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Global diversity lines - a five-continent reference panel of sequenced Drosophila melanogaster strains.

Grenier JK, Arguello JR, Moreira MC, Gottipati S, Mohammed J, Hackett SR, Boughton R, Greenberg AJ, Clark AG - G3 (Bethesda) (2015)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853.

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Related in: MedlinePlus

Gene annotation. The number of variant sites falling within exons was disproportionately reduced during the variant call pipeline for both (A) single-nucleotide polymorphisms (SNPs) and (B) small indels compared with variant site locations, particularly due to the GATK base quality recalibration step. The percent of variant sites retained after filtering is shown below the gene annotation category. (C) Similarly, SNP and small indel sites annotated as high impact were disproportionately reduced during the variant call pipeline compared to lower impact sites.
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fig3: Gene annotation. The number of variant sites falling within exons was disproportionately reduced during the variant call pipeline for both (A) single-nucleotide polymorphisms (SNPs) and (B) small indels compared with variant site locations, particularly due to the GATK base quality recalibration step. The percent of variant sites retained after filtering is shown below the gene annotation category. (C) Similarly, SNP and small indel sites annotated as high impact were disproportionately reduced during the variant call pipeline compared to lower impact sites.

Mentions: We next investigated the distribution of variant calls with respect to gene annotation. Variants with high predicted impact and located in exons were least likely to be retained in the variant call pipeline (Figure 3), indicating that as call quality increased due to recalibration and filtering, the false-positive rate of high impact sites decreased. Additionally, we observe a clear mod-3 pattern in small indels located in coding regions, which is magnified by the recalibration and filtering steps (Figure S7). These patterns of change in the distribution of variant annotations indicate the improved quality of the variant calls at each step of the pipeline.


Global diversity lines - a five-continent reference panel of sequenced Drosophila melanogaster strains.

Grenier JK, Arguello JR, Moreira MC, Gottipati S, Mohammed J, Hackett SR, Boughton R, Greenberg AJ, Clark AG - G3 (Bethesda) (2015)

Gene annotation. The number of variant sites falling within exons was disproportionately reduced during the variant call pipeline for both (A) single-nucleotide polymorphisms (SNPs) and (B) small indels compared with variant site locations, particularly due to the GATK base quality recalibration step. The percent of variant sites retained after filtering is shown below the gene annotation category. (C) Similarly, SNP and small indel sites annotated as high impact were disproportionately reduced during the variant call pipeline compared to lower impact sites.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390575&req=5

fig3: Gene annotation. The number of variant sites falling within exons was disproportionately reduced during the variant call pipeline for both (A) single-nucleotide polymorphisms (SNPs) and (B) small indels compared with variant site locations, particularly due to the GATK base quality recalibration step. The percent of variant sites retained after filtering is shown below the gene annotation category. (C) Similarly, SNP and small indel sites annotated as high impact were disproportionately reduced during the variant call pipeline compared to lower impact sites.
Mentions: We next investigated the distribution of variant calls with respect to gene annotation. Variants with high predicted impact and located in exons were least likely to be retained in the variant call pipeline (Figure 3), indicating that as call quality increased due to recalibration and filtering, the false-positive rate of high impact sites decreased. Additionally, we observe a clear mod-3 pattern in small indels located in coding regions, which is magnified by the recalibration and filtering steps (Figure S7). These patterns of change in the distribution of variant annotations indicate the improved quality of the variant calls at each step of the pipeline.

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853.

Show MeSH
Related in: MedlinePlus