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Searched refs:MQ (Results 1 – 25 of 3736) sorted by relevance

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/dports/biology/samtools/samtools-1.14/test/large_pos/
H A D	longref3.expected.sam	9 p1 99 1 1073741724 66 10M = 1073741924 210 GAAAAAAAAC * MQ:i:66 MC:Z:10M 12 x1 97 1 1073741727 66 10M 2 4073741927 0 GAAAAAAAAC * MQ:i:66 MC:Z:10M 13 p1 147 1 1073741924 66 10M = 1073741724 -210 GAAAAAAAAC * MQ:i:66 MC:Z:10M 15 p2 99 1 2147483548 66 10M = 2147483748 210 GAAAAAAAAC * MQ:i:66 MC:Z:10M 18 x2 97 1 2147483551 66 10M 2 5147483751 0 GAAAAAAAAC * MQ:i:66 MC:Z:10M 21 p3 99 1 3221225372 66 10M = 3221225572 210 GAAAAAAAAC * MQ:i:66 MC:Z:10M 24 x3 97 1 3221225375 66 10M 2 6221225575 0 GAAAAAAAAC * MQ:i:66 MC:Z:10M 27 p4 99 1 4294967196 66 10M = 4294967396 210 GAAAAAAAAC * MQ:i:66 MC:Z:10M 29 x4 97 1 4294967199 66 10M 2 7294967399 0 GAAAAAAAAC * MQ:i:66 MC:Z:10M 34 x5 97 1 5368709023 66 10M 2 8368709223 0 GAAAAAAAAC * MQ:i:66 MC:Z:10M [all …]
/dports/deskutils/calibre/calibre-src-5.34.0/src/tinycss/tests/
H A D	media3.py	8 from tinycss.media3 import CSSMedia3Parser, MediaQuery as MQ unknown 28 ('@media {}', [MQ()], []), 29 ('@media all {}', [MQ()], []), 30 ('@media screen {}', [MQ('screen')], []), 31 ('@media , screen {}', [MQ(), MQ('screen')], []), 32 ('@media screen, {}', [MQ('screen'), MQ()], []), 43 MQ('screen', (('color', None),)), MQ('projection', (('color', None),)),], []), 45 MQ('screen', (('color', None),), True)], []), 47 MQ('screen', (('color', None),))], []), 56 … ('@media (example, all,), speech {}', [MQ(negated=True), MQ('speech')], ['expected a :']), [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/
H A D	yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf	16 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 27 1 61969 . T C 98.69 GATK_STANDARD;HARD_TO_VALIDATE AC=2;AF=1.00;AN=2;DB=0;DP=83;Dels=0.00;HRun=0;MQ… 56 1 695744 . C T 287.83 PASS AB=0.53;AC=2;AF=0.33;AN=6;DB=0;DP=115;Dels=0.00;HRun=0;MQ=134.37;MQ0=4;Q… 70 1 726158 . A T 365.11 PASS AB=0.53;AC=2;AF=0.33;AN=6;DB=0;DP=73;Dels=0.01;HRun=6;MQ=84.48;MQ0=0;QD=… 86 1 746966 . C T 345.35 PASS AB=0.54;AC=1;AF=0.17;AN=6;DB=0;DP=149;Dels=0.00;HRun=0;MQ=133.97;MQ0=3;Q… 125 1 777212 . T C 114.16 PASS AB=0.58;AC=1;AF=0.17;AN=6;DB=0;DP=128;Dels=0.00;HRun=0;MQ=139.70;MQ0=1;Q… 141 1 794842 . A T 99.76 PASS AB=0.50;AC=1;AF=0.17;AN=6;DB=0;DP=89;Dels=0.00;HRun=2;MQ=147.12;MQ0=1;QD=… 149 1 801212 . G A 106.63 HARD_TO_VALIDATE AB=0.71;AC=1;AF=0.50;AN=2;DB=0;DP=36;Dels=0.00;HRun=0;MQ=148… 150 1 801256 . C T 345.58 HARD_TO_VALIDATE AB=0.52;AC=1;AF=0.50;AN=2;DB=0;DP=44;Dels=0.00;HRun=1;MQ=176… 364 1 869139 . A G 113.96 PASS AB=0.58;AC=1;AF=0.17;AN=6;DB=0;DP=83;Dels=0.00;HRun=0;MQ=115.04;MQ0=0;QD… [all …]
H A D	CEU.trio.callsForVE.vcf	3 …154;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7355;MQ=48.87;MQ0=4;QD=28.88;VQSLOD=3.6550;culprit=… 6 …140;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=1.4914;MQ=49.69;MQ0=1;QD=30.73;VQSLOD=4.3083;culprit=… 7 …243;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5776;MQ=51.69;MQ0=0;QD=33.65;VQSLOD=5.8432;culprit=… 8 …148;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.5063;MQ=48.78;MQ0=8;QD=16.87;VQSLOD=3.5744;culprit=… 9 …151;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5724;MQ=49.43;MQ0=6;QD=18.33;VQSLOD=3.3654;culprit=… 10 …206;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9674;MQ=53.43;MQ0=6;QD=24.77;VQSLOD=5.6627;culprit=… 12 …218;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=1.0648;MQ=42.93;MQ0=2;QD=29.95;VQSLOD=2.6384;culprit=… 20 …212;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=38.37;MQ0=33;QD=25.82;VQSLOD=2.2975;culprit… 23 …128;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=41.25;MQ0=24;QD=25.26;VQSLOD=2.5415;culprit… 24 …131;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.5752;MQ=35.65;MQ0=5;QD=23.13;VQSLOD=2.2903;culprit=… [all …]
