This utility explains SAM flags in plain English.
Flag:
Explanation:
read paired
read mapped in proper pair
read unmapped
mate unmapped
read reverse strand
mate reverse strand
first in pair
second in pair
not primary alignment
read fails platform/vendor quality checks
read is PCR or optical duplicate
read paired
read mapped in proper pair
read unmapped
mate unmapped
read reverse strand
mate reverse strand
first in pair
second in pair
not primary alignment
read fails platform/vendor quality checks
read is PCR or optical duplicate
Summary: