What BAM tags are generated?

Tag Type Description
ac B,i Detected and missing adapter counts
ec f Effective coverage
fi B,C Double-strand forward IPD (codec V1)
ff i Fail reads
fn i Double-strand forward number of complete passes (zero or more)
fp B,C Double-strand forward PulseWidth (codec V1)
ip B,C Single-strand IPD (codec V1)
ma i Missing adapters bitmask
np i Number of full-length subreads
pw B,C Single-strand PulseWidth (codec V1)
ri B,C Double-strand reverse IPD (codec V1)
rn i Double-strand reverse number of complete passes (zero or more)
rp B,C Double-strand reverse PulseWidth (codec V1)
rq f Predicted average read accuracy
sa B,I [Run-length encoded per-base coverage by subread alignments in form of ,,...](https://pacbiofileformats.readthedocs.io/en/13.0/BAM.html#use-of-read-tags-for-hifi-per-read-base-pileup-summary)
sm B,C Per-base number of aligned matches
sx B,C Per-base number of aligned mismatches
sn B,f Signal-to-noise ratios for each nucleotide
zm i ZMW hole number
RG z Read group

How does the output BAM file size scale with yield?

For each base, the output BAM file size scales as follows

  • 0.5 byte/base for the actual base (4-bit encoding)
  • 1 byte/base for the QV
  • 1 byte/base for the forward PW
  • 1 byte/base for the forward IPD
  • 1 byte/base for the reverse PW
  • 1 byte/base for the reverse IPD

For a normal ccs run without kinetics, the upper bound is 1.5 bytes/base. If ccs is run with kinetics, the upper bound is 5.5 bytes/base.

Per-read meta information add a fixed amount of 32 bytes per read:

  • ec,rq : float, each 4 bytes
  • sn: float array, 4x4 bytes
  • np, zm: int32_t, 4 byte
  • RG: string of length 8, 8x1 bytes

The actual output BAM that ccs generates is compressed. Compression is data-dependent and because of that, upper bounds can’t be provided.

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