Motif depletion in bacteriophages infecting hosts with CRISPR systems

BMC Genomics

Table 2 Summary of the statistical results using the Wilcoxon rank-sum test for CRISPR type I-C and PAM GAA

r _PAM
CRISPR^-	CRISPR⁺	Difference	p-value	Strain resampling	Method
Bacteria: 12 (47) CRISPR⁺, 117 (641) CRISPR^-
0.01883	-0.02136	0.04019	0.007858	99	res
0.1169	0.1082	0.008770	0.009564	99
Bacillus: 2 (18) CRISPR⁺, 4 (18) CRISPR^-
0.09768	0.1080	-0.01033	0.1916	-	res
0.08673	0.1773	-0.09062	0.0004285	100	sub
Lactobacillus: 1 (3) CRISPR⁺, 6 (13) CRISPR^-
-0.02019	-0.01306	-0.007136	0.6107	-	res
0.005076	-0.04924	0.05421	0.5214	-	sub
Streptococcus: 3 (9) CRISPR⁺, 7 (22) CRISPR^-
-0.04927	-0.5889	0.5397	4.464e-06	100	res
-0.03720	-0.4635	0.4263	1.19e-0.06	100	sub
Streptococcus (extended)
-0.06292	-0.3772	0.3143	1.965e-05	99	res
-0.04374	-0.3208	0.2771	1.223e-05	99	sub

For each data set, the number of species (strains) in CRISPR⁺ and CRISPR^-, respectively, is given. Median of r_PAM (log-ratio of the PAM) is given for CRISPR⁺ and CRISPR^-. “Difference” is the difference of these values, positive values indicate underrepresentation of the PAM in CRISPR⁺. Column “Strain resampling”: for significant results, resampling to a uniform species distribution, number of significant (p < 0.05) outcomes out of 100. Column “Method”: “res” - resampling method, “sub” - substring method.

ISSN: 1471-2164