Here is a sample stdout when using maq for paired-end reads.
# reads mapped in pairs is an odd number. How can that be?
94% reads mapped, but only 41% mapped in pairs, and about 1% can be rescued by 'moving' the reads. So the remaining 50% of 'mapped' reads, map to different chromosomes?
Are only the reads mapped in pairs used for SNP calling using downstream MAQ analysis?
-- 48 potential soa-indels pass the filter.
-- 3551 potential pe-indels pass the filter.
-- == statmap report ==
-- # single end (SE) reads: 0
-- # mapped SE reads: 0 (/ 0 = NA%)
-- # paired end (PE) reads: 21532606
-- # mapped PE reads: 20163428 (/ 21532606 = 93.64%)
-- # reads that are mapped in pairs: 8326749 (/ 20163428 = 41.29%)
-- # Q>=30 reads that are moved to meet mate-pair requirement: 899 (/ 8326749 = 0.01%)
-- # Q<30 reads that are moved to meet mate-pair requirement: 5519 (0.06%)
# reads mapped in pairs is an odd number. How can that be?
94% reads mapped, but only 41% mapped in pairs, and about 1% can be rescued by 'moving' the reads. So the remaining 50% of 'mapped' reads, map to different chromosomes?
Are only the reads mapped in pairs used for SNP calling using downstream MAQ analysis?
-- 48 potential soa-indels pass the filter.
-- 3551 potential pe-indels pass the filter.
-- == statmap report ==
-- # single end (SE) reads: 0
-- # mapped SE reads: 0 (/ 0 = NA%)
-- # paired end (PE) reads: 21532606
-- # mapped PE reads: 20163428 (/ 21532606 = 93.64%)
-- # reads that are mapped in pairs: 8326749 (/ 20163428 = 41.29%)
-- # Q>=30 reads that are moved to meet mate-pair requirement: 899 (/ 8326749 = 0.01%)
-- # Q<30 reads that are moved to meet mate-pair requirement: 5519 (0.06%)
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