[Samtools-help] samtools flagstat mapped read count

[Kate Im <kat...@gm...>]

I am using samtools flagstat to get some basic statistics on my alignment
and I noticed that the number of unmapped read (estimated by subtracting
the reported number of mapped reads from the reported number of total
reads) is always higher than the number of sequences with an " * " in the
third column of the SAM file. Shouldn't these be the same?

Thanks,
Kate