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The 21 species were selected based on genome coverage.
Ranking was based on genome coverage and accuracy.
We thus used an independent approach to identify autosomal and Z-linked regions based on genome coverage.
Based on genome coverage results compared with the D. ananassae rp49 gene, LOW was expected to have a 1.5-fold increase whereas HIGH was expected to have a 3.5-fold increase in copy number (fig. 4).
Gene deletions at either strain or lineage level were removed from the analysis by a Perl script (N = 223 genes); deletions were identified based on genome coverage using the respective strains genome, with a threshold of <90% gene coverage to define a deletion.
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In this case, investigating the variations of chloroplast genome based on higher genome coverage sequencing could decrease the number of missing values and heterozygotes, and thus obtain more accurate results.
The results were stored in a relational database that can readily be queried for coverage comparisons based on genome position.
Based on the genome coverage (∼70%) of this dataset, the total number of BsaXI sites in the C. farreri genome was estimated as ∼0.3 million.
The half-smooth tongue sole physical map assembly was judged to be reliable preliminarily based on enough genome coverage of valid clones, the very low cutoff value, and the very low fractions of Q clones and Q contigs.
As the previous analyzed microarray are mainly derived from ESTs and only a small fraction of NACs is present in these datasets, we further seek to use microarray based on whole genome coverage to provide deep insights into the expression patterns of NACs.
Based on the overall genome coverage and the unigene coverage, the A. syriaca genome likely contains a similar number of P3A-type ATPases.
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