H A D	pacbio.ts.recalibrated.vcf	17 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 29 20 1409612 . T A 579.26 PASS AC=1;AF=0.50;AN=2;DP=148;Dels=0.16;HRun=2;HaplotypeScore=372.8065;MQ=6… 38 20 3153236 . C G 304.30 PASS AC=1;AF=0.50;AN=2;DP=119;Dels=0.16;HRun=1;HaplotypeScore=320.3893;MQ=6… 40 20 3153605 . C T 151.39 PASS AC=1;AF=0.50;AN=2;DP=60;Dels=0.15;HRun=1;HaplotypeScore=161.0277;MQ=60… 147 20 25831374 . A T 93.18 PASS AC=1;AF=0.50;AN=2;DP=67;Dels=0.03;HRun=0;HaplotypeScore=153.4111;MQ=60… 164 20 26130942 . G C 92.07 PASS AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=25.2725;MQ=60.… 166 20 26131123 . G A 82.31 PASS AC=1;AF=0.50;AN=2;DP=70;Dels=0.01;HRun=0;HaplotypeScore=103.3413;MQ=60… 167 20 26131133 . A G 94.82 PASS AC=1;AF=0.50;AN=2;DP=70;Dels=0.04;HRun=0;HaplotypeScore=92.8547;MQ=60.… 185 20 26131872 . A G 33.79 PASS AC=1;AF=0.50;AN=2;DP=51;Dels=0.02;HRun=0;HaplotypeScore=38.3012;MQ=60.… 188 20 26132070 . A G 56.36 PASS AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=18.9358;MQ=60.… [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/
H A D	expected.testVCFMode.gatk3.8-4-g7b0250253.vcf	4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 18 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 28 20 10000439 . T G 2819.06 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 29 20 10000598 . T A 1956.06 . AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 31 20 10000758 . T A 3853.06 . AC=2;AF=1.00;AN=2;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 33 20 10001298 . T A 2932.06 . AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 35 20 10001474 . C T 2655.06 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 37 20 10001628 . G A 3913.06 . AC=2;AF=1.00;AN=2;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 38 20 10001661 . T C 3621.06 . AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 39 20 10001670 . T G 3688.06 . AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… [all …]
H A D	expected.testVCFMode.gatk4.nonstrict.vcf	4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 18 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 28 20 10000439 . T G 2819.06 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 29 20 10000598 . T A 1956.06 . AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 31 20 10000758 . T A 3853.06 . AC=2;AF=1.00;AN=2;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 33 20 10001298 . T A 2932.06 . AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 35 20 10001474 . C T 2655.06 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 37 20 10001628 . G A 3913.06 . AC=2;AF=1.00;AN=2;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 38 20 10001661 . T C 3621.06 . AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 39 20 10001670 . T G 3688.06 . AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… [all …]
H A D	expected.testVCFMode.gatk4.vcf	4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 18 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 28 20 10000439 . T G 2819.06 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 29 20 10000598 . T A 1956.06 . AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 31 20 10000758 . T A 3853.06 . AC=2;AF=1.00;AN=2;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 33 20 10001298 . T A 2932.06 . AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 35 20 10001474 . C T 2655.06 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 37 20 10001628 . G A 3913.06 . AC=2;AF=1.00;AN=2;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 38 20 10001661 . T C 3621.06 . AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 39 20 10001670 . T G 3688.06 . AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… [all …]
