Schema for Variants in lacO Mutants (Filtered) - Genetic Variations in lacO Mutants (Filtered) |
|---|
| |
Database: dm6 Primary Table: lacO_variants_filtered
VCF File: /gbdb/dm6/bbi/vcf/Dmel_lacO_screen_vep.filter_csq.vcf.gz
Format description: The fields of a Variant Call Format data line
See the Variant Call Format specification for more details
| field | description |
|---|
| chrom | An identifier from the reference genome | | pos | The reference position, with the 1st base having position 1 | | id | Semi-colon separated list of unique identifiers where available | | ref | Reference base(s) | | alt | Comma separated list of alternate non-reference alleles called on at least one of the samples | | qual | Phred-scaled quality score for the assertion made in ALT. i.e. give -10log_10 prob(call in ALT is wrong) | | filter | PASS if this position has passed all filters. Otherwise, a semicolon-separated list of codes for filters that fail | | info | Additional information encoded as a semicolon-separated series of short keys with optional comma-separated values | | format | If genotype columns are specified in header, a semicolon-separated list of of short keys starting with GT | | genotypes | If 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
|
|---|
| |
| chrom | pos | id | ref | alt | qual | filter | info | format | genotypes |
|---|
| chr2L | 31699 | . | G | A | 958.75 | PASS | AC=1;AF=0.017;AN=58;BaseQRankSum=-2.429;DP=1365;ExcessHet=3.0103;FS=1.435;InbreedingCoeff=-0.0175;MLEAC=1;MLEAF=0.017;MQ=60;MQRa ... | GT:AD:DP:GQ:PL | 0/0:62,0:62:99:0,120,1800 | 0/0:37,0:37:99:0,100,1280 | 0/0:40,0:40:99:0,103,1393 | 0/0:50,0:50:99:0,120,1800 | 0/0:37,0:37:99:0,102,1211 | 0/0:36,0:36:99:0,100,1327 | 0/0:44,0:44:99:0,113,1562 | 0/0:40,0:40:99:0,105,1453 | 0/0:41,0:41:99:0,100,1456 | 0/0:37,0:37:99:0,100,1381 | ... |
| chr2L | 34595 | . | C | T | 946.64 | PASS | AC=2;AF=0.034;AN=58;DP=1274;ExcessHet=0.0383;FS=0;InbreedingCoeff=1;MLEAC=2;MLEAF=0.034;MQ=60;QD=32.64;SOR=1.071;CSQ=T|missense_ ... | GT:AD:DP:GQ:PL | 0/0:50,0:50:99:0,102,1800 | 0/0:36,0:36:99:0,105,1575 | 0/0:31,0:31:90:0,90,1069 | 0/0:45,0:45:99:0,102,1687 | 0/0:38,0:38:99:0,105,1422 | 0/0:39,0:39:99:0,114,1308 | 0/0:48,0:48:99:0,102,1572 | 0/0:46,0:46:99:0,103,1613 | 0/0:37,0:37:99:0,100,1314 | 0/0:36,0:36:99:0,100,1350 | ... |
| chr2L | 34929 | . | C | T | 239.75 | PASS | AC=1;AF=0.017;AN=58;BaseQRankSum=-1.583;DP=1251;ExcessHet=3.0103;FS=0;InbreedingCoeff=-0.0175;MLEAC=1;MLEAF=0.017;MQ=60;MQRankSu ... | GT:AD:DP:GQ:PL | 0/0:50,0:50:99:0,102,1800 | 0/0:35,0:35:99:0,99,1230 | 0/0:36,0:36:99:0,104,1269 | 0/0:45,0:45:99:0,102,1687 | 0/0:34,0:34:94:0,94,1195 | 0/0:35,0:35:99:0,99,1245 | 0/0:49,0:49:99:0,111,1599 | 0/0:46,0:46:99:0,103,1613 | 0/0:39,0:39:99:0,104,1344 | 0/0:37,0:37:99:0,101,1292 | ... |
| chr2L | 66087 | . | C | T | 961.75 | PASS | AC=1;AF=0.017;AN=58;BaseQRankSum=-0.406;DP=2219;ExcessHet=3.0103;FS=8.164;InbreedingCoeff=-0.0175;MLEAC=1;MLEAF=0.017;MQ=60;MQRa ... | GT:AD:DP:GQ:PL | 0/0:59,0:59:99:0,110,1800 | 0/0:60,0:60:99:0,102,1800 | 0/0:69,0:69:99:0,115,1800 | 0/0:120,0:120:99:0,112,1800 | 0/0:100,0:100:99:0,120,1800 | 0/0:75,0:75:99:0,120,1800 | 0/0:118,0:118:99:0,106,1800 | 0/0:41,0:41:99:0,102,1495 | 0/0:83,0:83:99:0,120,1800 | 0/0:76,0:76:99:0,120,1800 | ... |
