880552e-01;AF1=0.4997;AC1=1;DP4=37,35,9,10;MQ=39;FQ=4.77;PV4=0.8,0.056,4.7e-45,0.19 GT:PL:DP:GQ 0/1:30,0,255:91:28
SL1344 3885592 . T G 4.13 . DP=97;VDB=5.067963e-02;RPB=-1.400699e+00;AF1=0.4998;AC1=1;DP4=36,33,9,11;MQ=38;FQ=6.2;PV4=0.62,0.48,5.9e-39,1 GT:PL:DP:GQ 0/1:32,0,255:89:31
SL1344 4033815 . C T 133 . DP=99;VDB=1.950578e-01;RPB=-2.898443e+00;AF1=0.5;AC1=1;DP4=33,37,7,16;MQ=26;FQ=118;PV4=0.23,2.9e-05,1,1 GT:PL:DP:GQ 0/1:163,0,145:93:99
SL1344 4033817 . G A 183 . DP=98;VDB=2.519198e-01;RPB=-2.598783e+00;AF1=0.5;AC1=1;DP4=32,35,9,18;MQ=27;FQ=112;PV4=0.25,0.11,1,1 GT:PL:DP:GQ 0/1:213,0,139:94:99
SL1344 4510440 . T C 36 . DP=100;VDB=1.265169e-01;RPB=7.759706e-01;AF1=0.5;AC1=1;DP4=34,36,10,9;MQ=29;FQ=39;PV4=0.8,0.0037,0.32,1 GT:PL:DP:GQ 0/1:66,0,255:89:69
SL1344 4510499 . C T 7.8 . DP=99;VDB=1.739060e-01;RPB=2.345257e+00;AF1=0.5;AC1=1;DP4=40,32,4,14;MQ=34;FQ=10.4;PV4=0.017,0.00081,1.9e-05,1 GT:PL:DP:GQ 0/1:37,0,255:90:39
SL1344 4510502 . A G 4.77 . DP=98;VDB=1.640491e-02;RPB=2.260907e+00;AF1=0.4999;AC1=1;DP4=39,36,2,16;MQ=34;FQ=6.99;PV4=0.0015,0.035,0.00012,1 GT:PL:DP:GQ 0/1:33,0,255:93:33
SL1344 4510506 . G A 10.4 . DP=99;VDB=6.934714e-02;RPB=2.673867e+00;AF1=0.5;AC1=1;DP4=40,35,3,16;MQ=34;FQ=13.2;PV4=0.0041,0.033,1.6e-05,1 GT:PL:DP:GQ 0/1:40,0,255:94:42
SL1344 4510509 . G C 6.98 . DP=99;VDB=1.718726e-01;RPB=2.646809e+00;AF1=0.4999;AC1=1;DP4=39,35,4,16;MQ=34;FQ=9.53;PV4=0.011,0.001,8e-07,0.4 GT:PL:DP:GQ 0/1:36,0,255:94:37
SL1344 4511817 . C T 6.98 . DP=88;VDB=1.819788e-01;RPB=1.372624e-01;AF1=0.4999;AC1=1;DP4=32,33,7,10;MQ=36;FQ=9.53;PV4=0.6,1,4.5e-16,1 GT:PL:DP:GQ 0/1:36,0,255:82:37