Table 2 Statistics of identified CRISPR cassettes and spacers
From: Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs
Metagenome dataset | JPN | HMP | DG |
|---|---|---|---|
Cassettes | |||
Identified by: | |||
  PILER-CR | 322 | 121 | 17 |
  CRT | 359 | 149 | 21 |
  CRISPRFinder | 361 | 235 | 22 |
  All three programs | 272 | 45 | 13 |
  1 or 2 programs, but adjacent to cas genes | 24 | 33 | 1 |
Final set of cassettes: | |||
  Total number | 296 | 78 | 14 |
  Cassettes adjacent to cas genes | 70 (24%) | 56 (71%) | 6 (43%) |
  Cassettes with assigned taxonomy | 73 (25%) | 69 (82%) | 9 (64%) |
  Cassettes with assigned CRISPR-cas type: | |||
    I type | 18 (6%) | 16 (20%) | 1 (7%) |
    II type | 9 (3%) | 4 (5%) | 1 (7%) |
    III type | 6 (2%) | 18 (23%) | 1 (7%) |
Spacers | |||
Total number | 3410 | 378 | 175 |
Unique spacers | 2992 | 352 | 174 |
Spacers with protospacers in: | |||
  The same metagenomic dataset | 136 | 59 | 0 |
  NR database | 17 | 9 | 0 |
Repeats | |||
Unique | 170 | 74 | 11 |
Repeats with matches in CRISPRdb | 23 | 0 | 0 |
Repeats from known clusters according to the CRISPRmap algorithm | 122 | 18 | 8 |