What are missing adapter tags ma and ac?

The ma and ac tags indicate whether the molecule that produces a CCS read is missing a SMRTbell adapter on its left/start or right/end. The tags produced by ccs v6.3.0 and newer are based on the ADAPTER_BEFORE_BAD and ADAPTER_AFTER_BAD information in the subread cx tag.

Tag ac

Array containing four counts, in order:

  • detected adapters on left/start
  • missing adapters on left/start
  • detected adapters on right/end
  • missing adapter on right/end

Tag ma

Bitmask storing if an adapter is missing on either side of the molecule. A value of 0 indicates neither end has a confirmed missing adapter.

  • 0x1 if adapter is missing on left/start
  • 0x2 if adapter is missing on right/end

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