Schema for Variants in lacO Mutants (All) - Genetic Variations in lacO Mutants (All)
  Database: dm6    Primary Table: lacO_variants
VCF File: /gbdb/dm6/bbi/vcf/Dmel_lacO_screen.vep.ucsc.vcf.gz
Format description: The fields of a Variant Call Format data line
See the Variant Call Format specification for more details
fielddescription
chromAn identifier from the reference genome
posThe reference position, with the 1st base having position 1
idSemi-colon separated list of unique identifiers where available
refReference base(s)
altComma separated list of alternate non-reference alleles called on at least one of the samples
qualPhred-scaled quality score for the assertion made in ALT. i.e. give -10log_10 prob(call in ALT is wrong)
filterPASS if this position has passed all filters. Otherwise, a semicolon-separated list of codes for filters that fail
infoAdditional information encoded as a semicolon-separated series of short keys with optional comma-separated values
formatIf genotype columns are specified in header, a semicolon-separated list of of short keys starting with GT
genotypesIf genotype columns are specified in header, a tab-separated set of genotype column values; each value is a colon-separated list of values corresponding to keys in the format column

Sample Rows
 
chromposidrefaltqualfilterinfoformatgenotypes
chr2L5038.TCGACAAT41597.6PASSAC=54;AF=0.931;AN=58;BaseQRankSum=0.883;DP=937;ExcessHet=0.2348;FS=0;InbreedingCoeff=0.461;MLEAC=54;MLEAF=0.931;MQ=52.63;MQRankS ...GT:AD:DP:GQ:PGT:PID:PL:PS1|1:0,46:46:99:1|1:5038_TCGACAA_T:2072,139,0:50381|1:0,22:22:66:1|1:5038_TCGACAA_T:975,66,0:50381|1:0,21:21:63:1|1:5038_TCGACAA_T:945,63,0:50381|1:0,29:29:90:1|1:5038_TCGACAA_T:1350,90,0:50381|1:0,30:30:94:1|1:5038_TCGACAA_T:1387,94,0:50381|1:0,29:29:88:1|1:5038_TCGACAA_T:1306,88,0:50381|1:0,47:47:99:1|1:5038_TCGACAA_T:2117,142,0:50380|1:1,35:36:99:0|1:5038_TCGACAA_T:1551,0,410:50381|1:0,28:28:88:1|1:5038_TCGACAA_T:1306,88,0:50381|1:0,34:34:99:1|1:5038_TCGACAA_T:1530,102,0:5038...
chr2L5045.TGCACGACAGAGGT43025.4PASSAC=52;AF=0.897;AN=58;BaseQRankSum=1.82;DP=950;ExcessHet=0.6125;FS=0;InbreedingCoeff=0.256;MLEAC=52;MLEAF=0.897;MQ=52.88;MQRankSu ...GT:AD:DP:GQ:PGT:PID:PL:PS1|1:0,46:46:99:1|1:5038_TCGACAA_T:2160,144,0:50381|1:0,22:22:72:1|1:5038_TCGACAA_T:1065,72,0:50381|1:0,21:21:63:1|1:5038_TCGACAA_T:945,63,0:50381|1:0,30:30:96:1|1:5038_TCGACAA_T:1440,96,0:50380|1:1,31:32:99:0|1:5038_TCGACAA_T:1373,0,190:50381|1:0,29:29:87:1|1:5038_TCGACAA_T:1305,87,0:50381|1:0,47:47:99:1|1:5038_TCGACAA_T:2115,141,0:50380|1:1,37:38:99:0|1:5038_TCGACAA_T:1593,0,407:50381|1:0,29:29:90:1|1:5038_TCGACAA_T:1350,90,0:50381|1:0,34:34:99:1|1:5038_TCGACAA_T:1575,105,0:5038...
