Hi
I'm trying to recover whole chloroplast sequence data from paired-end Illumina reads from a pool-seq project (25 individuals per pool). We have access to a close reference but not a species-specific chloroplast reference. Following alignment and filtering of reads from one lane (basically following the Popoolation pipeline), I'm getting coverage of about 10% of chloroplast genome at a read depth of 10. This seems very low to me...I expected that because there are many more copies of the cp genome than the nuclear genome, I would get higher cp coverage (our nuclear coverage is at about 70% at a read depth of 25-500). Does anyone have any numbers that I can compare to (e.g. cp coverage from paired-end Illumina data, not necessarily pooled)?
Thanks!