Schema for FlyVar EMS Screen - Variants Identified in FlyVar EMS Mutagenesis Screen
  Database: dm6    Primary Table: hgsc_all_Hugo_EMS_indels
VCF File: /gbdb/dm6/bbi/vcf/filter_hgsc_all_Hugo_EMS_indels.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
chr2L263.GGCTCT13.58PASSAC=3;AN=6;P=0.9597;SF=0GT:GQ:DP:RR:VR.:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:....
chr2L721.GGCTCT14.32PASSAC=2;AN=4;P=0.9732;SF=0GT:GQ:DP:RR:VR.:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:....
chr2L915.ANTCG46.08PASSAC=36;AN=40;P=1;SF=0GT:GQ:DP:RR:VR.:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:.1/1:.:143:51:92...
chr2L1140.TTTAA5PASSAC=1;AN=2;P=0.7111;SF=0GT:GQ:DP:RR:VR.:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:....
chr2L1179.GGCTCT11PASSAC=3;AN=6;P=0.917;SF=0GT:GQ:DP:RR:VR.:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:....
chr2L1598.TTTAA13PASSAC=1;AN=2;P=0.9522;SF=0GT:GQ:DP:RR:VR.:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:....
chr2L2095.GGCTCT11PASSAC=1;AN=2;P=0.9254;SF=0GT:GQ:DP:RR:VR.:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:....
chr2L2514.TTTAA10PASSAC=1;AN=2;P=0.8965;SF=0GT:GQ:DP:RR:VR.:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:....
chr2L2601.AATAAC4.5PASSAC=2;AN=4;P=0.6699;SF=0GT:GQ:DP:RR:VR.:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:....
chr2L3011.GGCTCT13PASSAC=1;AN=2;P=0.9546;SF=0GT:GQ:DP:RR:VR.:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:..:.:.:.:....

FlyVar EMS Screen (flyvar_ems) Track Description
 

Description

These tracks show the sequence (e.g., single nucleotide polymorphisms) and structural variants identified in 394 mutant strains from a EMS-mutagenesis screen and in their parental strain (FRT19A). The mutant strains carry lethal mutations on the X chromosome. The parental strain (FRT19A) was isogenized for only the X chromosome.

The datasets were obtained from the FlyVar web site. The variants were lifted from the D. melanogaster release 5 assembly to the release 6 assembly.

References

Haelterman NA, Jiang L, Li Y, Bayat V, Sandoval H, Ugur B, Tan KL, Zhang K, Bei D, Xiong B, Charng WL, Busby T, Jawaid A, David G, Jaiswal M, Venken KJ, Yamamoto S, Chen R, Bellen HJ. Large-scale identification of chemically induced mutations in Drosophila melanogaster. Genome Res. 2014 Oct;24(10):1707-18.

Wang F, Jiang L, Chen Y, Haelterman NA, Bellen HJ, Chen R. FlyVar: a database for genetic variation in Drosophila melanogaster. Database (Oxford). 2015 Aug 19;2015. pii: bav079.