chr2L5059.AGCAGAACAGA43934.8PASSAC=51;AF=0.879;AN=58;BaseQRankSum=1.01;DP=986;ExcessHet=0.8825;FS=0;InbreedingCoeff=0.1884;MLEAC=51;MLEAF=0.879;MQ=53.25;MQRankS ...GT:AD:DP:GQ:PGT:PID:PL:PS1|1:0,48:48:99:1|1:5038_TCGACAA_T:2295,154,0:50381|1:0,23:23:72:1|1:5038_TCGACAA_T:1080,72,0:50381|1:0,21:21:63:1|1:5038_TCGACAA_T:945,63,0:50381|1:0,32:32:99:1|1:5038_TCGACAA_T:1485,99,0:50380|1:1,32:33:99:0|1:5038_TCGACAA_T:1341,0,193:50381|1:0,29:29:90:1|1:5038_TCGACAA_T:1350,90,0:50381|1:0,46:46:99:1|1:5038_TCGACAA_T:2160,144,0:50380|1:1,38:39:99:0|1:5038_TCGACAA_T:1677,0,401:50381|1:0,30:30:93:1|1:5038_TCGACAA_T:1395,93,0:50381|1:0,35:35:99:1|1:5038_TCGACAA_T:1575,105,0:5038...
chr2L5073.TTAGATTGCCTCTCT46181.4PASSAC=49;AF=0.845;AN=58;BaseQRankSum=1.76;DP=1052;ExcessHet=1.6248;FS=0;InbreedingCoeff=-0.0229;MLEAC=50;MLEAF=0.862;MQ=53.94;MQRan ...GT:AD:DP:GQ:PGT:PID:PL:PS1|1:1,51:52:99:1|1:5038_TCGACAA_T:2459,153,0:50381|1:0,22:22:72:1|1:5038_TCGACAA_T:1080,72,0:50381|1:0,24:24:78:1|1:5038_TCGACAA_T:1170,78,0:50381|1:0,38:38:99:1|1:5038_TCGACAA_T:1710,114,0:50380|1:1,32:33:99:0|1:5038_TCGACAA_T:1383,0,190:50381|1:0,30:30:90:1|1:5038_TCGACAA_T:1350,90,0:50381|1:0,50:50:99:1|1:5038_TCGACAA_T:2289,154,0:50380|1:1,39:40:99:0|1:5038_TCGACAA_T:1761,0,395:50381|1:0,32:32:99:1|1:5038_TCGACAA_T:1485,99,0:50381|1:0,36:36:99:1|1:5038_TCGACAA_T:1665,111,0:5038...
chr2L5092.CT48790.5PASSAC=50;AF=0.862;AN=58;BaseQRankSum=1.86;DP=1123;ExcessHet=1.2169;FS=0;InbreedingCoeff=-0.002;MLEAC=51;MLEAF=0.879;MQ=54.62;MQRank ...GT:AD:DP:GQ:PGT:PID:PL:PS1|1:1,52:53:99:1|1:5038_TCGACAA_T:2371,149,0:50381|1:0,23:23:72:1|1:5038_TCGACAA_T:1073,72,0:50381|1:0,25:25:81:1|1:5038_TCGACAA_T:1196,81,0:50381|1:0,45:45:99:1|1:5038_TCGACAA_T:2068,138,0:50380|1:1,35:36:99:0|1:5038_TCGACAA_T:1496,0,181:50381|1:0,27:27:87:1|1:5038_TCGACAA_T:1286,87,0:50381|1:0,52:52:99:1|1:5038_TCGACAA_T:2441,166,0:50380|1:1,42:43:99:0|1:5038_TCGACAA_T:1794,0,392:50381|1:0,34:34:99:1|1:5038_TCGACAA_T:1566,105,0:50381|1:0,38:38:99:1|1:5038_TCGACAA_T:1747,117,0:5038...
chr2L5095.TA48549PASSAC=50;AF=0.862;AN=58;BaseQRankSum=1.82;DP=1159;ExcessHet=1.2169;FS=2.781;InbreedingCoeff=0.0021;MLEAC=51;MLEAF=0.879;MQ=55.05;MQ ...GT:AD:DP:GQ:PGT:PID:PL:PS1|1:1,55:56:99:1|1:5038_TCGACAA_T:2406,152,0:50381|1:0,25:25:76:1|1:5038_TCGACAA_T:1110,76,0:50381|1:0,27:27:83:1|1:5038_TCGACAA_T:1199,83,0:50381|1:0,44:44:99:1|1:5038_TCGACAA_T:1979,133,0:50380|1:1,35:36:99:0|1:5038_TCGACAA_T:1490,0,180:50381|1:0,30:30:91:1|1:5038_TCGACAA_T:1323,91,0:50381|1:0,55:55:99:1|1:5038_TCGACAA_T:2442,166,0:50380|1:1,45:46:99:0|1:5038_TCGACAA_T:1860,0,385:50381|1:0,35:35:99:1|1:5038_TCGACAA_T:1551,105,0:50381|1:0,38:38:99:1|1:5038_TCGACAA_T:1748,118,0:5038...