H A D	expected.testLinkedDebruijnMode.gatk4.vcf	4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 18 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 28 20 10000439 . T G 2819.06 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 29 20 10000598 . T A 1956.06 . AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 31 20 10000758 . T A 4015.06 . AC=2;AF=1.00;AN=2;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 33 20 10001298 . T A 2932.06 . AC=2;AF=1.00;AN=2;DP=79;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 35 20 10001474 . C T 3130.06 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 37 20 10001628 . G A 4273.06 . AC=2;AF=1.00;AN=2;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 38 20 10001661 . T C 3792.06 . AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 39 20 10001670 . T G 3700.06 . AC=2;AF=1.00;AN=2;DP=86;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… [all …]
H A D	expected.testVCFMode.gatk3.5.vcf	4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 21 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 32 20 10000439 . T G 2804.77 . AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 33 20 10000598 . T A 1941.77 . AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 35 20 10000758 . T A 3838.77 . AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 37 20 10001298 . T A 2917.77 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 39 20 10001474 . C T 2640.77 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 41 20 10001628 . G A 3898.77 . AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 42 20 10001661 . T C 3606.77 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 43 20 10001670 . T G 3673.77 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… [all …]
H A D	expected.testVCFMode.gatk4.DRAGEN.vcf	4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 22 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 32 20 10000439 . T G 277.22 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… 33 20 10000598 . T A 187.22 . AC=2;AF=1.00;AN=2;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… 35 20 10000758 . T A 323.22 . AC=2;AF=1.00;AN=2;DP=97;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… 37 20 10001298 . T A 256.22 . AC=2;AF=1.00;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… 39 20 10001474 . C T 256.22 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… 41 20 10001628 . G A 322.22 . AC=2;AF=1.00;AN=2;DP=99;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… 42 20 10001661 . T C 286.22 . AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… 43 20 10001670 . T G 287.22 . AC=2;AF=1.00;AN=2;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… [all …]
H A D	expected.testVCFMode.gatk3.8-4-g7b0250253f.alleleSpecific.vcf	4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 29 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 40 …S_MQ=59.06;AS_SOR=1.236;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;QD=34.24;SOR=1… 41 …S_MQ=55.26;AS_SOR=1.225;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.26;QD=30.63;SOR=1… 43 …S_MQ=53.37;AS_SOR=0.802;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.37;QD=29.09;SOR=0… 45 …S_MQ=54.54;AS_SOR=0.963;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.34;QD=32.93;SOR=0… 47 …S_MQ=43.89;AS_SOR=1.516;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.72;QD=29.67;SOR=1… 49 …S_MQ=59.17;AS_SOR=1.053;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.17;QD=34.04;SOR=1… 50 …S_MQ=58.33;AS_SOR=1.193;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.33;QD=32.42;SOR=1… 51 …S_MQ=57.45;AS_SOR=0.995;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.45;QD=37.76;SOR=0… [all …]
H A D	expected.testVCFMode.gatk3.5.alleleSpecific.vcf	4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 29 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 40 …S_MQ=59.06;AS_SOR=1.236;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;QD=34.24;SOR=1… 41 …S_MQ=55.26;AS_SOR=1.225;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.26;QD=30.63;SOR=1… 43 …S_MQ=53.37;AS_SOR=0.802;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.37;QD=29.09;SOR=0… 45 …S_MQ=54.54;AS_SOR=0.963;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.34;QD=32.93;SOR=0… 47 …S_MQ=43.89;AS_SOR=1.516;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.72;QD=29.67;SOR=1… 49 …S_MQ=59.17;AS_SOR=1.053;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.17;QD=34.04;SOR=1… 50 …S_MQ=58.33;AS_SOR=1.193;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.33;QD=32.42;SOR=1… 51 …S_MQ=57.45;AS_SOR=0.995;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.45;QD=37.76;SOR=0… [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/
