Questions tagged [mapq]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
2 votes
2 answers
50 views

Is the Bowtie2 MAPQ score dependent on the database index?

I have two very similar genomes in my bowtie2 database (nuc similarity > 90 %). When mapping with bowtie2 against this database, most of the reads that are mapped to one of these genomes have a ...
user avatar
  • 23
6 votes
2 answers
55 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 ...
user avatar
  • 2,234
4 votes
2 answers
142 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:...
user avatar
  • 952
4 votes
3 answers
365 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 ...
user avatar
  • 2,234