maq格式

map格式：

       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.

snp格式：

       chromosome,

       position,

       reference base,

       consensus base,

       Phred-like consensus quality,

       read depth,

       the average number of hits of reads covering this position,

       the highest mapping quality of the reads covering the position,

       the minimum consensus quality in the 3bp flanking regions at each side of the site (6bp in total),

       the second best call,

       log likelihood ratio of the second best and the third best call,

       the third best call.

 

 

 

参考网址：http://maq.sourceforge.net/maq-manpage.shtml