Next-generation sequencing tool

Explain SAM FLAG tool

Instruction: enter a valid SAM FLAG value (e.g. 99) to get a detailed interpretation of its meaning. FLAG values can additionally be used in filtering operations to include and/or exclude reads of interest. Filtering can be adjusted to achieve fine-grained control of the slicing operation. Notice that the FLAG bit values are simply binary representations of a series of concatenated Booleans. You can create dynamic links to this page for easy sharing.


Examples: exclude invalids, unmapped only

Include f =
Exclude F =
  • 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
  • supplementary alignment

Additional information

Include binary
Exclude binary
Binary comparison mask