H A D	newMQcalc.singleSample.genotyped.vcf	5 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 27 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 38 20 10000439 . T G 2819.06 . AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 39 20 10000598 . T A 1956.06 . AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 41 20 10000758 . T A 3853.06 . AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 43 20 10001298 . T A 2932.06 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 45 20 10001474 . C T 2655.06 . AC=2;AF=1.00;AN=2;DP=73;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 47 20 10001628 . G A 3913.06 . AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 55 20 10002470 . C T 2537.06 . AC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 119 20 10012362 . G T 850.06 . AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… [all …]
H A D	CEUTrio.20.gatk3.7_30_ga4f720357.expected.vcf	6 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 30 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 42 20 10000439 . T G 2819.06 . AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 43 20 10000598 . T A 1956.06 . AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 45 20 10000758 . T A 3853.06 . AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 47 20 10001298 . T A 2932.06 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 49 20 10001474 . C T 2655.06 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 51 20 10001628 . G A 3913.06 . AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 123 20 10012362 . G T 850.06 . AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… 125 20 10012387 . T C 548.06 . AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… [all …]
H A D	CEUTrio.21.gatk3.7_30_ga4f720357.expected.vcf	6 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 30 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 81 21 10014357 . A G 66.84 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=2… 231 21 10088339 . A T 55.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=2… 240 21 10101225 . A AT 49.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=… 252 21 10113095 . C A 56.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=2… 299 21 10131915 . A G 63.84 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=2… 357 21 10139335 . G A 37.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=2… 410 21 10143574 . C T 40.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=2… 411 21 10143588 . C T 40.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=2… [all …]
H A D	CEUTrio.20.21.gatk3.7_30_ga4f720357.expected.vcf	5 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 30 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 39 ….03 . AC=2;AF=1.00;AN=2;DP=84;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.44;QD=25.36;SOR=1… 576 21 10014357 . A G 66.84 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=2… 660 21 10028325 . C A 137.97 . AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=2… 735 21 10101225 . A AT 49.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=… 852 21 10139335 . G A 37.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=2… 904 21 10143381 . G A 85.14 . AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20… 906 21 10143588 . C T 40.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=2… 911 21 10144183 . C T 56.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=2… [all …]
