QTLdb: entrichment tests

Release 56
(Apr 24, 2025)

Whole genome analysis for QTL/association enrichment

Running...

Version: Enrich S: beta v0.8

Search:	to limit the list of your trait choices:
	(optional) focus on chromosome with Mb windows across its length

Data:

Number of milk production & yield traits:	6
Number of QTL / associations found:	9,301
Number of chromosomes where QTL / associations are found:	30

Chi-squared (χ²) test: are milk production & yield traits over-represented on some chromosomes?

Chromosomes	Total χ²	df	p-values	FDR ^*	Size of χ²
Chromosome X	1474.57176	29	1.440266e-292	2.160399e-291
Chromosome 1	837.54612	29	1.501799e-157	4.095815e-157
Chromosome 2	566.11464	29	6.72586e-101	1.345172e-100
Chromosome 3	363.40866	29	1.811755e-59	2.860666e-59
Chromosome 4	1069.05924	29	2.147706e-206	9.204454e-206
Chromosome 5	2606.13012	29	9e-41	1.173913e-40
Chromosome 6	1516.89498	29	1.360682e-301	4.082046e-300
Chromosome 7	9.33840	29	0.9997992	9.997992e-01
Chromosome 8	514.39374	29	3.156862e-90	5.570933e-90
Chromosome 9	634.24926	29	4.97153e-115	1.147276e-114
Chromosome 10	42.81090	29	0.04739254	5.265838e-02
Chromosome 11	0.17808	29	0.998329325823115	9.997992e-01
Chromosome 12	1359.38934	29	4.941111e-268	3.705833e-267
Chromosome 13	395.92908	29	4.966602e-66	8.277670e-66
Chromosome 14	138581.18142	29	9e-41	1.173913e-40
Chromosome 15	32.58492	29	0.2947948	3.158516e-01
Chromosome 16	146.59332	29	1.173998e-17	1.408798e-17
Chromosome 17	829.51338	29	7.320428e-156	1.830107e-155
Chromosome 18	613.40244	29	1.066661e-110	2.285702e-110
Chromosome 19	205.44630	29	1.747555e-28	2.184444e-28
Chromosome 20	21375.71964	29	9e-41	1.173913e-40
Chromosome 21	861.87636	29	1.150404e-162	3.451212e-162
Chromosome 22	1278.56190	29	7.699044e-251	4.619426e-250
Chromosome 23	139.93338	29	1.769119e-16	2.041291e-16
Chromosome 24	1594.43760	29	9e-41	1.173913e-40
Chromosome 25	971.33298	29	9.818327e-186	3.681873e-185
Chromosome 26	533.49876	29	3.66108e-94	6.864525e-94
Chromosome 27	1359.38934	29	4.941111e-268	3.705833e-267
Chromosome 28	1078.17570	29	2.523776e-208	1.261888e-207
Chromosome 29	928.46016	29	1.090580e-176	3.635267e-176

Chi-squared (χ²) test: Which of the 6 milk production & yield traits are over-represented in the QTLdb

Traits	Total χ²	df	p-values	FDR ^*	Size of χ²
Dry period length	79.9356	5	8.656235e-16	1.038748e-15
Lactation length	68.7268	5	1.885771e-13	1.885771e-13
Lactation persistency	346.42502	5	1.029795e-72	3.089385e-72
Milk profitability index	86.01869	5	4.603026e-17	6.904539e-17
Milk yield	363.25433	5	2.449296e-76	1.469578e-75
Milking speed	2445.60341	5	9e-41	1.800000e-40

Correlations found between some of these traits for your reference

No correlation data found on these traits

Overall Test

Data		Chi'Square Test			Fisher's Exact Test
Number of chrom.:	30	χ²	=	181920.121920
Number of traits:	6	df	=	145
Number of QTLs:	9,301	p-value	=	0

FOOT NOTE: * : FDR is short for "false discovery rate", representing the expected proportion of type I errors. A type I error is where you incorrectly reject the null hypothesis, i.e. you get a false positive. It's statistical definition is FDR = E(V/R | R > 0) P(R > 0), where V = Number of Type I errors (false positives); R = Number of rejected hypotheses. Benjamini–Hochberg procedure is a practical way to estimate FDR.