Global diversity lines - a five-continent reference panel of sequenced Drosophila melanogaster strains.
Bottom Line: Another key feature of these strains is their widespread geographic origin, coming from Beijing, Ithaca, Netherlands, Tasmania, and Zimbabwe.We found 83 segregating inversions among the lines, and as expected these were especially abundant in the African sample.We anticipate that this will make a useful addition to the set of reference D. melanogaster strains, thanks to its geographic structuring and unusually high level of genetic diversity.
Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853.Show MeSH
Related in: MedlinePlus
Mentions: We investigated whether the variant quality score (VQS) per site or the genotype quality score (GQ) for individual genotype calls correlated with validation rate. Using the “100×” ZW155 validation set, we found that GQ clearly correlated with validation (Figure S3) but VQS did not (data not shown). Genotype calls with a greater GQ validated at a greater rate. We did find that, following variant quality score recalibration, the sites with the lowest VQS-recalibrated also had lower validation rates, especially heterozygous sites. We used a combination of GQ score, VQS recalibrated-flag, and genotype to filter out classes of genotype calls with validation rates below 90%, including all heterozygous calls outside of “het blocks.” This filtering reduced the number of nonreference SNP genotypes by 12% and the number of variant SNP sites by 5%. Finally, we masked SNP genotype calls if the SNP was within 5 nt of an indel call in the same line. There are more than 5.75 M euchromatic SNPs in the final set of variant sites (Figure 2 and Table S3), with 97% of genotypes called across 84+1 lines.
Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853.