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Old 09-10-2009, 10:47 AM   #3
AlexB
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Location: Netherlands

Join Date: Sep 2009
Posts: 18
Default coverage quantitative?

Hi kmcarr,
yes indeed its a bacterial (streptococcus) genome. I guess that since for transcriptomics the technique is quantitative so my guess it should be for genomes as well. Just wondered whether such "artefacts" might be the result of library generation and or the used chemistry for sequence analysis (I am not so much in those details).
Regarding the 4-5 fold more coverage I indeed expect the example to be a multiple duplicated gene (have to look for transposon elements and so) or indeed as you say extra chromosomal like plasmid. The example (I looked it up was a transposase of 1163bp and flanking 270 post and 100 pre). Another contains IS630-spnl. Most indeed transposable elements.... But how to find where they belong????? Looking at the assembly and flanking sequences/SNPs???

In addition I just finished some pre-processing of another strain this afternoon that also has an average coverage of roughly 20-35 times but has several larger regions that have coverage over multiple contigs in synteny with about 100 fold. More extreme even a region with even 800 coverage (really smells like plasmid...?). Don't know yet what they contain but I hope to know soon.

So is it generally true that the coverage ratio approx resembles copy number per genome???

Thanks
ALex
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