Variation average coverage depth between samples

[Fasyr]

Hi,

I sequenced several bacterial strains from the same species using Illumina Hiseq 2500 (multiplexing). I then aligned the cleaned reads for each sample to a reference genome with Bowtie2. I observed an important variation in average coverage depth between samples ranging from 70X to 700X for one sample.
Do you have any idea what could be the source(s) of such variation?

Thanks

[nucacidhunter]

if you mean differences in average coverage between samples (sample 1: 70x and sample 2: 700x), it is most likely due to differences in library input (unequal pooling) for sequencing which have resulted in different number of reads for each sample. So my guess is that sample with 700x coverage has around 10x more read than the sample with 70x coverage.

If you mean differences in different region of the same sample then it is most likely due to bias in library prep.

[Fasyr]

Hello,
I mean differences in average coverage between samples.
I confirm the sample at 700X coverage has a higher % of read identified (5.5) after sequencing than the sample at 70X (0.58).
Thanks