Schema for DGRP v2 (R5) - Drosophila Genetics Reference Panel 2 (R5)
  Database: dm6    Primary Table: dgrp2
VCF File: /gbdb/dm6/bbi/vcf/dgrp2.r6.sorted.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
chr2L49982L_4998_SNPGA999PASSREFCOUNT=117;ALTCOUNT=5;ANNOTATION=|||;REFLINE=21,28,31,38,40,41,45,48,49,69,73,75,83,85,88,91,93,100,109,129,136,153,158,161,17 ...GT0/0./.0/00/0./.0/00/00/0./.0/0...
chr2L50022L_5002_SNPGT999PASSREFCOUNT=127;ALTCOUNT=1;ANNOTATION=|||;REFLINE=21,28,31,38,40,41,45,48,49,69,73,75,83,85,88,91,93,100,109,129,136,153,158,161,17 ...GT0/0./.0/00/0./.0/00/00/0./.0/0...
chr2L50392L_5039_SNPCT999PASSREFCOUNT=1;ALTCOUNT=118;ANNOTATION=|||;REFLINE=176;ALTLINE=21,28,31,38,40,41,45,49,69,73,83,85,93,109,129,136,153,158,161,189,22 ...GT1/1./.1/11/1./.1/11/11/1./.1/1...
chr2L50402L_5040_SNPGA999PASSREFCOUNT=1;ALTCOUNT=118;ANNOTATION=|||;REFLINE=176;ALTLINE=21,28,31,38,40,41,45,49,69,73,83,85,93,109,129,136,153,158,161,189,22 ...GT1/1./.1/11/1./.1/11/11/1./.1/1...
chr2L50922L_5092_SNPCT999PASSREFCOUNT=6;ALTCOUNT=119;ANNOTATION=|||;REFLINE=176,379,437,551,705,765;ALTLINE=21,28,31,38,40,41,45,48,49,69,73,83,85,93,100,109 ...GT1/1./.1/11/1./.1/11/11/1./.1/1...
chr2L50952L_5095_SNPTA999PASSREFCOUNT=4;ALTCOUNT=115;ANNOTATION=|||;REFLINE=176,340,379,437;ALTLINE=21,28,31,38,40,41,45,48,69,73,83,85,93,100,109,129,136,15 ...GT1/1./.1/11/1./.1/11/11/1./.1/1...
chr2L51532L_5153_SNPAC999PASSREFCOUNT=155;ALTCOUNT=2;ANNOTATION=|||;REFLINE=21,26,28,31,32,38,40,41,48,49,59,73,83,85,100,109,136,149,153,158,161,189,195,208 ...GT0/00/00/00/00/00/00/00/0./../....
chr2L52322L_5232_SNPCT999PASSREFCOUNT=191;ALTCOUNT=1;ANNOTATION=|||;REFLINE=21,26,28,31,32,38,40,41,42,45,48,49,57,59,69,73,75,83,85,88,91,93,100,101,109,129 ...GT0/00/00/00/00/00/00/00/00/00/0...
chr2L52332L_5233_SNPGC999PASSREFCOUNT=189;ALTCOUNT=2;ANNOTATION=|||;REFLINE=21,26,28,31,32,38,40,41,42,45,48,49,57,59,69,73,75,83,85,88,91,93,100,101,109,129 ...GT0/00/00/00/00/00/00/00/00/00/0...
chr2L53172L_5317_SNPGA999PASSREFCOUNT=177;ALTCOUNT=11;ANNOTATION=|||;REFLINE=21,26,28,32,38,40,41,42,45,48,49,57,59,69,73,75,83,88,93,100,101,109,129,138,142 ...GT0/00/00/01/10/00/00/00/00/00/0...

DGRP v2 (R5) (dgrp2) Track Description
 

Description

This track shows the sequence (e.g., single nucleotide polymorphisms) and structural variants in 205 inbred lines of Drosophila melanogaster that are part of version 2 of the Drosophila melanogaster Genetic Reference Panel (DGRP).

The VCF file for the DGRP Freeze 2.0 calls was obtained from the DGRP web site. The variants were then lifted from the D. melanogaster release 5 assembly to the release 6 assembly.

References

Huang W et al. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Res. 2014 Jul;24(7):1193-208.