chr2L5372.TA14928.6PASSAC=13;AF=0.224;AN=58;BaseQRankSum=-0.353;DP=1589;ExcessHet=0.0014;FS=0.7;InbreedingCoeff=0.7026;MLEAC=13;MLEAF=0.224;MQ=59.71;MQ ...GT:AD:DP:GQ:PGT:PID:PL:PS1/1:0,80:80:99:.:.:2799,240,0:.0/0:41,0:41:99:.:.:0,100,1406:.0/0:49,0:49:99:.:.:0,105,1578:.0/0:54,0:54:99:.:.:0,109,1800:.0/0:48,0:48:99:.:.:0,100,1563:.0/0:41,0:41:99:.:.:0,101,1363:.0/0:51,0:51:99:.:.:0,120,1800:.0/0:43,0:43:99:.:.:0,105,1481:.0/0:49,0:49:99:.:.:0,106,1706:.0/0:53,0:53:83:.:.:0,83,1645:....
chr2L5390.TA14564.9PASSAC=12;AF=0.207;AN=58;BaseQRankSum=-2.124;DP=1549;ExcessHet=0.0124;FS=0;InbreedingCoeff=0.5975;MLEAC=12;MLEAF=0.207;MQ=59.79;MQRa ...GT:AD:DP:GQ:PGT:PID:PL:PS1/1:0,69:69:99:.:.:2390,207,0:.0/0:41,0:41:99:.:.:0,100,1406:.0/0:49,0:49:99:.:.:0,105,1578:.0/0:54,0:54:99:.:.:0,109,1800:.0/0:48,0:48:99:.:.:0,100,1563:.0/0:41,0:41:99:.:.:0,101,1363:.0/0:51,0:51:99:.:.:0,120,1800:.0/0:43,0:43:99:.:.:0,105,1481:.0/0:49,0:49:99:.:.:0,106,1706:.0/0:45,0:45:99:.:.:0,120,1800:....
chr2L5403.CG14362.8PASSAC=12;AF=0.207;AN=58;BaseQRankSum=-0.706;DP=1535;ExcessHet=0.0124;FS=0;InbreedingCoeff=0.5837;MLEAC=12;MLEAF=0.207;MQ=59.87;MQRa ...GT:AD:DP:GQ:PGT:PID:PL:PS1/1:0,70:70:99:.:.:2427,209,0:.0/0:39,0:39:99:.:.:0,105,1332:.0/0:49,0:49:99:.:.:0,105,1578:.0/0:54,0:54:99:.:.:0,109,1800:.0/0:48,0:48:99:.:.:0,100,1563:.0/0:41,0:41:99:.:.:0,101,1363:.0/0:51,0:51:99:.:.:0,120,1800:.0/0:43,0:43:99:.:.:0,105,1481:.0/0:49,0:49:99:.:.:0,106,1706:.0/0:43,0:43:99:.:.:0,114,1710:....
chr2L5465.CA15304.6PASSAC=13;AF=0.224;AN=58;BaseQRankSum=-2.48;DP=1513;ExcessHet=0.0014;FS=0.705;InbreedingCoeff=0.7025;MLEAC=13;MLEAF=0.224;MQ=60;MQRa ...GT:AD:DP:GQ:PL1/1:0,77:77:99:2727,230,00/0:38,0:38:99:0,102,12320/0:38,0:38:99:0,100,12240/0:54,0:54:99:0,109,18000/0:48,0:48:99:0,100,15630/0:41,0:41:99:0,101,13630/0:51,0:51:99:0,120,18000/0:43,0:43:99:0,105,14810/0:46,0:46:99:0,103,15690/0:44,0:44:99:0,102,1565...

Variants in lacO Mutants (All) (lacO_variants) Track Description
 

Description

This track shows the locations of sequence variants in the D. melanogaster lacO mutants that were identified by GATK 4. The effect of the variants were predicted by the Ensembl Variant Effect Predictor (VEP).

References

McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biol. 2016 Jun 6;17(1):122.

Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43:11.10.1-11.10.33.