Skip to main content

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
  1. Columns correspond to three metagenome datasets.