Drosophila Genome Variant Analysis

Sequences of the 623 genomes provided by the Drosophila Genome Nexus (Lack et al. 2015 (link)) were downloaded and and repeat regions masked. Additionally, the DGN indel VCFs were downloaded and indel locations masked (±5 bp). Resequence data used to confirm a subset of the variants was obtained from the DPGP1 project's Solexa (now Illumina) sequencing (Solexa_release_1/dpgp_Solexa_r1.0.tar">http://www.dpgp.org/Solexa_release_1/dpgp_Solexa_r1.0.tar) and from the DGRP (Mackay et al. 2012 (link)) project's Roche 454 sequencing (ftp://ftp.hgsc.bcm.edu/DGRP/freeze1_July_2010/snp_calls/454/). Pooled Nescent data were from Bergland et al. (2014) (link), Kapun and Fabian (2017) , and SRA accession SRP075757.

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Assaf Z.J., Tilk S., Park J., Siegal M.L, & Petrov D.A. (2017). Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations. Genome Research, 27(12), 1988-2000.

Publication 2017

Solexa

Dpgp Drosophila Genome Indel Nexus Vcfs

Corresponding Organization :

Other organizations : Stanford University, New York University

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Protocol cited in 2 other protocols

Variable analysis

independent variables

Sequences of the 623 genomes provided by the Drosophila Genome Nexus (Lack et al. 2015)
Indel locations masked (±5 bp) from the DGN indel VCFs
Resequence data used to confirm a subset of the variants obtained from the DPGP1 project's Solexa (now Illumina) sequencing and the DGRP (Mackay et al. 2012) project's Roche 454 sequencing
Pooled Nescent data from Bergland et al. (2014), Kapun and Fabian (2017), and SRA accession SRP075757

dependent variables

Not explicitly mentioned

control variables

Repeat regions masked
Indel locations masked (±5 bp) from the DGN indel VCFs

controls

Positive controls: Not specified
Negative controls: Not specified

Annotations

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