SAM (Sequence Alignment/Map) format is one of the most popular formats used for storing aligment information of high-throughput sequencing data. I’ve used it extensively, but still sometimes I find it hard to recognize the columns at first glance. So I annotated an example from the SAM format specification (Version: 1 Jun 2017) for quick reference.

Other related specification can be found at

SAM format example

An annotated example of SAM format. (A) An example alignment result. (B) The alignment result represented in SAM format. Black color represents the SAM information, and colorful text is the annotation.