SAM file format

1. About SAM format

SAM is (Sequence Alignment/Map) format

2. Field introduction
Office File



3. Flag expalin
  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
Reference: Web SAM Flag



3. Example
 Reference: Detail Example



4. Paired-End Flag

• 163: read paired, read mapped in proper, mate reverse, second in pair
• 83  : rad paired, read mapped in proper, read reverse, first in pair

• 67: read paired, read mapped in proper, fist in parir
• 131: read paired, read mapped in proper, second in pair 

• 99: read pair, read mapped in proper, mate reverse, fist in pair
• 147: read pair, read mapped in proper, read reverse, second in pair

5. Paired insert length calculation
 Reference: Paired insert length