Genomic DNA alignment Oregon-R Bloomington

Dm Strain Genomic Sequencing OreR-modencode alignments and assembly (Celniker project, Graveley subgroup)

Details

Reads from genomic DNA libraries created from the D. melanogaster Oregon R strain virgin female from Bloomington stock, were aligned to the D. melanogaster r5 genome using BWA. Tracks show read alignments and density. Based on the alignments, a consensus FASTA sequence for the cell-line genome was created with a guided assembly.
Total read count: 39751528
Mapped read count: 35118523
Alignment rate: 88.3%

General Description

Rather than doing a de novo assembly, we have done a guided assembly for D. melanogaster strains and tissue culture cell lines using the dm3 reference to build a new assembly in which we change the appropriate SNPs and insert or delete sequences as appropriate for indels. Our assembly, then, is full chromosome sequence (e.g., 2R, 2L, etc.) with the changes inserted.

Protocols

  1. Other Protocols: BWA alignment of D. melanogaster genomic reads, Guided Assembly of D. melanogaster Genomes
  1. External Links: SRR497727

Referenced modENCODE submissions:


Release Date: 2012-08-30 Submission 5518 Release Date: 2012-08-30 Submission 5518