Subject: Re: genome sequence coverages
Date:  14 Nov 2006

To: drospege@eugenes.org
|I am trying to find out what the relative sequence coverage was for 
|specific species in the 12 Drosophila genome project.  Specifically 
|we would like to know the sequence coverage in D. simulans, D. 
|sechellia, D. yakuba and D. erecta.  Can you tell me if and where 
|this information exists on the web.

Your question on sequence coverage could mean different things.  

One way is how many times did the whole genome shutgun sequencing
and assembly overlap or cover genome regions, on average.  This for
most of the Dros. genomes is 8 to 9 fold coverage.  This includes
all the Agencourt assemblies (Dere, Dana, Dvir, Dmoj, Dgri),
and Dyak (WUSTL).

These had 4X WGS coverage: Dsec (4.86X Broad), Dper (4.10X Broad), 
Dwil (Venter).

Dpse (Baylor) was 8X I believe, as was Dmel (probably).
Dsim (WUSTL) is a special case of a mosaic assembly of several
strains, one strain at 4X coverage, and 3 or 4 others at 1X coverage.
This Dsim assembly shows phylogenetic oddities due to that.

If you mean how well do the species genomes cover or match Dmel
genome, here is an answer from DroSpeGe.  Figure 1 here, the
middle green line displays DNA genome coverage in summary form:
http://insects.eugenes.org/species/news/genome-summaries/dnacoverage.html

This green line shows "genome coverage" in the sense of overall
matching of DNA segments. This is based on BLAST matches of genome
dna, which is one way, but not neccessarily the most precise way, to
measure this. These BLAST match statistics are for the matching base
range, not identity, so it is a rough measure.

Here is another way to look at the same BLAST match of genomes:  of
the regions that align well, what percent of bases are identical? This
doesn't count those regions that don't align well, but still can have
some matching bases.  Note also that there are multiple, duplicate
alignments so the species near Dmel have more than a full genome of
matches.

   BLAST-aligned to Dmel genome (118357599 Dmel bases)   
         Aligned   Identical      I/A 
           bases       bases    ratio
dsec   167573291   156630658   0.9347
dsim   214792784   202084159   0.9408
dyak   115449735   105385696   0.9128
dere   107867313    98257255   0.9109
dana    40494218    35796226   0.8840
dper    51626464    45858199   0.8883
dpse    26131078    23267705   0.8904
dwil    18893458    16534575   0.8751
dmoj    14231831    12445329   0.8745
dvir    18432531    16072818   0.8720
dgri    15129933    13232344   0.8746

- Don Gilbert
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd@indiana.edu--http://marmot.bio.indiana.edu/