Likelihood ratio tests reveal a large, highly significant effect of third chromosome line on phenotypic variation in bacterial load against all four bacteria ( S. marcescens : χ 2 = 128.42, d.f. = 1, P <2.2×10 -16 ; P. rettgeri : χ 2 = 263.88, d.f. = 1, P <2.2×10 −16 ; E. faecalis : χ 2 = 51.533, d.f. = 1, P = 7.04×10 −13 ; L. lactis : χ 2 = 35.391, d.f. = 1, P = 2.70×10 −9 ).
While 6.93% of tests are significant at a nominal α of 0.05, a weakly significant excess over the null expectation (χ 2 = 4.32, d. f. = 1, P = 0.0377), only 0.91% of tests are significant at a nominal α of 0.01, which is not different from the null expectation (χ 2 = 0.042, d. f. = 1, P = 0.8367).
In this case, genotypes at two out of 10 SNPs are associated with variation in bacterial load against at least two different bacteria at a nominal α of 0.05, and a third marker has marginal significance.
Nominally significant associations are also not evenly distributed within functional classes of the immune system.