[nilshomer]

Originally Posted by zcrself

read name, chromosome, position, strand, insert size from the outer coorniates of a pair, paired flag, mapping quality, single-end mapping quality, alternative mapping quality, number of mismatches of the best hit, sum of qualities of mismatched bases of the best hit, number of 0-mismatch hits of the first 24bp, number of 1-mismatch hits of the first 24bp on the reference, length of the read, read sequence and its quality

See:
http://maq.sourceforge.net/maq-manpage.shtml
http://maq.sourceforge.net/maqmap_format.shtml