[chenyao]

They should give the same number, and that is the case with the handful of bam files I have checked myself. Again the # reported for mapped with flagstat is not the number of reads which mapped but the number of alignments reported in the file. When output as a sam text file there is one line for each alignment which you count with wc -l. The numbers should be equal.

How can I get uniquely mapped reads? I konw I can use -q to get realiable reads, but I still want to know how many reads are unique not matter they are paired or not?