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7 species at high (8.4 - 11X) coverage

7 species at high (8.4 - 11X) coverage 2 species ( D. sech. & D. persim ) at intermediate (4.9 and 4.1X) coverage why these two? 7 inbred lines of D. simulans at low coverage (1 - 3X) why do these and why at low coverage?. Quality score: Q20 = 99% accurate, Q40 = 99.99% accurate.

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7 species at high (8.4 - 11X) coverage

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  1. 7 species at high (8.4 - 11X) coverage 2 species (D. sech. & D. persim) at intermediate (4.9 and 4.1X) coverage why these two? 7 inbred lines of D. simulans at low coverage (1 - 3X) why do these and why at low coverage?

  2. Quality score: Q20 = 99% accurate, Q40 = 99.99% accurate N50 score: 50% of assembled basepairs are in contigs of this length or greater

  3. ORF annotation by: 4 de novo gene prediction models 3 homology-based predictors 1 combo method used GLEAN program to analyze combined set to predict optimal start, stop, intron splice sites

  4. Why look at “TE-derived expression”?

  5. Homology assessment Orthology by: fuzzy RBH (FRB) & Synpipe (incorporates synteny) 8,563 genes with 1:1 orthologs in melanogaster group 6,698 genes with 1:1 orthologs in all 12 species ** Caveats: missing genes - “plausible homologs” for 61% of genes ‘without’ orthologs - “confirmed” 20.7% gene losses - unable to resolve ~18% “probably underestimating the number of genuine absences”

  6. Red = same direction Green = inversion Blue = translocation

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