SAM Flags Explained Improved

SAM Flags Explained

This utility improves on the Broad utility that explains SAM flags in plain English.
It also allows switching easily from a read to its mate.

Flag:

Read Paired

Read Mapped in Proper Pair

Read Unmapped

Mate Unmapped

Read Reverse Strand

Mate Reverse Strand

First in Pair

Second in Pair

Secondary Alignment

Read Fails Platform/Vendor Quality Checks

Read is PCR or Optical Duplicate

Supplementary Alignment

Summary: