Miscellaneous OCTU stats

Typing up some old pages, and here are some stats I calculated for the OCTUs.

Results from Chimera check on 95% OCTUs:

  • 95A had 2769 chimeric OCTUs, and 1179 non-chimeric OCTUs
  • 95B had 1883 chimeric OCTUs, and 2169 non-chimeric OCTUs

Contaminant OCTUs detected in 95 and 99 datasets:

99A Dataset:

  • Vector OCTU 10409 (Blast match 100%)
  • Human OCTU 23900 (Blast match 99.55%), shared Pacific/Atlantic
  • Human OCTU 31567 (Blast match 99.11%)
  • Human OCTU 30401 (Blast match 98.41), shared Pacific/Atlantic
  • Human OCTU 79050 (Blast match 97.87%)
  • Human OCTU 78664 (Blast match 98.67%), shared Pacific/Atlantic
  • LOTS more (55 overall total) in 99A dataset–check spreadsheet for exact OCTU numbers

95A Dataset:

  • Vector OCTU 1312 (Blast match 100%)
  • Human OCTU 807 (Blast match 95.37%)
  • Human OCTU 1829 (Blast match 99.78%), shared Pacific/Atlantic
  • Human OCTU 1860 (Blast mach 97.39%), shared Pacific/Atlantic
  • Human OCTU 2917 (Blast match 99.56%), shared Pacific/Atlantic
  • Human OCTU 2453 (Blast match 92.39%)
  • Human OCTU 2335 (Blast match 97.39%)

95B Dataset:

  • Human OCTU 1034 (Blast match 100%), shared Deep/Shallow and Pacific/Atlantic
  • Human OCTU 2850 (Blast match 99.12%), shared Pacific/Atlantic
  • Human OCTU 3017 (Blast match 92.87%)
  • Human OCTU 2291 (Blast match 100%)

Shared OCTUs below base error frequency:

  • 95A deep/shallow (3) = OCTUs 30, 37, 81 ; Pacific/Atlantic (0)
  • 95B deep/shallow (7) = OCTUs 6, 8, 26, 84, 108, 113, 332 ; Pacific/Atlantic (1) = OCTU 381
  • 99A deep/shallow (1) = OCTU 142  ; Pacific/Atlantic (1) = 16413

19 March Daimi StemLoops combo submitted to CIPRES; partition is Helix (alignment sites 1-1175) and Loops (alignment sites 1176-2154)

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