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Old 09-10-2009, 06:38 AM   #1
AlexB
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Location: Netherlands

Join Date: Sep 2009
Posts: 18
Question How quantitative is contig coverage?

Hi All,
I am working on draft (resequencing) genomes of about 2Mb. In one run we multiplexed three strains and that works quite ok (as far as i can see now).
I noticed one thing which I find odd and which might be an artefact or meaningful observation.
When I plotted the sequence coverage (contrib to consensus) I noticed that in my draft which has on average about 20-25 fold coverage that some contigs have extreme high coverage (over that complete contig). this can be as high as 125 fold coverage. .... Aaah repeats..... no.
I looked at it and one example for instance is of size 1kb containing one complete ORF. But there are more regions similar to this.

Does this mean this ORF is about 4-5 fold present in the genome or is this a too simple conclusion. Could there be amplification or assembly artefacts???

Thanks for sharing any thoughts on this!

Alex
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