H A D	newMQcalc.combined.genotyped.vcf	5 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 29 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 122 …13 . AC=4;AF=1.00;AN=4;DP=109;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.14;QD=33.02;SOR=1… 124 20 10000598 . T A 2946.13 . AC=4;AF=1.00;AN=4;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ… 128 …13 . AC=4;AF=1.00;AN=4;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=55.71;QD=30.97;SOR=0… 140 20 10002470 . C T 3791.13 . AC=4;AF=1.00;AN=4;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ… 141 20 10002625 . G T 3707.13 . AC=4;AF=1.00;AN=4;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ… 142 20 10003021 . C T 3224.13 . AC=4;AF=1.00;AN=4;DP=90;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ… 145 …13 . AC=4;AF=1.00;AN=4;DP=128;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.42;QD=29.11;SOR=1… 146 …13 . AC=4;AF=1.00;AN=4;DP=102;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=59.63;QD=28.08;SOR=1… [all …]
H A D	expected.posteriors.genotyped.vcf	5 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 28 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 40 20 10000439 . T G 2819.06 . AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 41 20 10000598 . T A 1956.06 . AC=2;AF=1.00;AN=2;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 43 20 10000758 . T A 3853.06 . AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 45 20 10001298 . T A 2932.06 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 47 20 10001474 . C T 2655.06 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 49 20 10001628 . G A 3913.06 . AC=2;AF=1.00;AN=2;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ… 121 20 10012362 . G T 850.06 . AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… 123 20 10012387 . T C 548.06 . AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=… [all …]
/dports/biology/haplohseq/haplohseq-0.1.2/example/example_input/
H A D	tumor_exome.vcf	7302 1 89887468 . TGAAAAA T 168.87 . AC=2;AF=1.00;AN=2;DP=5;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=58.42;… 23434 2 136552615 . G GCGCA 165.87 . AC=2;AF=1.00;AN=2;DP=6;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=66.83;M… 27241 2 220341938 . C CT 388.73 . AC=2;AF=1.00;AN=2;DP=11;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=53.02;MQ0… 32277 3 69059099 . AAC A 208.76 . AC=2;AF=1.00;AN=2;DP=10;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=57.94;MQ0… 35178 3 150916128 . TG T 396.73 . AC=2;AF=1.00;AN=2;DP=22;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=50.62;MQ0… 40578 4 73933599 . TATAA T 193.77 . AC=2;AF=1.00;AN=2;DP=7;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=77.28;MQ… 49392 5 175721967 . C CCA 171.77 . AC=2;AF=1.00;AN=2;DP=9;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=25.23;MQ0… 53053 6 32441391 . G GT 621.94 . AC=2;AF=1.00;AN=2;DP=24;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=31.65;MQ0=… 76501 9 40700121 . C CA 189.87 . AC=2;AF=1.00;AN=2;DP=7;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=22.35;MQ0=0… 76546 9 43998330 . T TGGG 272.87 . AC=2;AF=1.00;AN=2;DP=19;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=9.90;MQ0… [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/
H A D	multiallelic.vcf	3 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 19 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 27 …93 . AC=5,3;AF=0.0163,0.0098;AN=306;DP=1545;Dels=0.00;InbreedingCoeff=0.0182;MQ=59.21;MQ0=0;QD=9.18 30 …. AC=6,14;AF=0.0196,0.0458;AN=306;DP=6465;Dels=0.00;InbreedingCoeff=-0.0088;MQ=57.16;MQ0=7;QD=13.75 31 …8 . AC=2,1;AF=0.0065,0.0033;AN=306;DP=8030;Dels=0.00;InbreedingCoeff=-0.0000;MQ=58.99;MQ0=0;QD=9.96 33 ….57 . AC=9,9;AF=0.0294,0.0294;AN=306;DP=792;Dels=0.00;InbreedingCoeff=0.1229;MQ=58.84;MQ0=0;QD=9.69 38 …7 . AC=1,1;AF=0.0033,0.0033;AN=306;DP=10365;Dels=0.00;InbreedingCoeff=0.0033;MQ=58.86;MQ0=0;QD=9.20 42 … . AC=9,13;AF=0.0294,0.0425;AN=306;DP=6729;Dels=0.00;InbreedingCoeff=0.0179;MQ=59.35;MQ0=0;QD=14.15 47 … . AC=1,3;AF=0.0033,0.0098;AN=306;DP=2844;Dels=0.00;InbreedingCoeff=-0.0025;MQ=59.47;MQ0=0;QD=10.24 56 … . AC=2,5;AF=0.0065,0.0163;AN=306;DP=3099;Dels=0.00;InbreedingCoeff=-0.0034;MQ=59.36;MQ0=0;QD=13.67 [all …]
