View Single Post
Old 06-11-2017, 12:39 PM   #14
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

"perfect" means every base in the read matched the reference (no mismatches, indels, or Ns). "semiperfect" is similar but it allows Ns in the reference.

The "num reads" column in "mapped" row indicates the number of reads that were mapped.

Don't worry about the high error rate. That just indicates that 63.8% of your reads had at least one error (mismatching base, indel, etc). The more important number is the % of bases, which is only 0.46%, so the reads have roughly 99.5% identity to the reference.
Brian Bushnell is offline   Reply With Quote