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I have 11 mpileups generated by novoalign from whole genome sequencing of Daphnia, which has a genome size of ~200MB. Each is the result of alignment of about 130M paired-end illumina reads. I find that all of the mpileups have about 110M lines, implying that we have info for about 55% of the reference. I want to quantify the degree of overlap in coverage among the mpileups. Is there an easy way to do this with samtools or something similar? Also, is there a way to construct an mpileup file that has a line for every site in the reference, rather than just those with read coverage?
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