Questions tagged [mapq]

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6
votes
2answers
45 views

Does the MAPQ=0 fraction of a BAM file depend on the insert sizes?

When doing Illumina 2x150bp sequencing of genomic DNA, and after aligning the reads to GRCh38, does the percentage of the non-N fraction of the human genome as MAPQ=0 depend on the insert sizes of the ...
4
votes
2answers
127 views

sum of products of mapq and mapped bases for each read in a from a BAM file

Given a BAM file, I'd like to calculate the sum, over all reads, of the mapping quality and the number of mapped bases (i.e. number of M's in the CIGAR string). For example, given two reads like this:...
4
votes
3answers
324 views

what percentage of the human genome is MAPQ=0?

When doing Illumina 2x150bp sequencing of genomic DNA, and after aligning the reads to GRCh38, what percentage of the non-N fraction of the human genome is MAPQ=0? This is, what part corresponds to ...