/dports/biology/vcf2hap/vcf2hap-0.1.4/
H A D	tumor-exome-small.vcf	8 …=2;DP=2;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.00;MQ0=0;QD=15.87… 88 1 957967 . T TTGTAGTCTGACCT 4656.73 . AC=2;AF=1.00;AN=2;DP=50;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ… 386 4 666385 . ATT A 418.73 . AC=2;AF=1.00;AN=2;DP=43;FS=0.000;HRun=20;MLEAC=2;MLEAF=1.00;MQ=56.56;MQ0=… 389 …AA 4144.73 . AC=2;AF=1.00;AN=2;DB;DP=82;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=51.71;MQ0=0;QD=25.27… 832 9 325811 rs3831138 T TC 2207.73 . AC=2;AF=1.00;AN=2;DB;DP=55;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=… 921 …TT 4228.73 . AC=2;AF=1.00;AN=2;DB;DP=75;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=54.49;MQ0=0;QD=14.10… 986 …AC 1731.73 . AC=2;AF=1.00;AN=2;DB;DP=31;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=50.63;MQ0=0;QD=18.62… 1135 12 250089 rs11355066 AT A 371.74 . AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=… 1262 …TTC 793.73 . AC=2;AF=1.00;AN=2;DB;DP=17;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ=60.56;MQ0=0;QD=23.35… 1731 18 196926 rs35399373 T TC 883.73 . AC=2;AF=1.00;AN=2;DB;DP=21;FS=0.000;HRun=0;MLEAC=2;MLEAF=1.00;MQ… [all …]
/dports/biology/vcftools/vcftools-0.1.16/examples/
H A D	contrast.vcf	5 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads… 44 ##FILTER=<ID=MinMQ,Description="Minimum RMS mapping quality for SNPs (INFO/MQ) [30]"> 48 1 10250 . A C 61 MinMQ DP=271;VDB=0.0265;AF1=0.125;AC1=1;DP4=87,78,18,9;MQ=17;FQ=61;PV4=0.21,1,1,0.… 55 1 10821 . T A 49.7 MinMQ DP=9;VDB=0.0091;AF1=1;AC1=5;DP4=1,3,0,4;MQ=12;FQ=7.75;PV4=1,1,1,1;AN=8;AC=… 62 1 15903 . GCC GCCC 158 MinMQ INDEL;DP=14;VDB=0.0182;AF1=1;AC1=8;DP4=0,0,0,7;MQ=29;FQ=-18.2;AN=8;AC=… 90 1 55926 . T C 999 MinMQ DP=56;VDB=0.0269;AF1=1;AC1=8;DP4=0,0,23,32;MQ=14;FQ=-11.9;AN=8;AC=8 GT:PL:D… 120 1 79033 . A G 217 MinMQ DP=19;VDB=0.0139;AF1=1;AC1=8;DP4=0,0,12,7;MQ=18;FQ=-12.7;AN=8;AC=8 GT:PL:DP… 121 1 79050 . G T 258 MinMQ DP=29;VDB=0.0203;AF1=1;AC1=8;DP4=0,0,15,11;MQ=16;FQ=-18.3;AN=8;AC=8 GT:PL:D… 150 X 1 . A G 89 PASS DP=304;VDB=0.0327;AF1=0.125;AC1=1;DP4=99,171,10,15;MQ=30;FQ=89;PV4=0.83,0.3,0.035… 151 X 2 . A G 89 PASS DP=304;VDB=0.0327;AF1=0.125;AC1=1;DP4=99,171,10,15;MQ=30;FQ=89;PV4=0.83,0.3,0.035… [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/
H A D	fiveSampleTest.lowerCallThreshold.vcf	6 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or wit… 27 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> 29 ##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calcul… 43 chr20 251377 . T C 307 . AC=1;AF=0.500;AN=2;DP=26;ExcessHet=11.9728;FS=45.405;MQ=60.00;MQRankSum=1.… 49 chr20 252881 . G GAAAAAAA 69.97 . AC=1;AF=0.167;AN=6;DP=58;ExcessHet=6.9897;FS=7.404;MQ=59.46;MQRan… 140 chr20 273894 . A G 458 . AC=1;AF=0.167;AN=6;DP=55;ExcessHet=6.9897;FS=0.000;MQ=60.00;MQRankSum=0.42… 142 chr20 273904 . AG A 316.97 . AC=1;AF=0.250;AN=4;DP=41;ExcessHet=9.4201;FS=3.222;MQ=60.00;MQRankSum=… 268 chr20 304504 . CA C 1193.97 . AC=4;AF=1.00;AN=4;DP=70;ExcessHet=4.7712;FS=3.087;MQ=59.47;MQRankSum=… 286 chr20 306376 . A G 276 . AC=2;AF=0.500;AN=4;DP=47;ExcessHet=11.9728;FS=7.243;MQ=59.08;MQRankSum=0.7… 333 chr20 314925 . G T 30 . AC=1;AF=0.500;AN=2;DP=15;ExcessHet=11.9728;FS=15.911;MQ=56.67;MQRankSum=-1.… [all …]
/dports/science/dalton/dalton-66052b3af5ea7225e31178bf9a8b031913c72190/DALTON/test/qmcmm/result/
H A D	qmcmm_qr_damped_qmcmm.out	`631 * Computed MQ vector end * 648 * Computed MQ vector end * 770 * Computed MQ vector end * 787 * Computed MQ vector end * 909 * Computed MQ vector end * 926 * Computed MQ vector end * 1048 * Computed MQ vector end * 1065 * Computed MQ vector end * 1187 * Computed MQ vector end * 1204 * Computed MQ vector end * [all …]`

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