Suppose the two reads in a read pair have the "XT" tag (Type: Unique/Repeat/N/Mate-sw) set to "U" and "M" respectively, which means one read is rescued by the other.
Then it seems to me that BWA sets the mapping quality of both to 0, which I couldn't understand. Since even if only 1 read is mapped (an orphan read), the mapping quality of this mapped read will not be 0.
Any idea would be appreciated.
Then it seems to me that BWA sets the mapping quality of both to 0, which I couldn't understand. Since even if only 1 read is mapped (an orphan read), the mapping quality of this mapped read will not be 0.
Any idea would be appreciated.