Can anyone please explain in one sentence the meaning of these two flags (mate unmapped and mate reverse strand)? If I have paired-end sequencing data in samtools flagstat the values should be 0 because it is not mate pair sequencing? Thanks a lot for explanation.
In the BAM specification "mate" is not the same thing as "mate" in mate-pair sequencing. It, more or less, mean "pair".
The meanings are
read1 mapped + read2 mapped -
"mate unmapped" is unset and "mate revserse strand" is set.
read1 mapped - read2 unmapped +
"mate umapped" is set and "mate reverse strand" is not set.
The specification has slowly been changing over to using the term "next read in template" rather than "mate", but the flags still use the old language.