Significant difference in SNV count between replicates

Question

[dana]

Hi,

I have several samples that were treated, and single clones were sent for exome sequencing.

After filtering out germline mutations, for two of the samples I have twice as many SNVs (and I have additional samples from the same conditions that have roughly the same number of mutations). These single clones were grown from the same original population as the other replicates, so I don't except that much of a difference.

I looked at the allele frequency and allele count fields, and there's no significant difference between the samples that stood out and the other ones.

Any idea as for what may cause this and what else to check?

Thanks!