| chr2L | 67188 | . | T | C | 866.75 | PASS | AC=1;AF=0.017;AN=58;BaseQRankSum=2.93;DP=2416;ExcessHet=3.0103;FS=0.84;InbreedingCoeff=-0.0175;MLEAC=1;MLEAF=0.017;MQ=60;MQRankS ... | GT:AD:DP:GQ:PL | 0/0:55,0:55:99:0,120,1800 | 0/0:65,0:65:99:0,120,1800 | 0/0:83,0:83:99:0,120,1800 | 0/0:125,0:125:99:0,120,1800 | 0/0:97,0:97:99:0,120,1800 | 0/0:77,0:77:99:0,120,1800 | 0/0:138,0:138:99:0,120,1800 | 0/0:37,0:37:99:0,102,1530 | 0/0:90,0:90:99:0,120,1800 | 0/0:81,0:81:99:0,120,1800 | ... |
| chr2L | 71992 | . | C | G | 947.75 | PASS | AC=1;AF=0.017;AN=58;BaseQRankSum=-0.092;DP=2865;ExcessHet=3.0103;FS=0;InbreedingCoeff=-0.0175;MLEAC=1;MLEAF=0.017;MQ=60;MQRankSu ... | GT:AD:DP:GQ:PL | 0/0:127,0:127:99:0,120,1800 | 0/0:72,0:72:99:0,120,1800 | 0/0:99,0:99:99:0,120,1800 | 0/0:120,0:120:99:0,120,1800 | 0/0:92,0:92:99:0,120,1800 | 0/0:78,0:78:99:0,120,1800 | 0/0:123,0:123:99:0,120,1800 | 0/0:118,0:118:99:0,120,1800 | 0/0:90,0:90:99:0,120,1800 | 0/0:98,0:98:99:0,120,1800 | ... |
| chr2L | 74167 | . | A | G | 916.75 | PASS | AC=1;AF=0.017;AN=58;BaseQRankSum=2.73;DP=2227;ExcessHet=3.0103;FS=0.848;InbreedingCoeff=-0.0175;MLEAC=1;MLEAF=0.017;MQ=60;MQRank ... | GT:AD:DP:GQ:PL | 0/0:137,0:137:99:0,120,1800 | 0/0:50,0:50:99:0,120,1708 | 0/0:75,0:75:99:0,99,1485 | 0/0:75,0:75:99:0,120,1800 | 0/0:79,0:79:99:0,105,1575 | 0/0:64,0:64:99:0,106,1800 | 0/0:106,0:106:99:0,120,1800 | 0/0:91,0:91:99:0,111,1665 | 0/0:58,0:58:99:0,120,1800 | 0/0:68,0:68:99:0,120,1800 | ... |
| chr2L | 82745 | . | C | T | 668.75 | PASS | AC=1;AF=0.017;AN=58;BaseQRankSum=3.67;DP=2575;ExcessHet=3.0103;FS=8.149;InbreedingCoeff=-0.0175;MLEAC=1;MLEAF=0.017;MQ=60;MQRank ... | GT:AD:DP:GQ:PL | 0/0:134,0:134:99:0,120,1800 | 0/0:64,0:64:99:0,120,1800 | 0/0:72,0:72:99:0,120,1800 | 0/0:116,0:116:99:0,120,1800 | 0/0:86,0:86:99:0,120,1800 | 0/0:69,0:69:99:0,120,1800 | 0/0:130,0:130:99:0,120,1800 | 0/0:102,0:102:99:0,120,1800 | 0/0:89,0:89:99:0,120,1800 | 0/0:84,0:84:99:0,120,1800 | ... |
| chr2L | 106728 | . | C | G | 1661.75 | PASS | AC=1;AF=0.017;AN=58;BaseQRankSum=1.87;DP=2592;ExcessHet=3.0103;FS=0.701;InbreedingCoeff=-0.0175;MLEAC=1;MLEAF=0.017;MQ=60;MQRank ... | GT:AD:DP:GQ:PL | 0/0:122,0:122:99:0,120,1800 | 0/0:56,0:56:99:0,120,1800 | 0/0:90,0:90:99:0,120,1800 | 0/0:131,0:131:99:0,120,1800 | 0/0:85,0:85:99:0,120,1800 | 0/0:63,0:63:99:0,118,1800 | 0/0:113,0:113:99:0,120,1800 | 0/0:95,0:95:99:0,107,1800 | 0/0:83,0:83:99:0,120,1800 | 0/0:89,0:89:99:0,110,1800 | ... |
| chr2L | 107005 | . | TAGAAA | T | 995.75 | PASS | AC=1;AF=0.017;AN=58;BaseQRankSum=0.306;DP=2669;ExcessHet=3.0103;FS=1.88;InbreedingCoeff=-0.0175;MLEAC=1;MLEAF=0.017;MQ=60;MQRank ... | GT:AD:DP:GQ:PGT:PID:PL:PS | 0/0:130,0:130:99:.:.:0,120,1800:. | 0/0:56,0:56:99:.:.:0,120,1800:. | 0/0:90,0:90:99:.:.:0,120,1800:. | 0/0:131,0:131:99:.:.:0,120,1800:. | 0/0:85,0:85:99:.:.:0,120,1800:. | 0/0:63,0:63:99:.:.:0,118,1800:. | 0/0:113,0:113:99:.:.:0,120,1800:. | 0/0:95,0:95:99:.:.:0,107,1800:. | 0/0:83,0:83:99:.:.:0,120,1800:. | 0/0:89,0:89:99:.:.:0,110,1800:. | ... |
|
| |
|
|
|
Variants in lacO Mutants (Filtered) (lacO_variants_filtered) Track Description
|
|---|
| |
Description
This track shows the sequence variants in the D. melanogaster lacO mutants that cause changes in the transcribed exons (e.g., UTR variants, missense variants, frame shifts). Variants found in the control samples were excluded from this evidence track.
The sequence variants 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.
| |
|
|
|