QTLdb: entrichment tests

Release 57
(Aug 26, 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:	9,620
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	1495.01874	29	6.29603e-297	1.888809e-295
Chromosome 1	799.16838	29	1.721563e-149	4.695172e-149
Chromosome 2	544.99794	29	1.552885e-96	2.911659e-96
Chromosome 3	334.30560	29	1.234117e-53	2.056862e-53
Chromosome 4	1083.75054	29	1.665980e-209	9.995880e-209
Chromosome 5	3353.22246	29	9e-41	1.173913e-40
Chromosome 6	1721.62164	29	9e-41	1.173913e-40
Chromosome 7	2.40330	29	0.998329325823115	9.983293e-01
Chromosome 8	557.84616	29	3.44573e-99	6.891460e-99
Chromosome 9	638.07900	29	7.944252e-116	1.986063e-115
Chromosome 10	40.74846	29	0.0724232	8.047022e-02
Chromosome 11	0.05196	29	0.998329325823115	9.983293e-01
Chromosome 12	1391.11020	29	8.72501e-275	8.725010e-274
Chromosome 13	430.40538	29	4.973121e-73	8.776096e-73
Chromosome 14	137855.40330	29	9e-41	1.173913e-40
Chromosome 15	35.67774	29	0.1831425	1.962241e-01
Chromosome 16	153.81288	29	6.017448e-19	6.943209e-19
Chromosome 17	870.28896	29	1.953854e-164	6.512847e-164
Chromosome 18	624.33264	29	5.724906e-113	1.321132e-112
Chromosome 19	153.81288	29	6.017448e-19	6.943209e-19
Chromosome 20	20563.46154	29	9e-41	1.173913e-40
Chromosome 21	919.38672	29	8.92236e-175	3.345885e-174
Chromosome 22	1320.60084	29	8.854667e-260	6.641000e-259
Chromosome 23	171.24534	29	4.115799e-22	5.144749e-22
Chromosome 24	1624.64862	29	9e-41	1.173913e-40
Chromosome 25	1030.38672	29	3.265926e-198	1.399683e-197
Chromosome 26	583.99170	29	1.340955e-104	2.873475e-104
Chromosome 27	1411.59252	29	3.790163e-279	5.685244e-278
Chromosome 28	1030.38672	29	3.265926e-198	1.399683e-197
Chromosome 29	862.23702	29	9.660087e-163	2.898026e-162

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	73.52444	5	1.889879e-14	1.889879e-14
Lactation length	166.25715	5	4.586914e-34	6.880371e-34
Lactation persistency	348.88733	5	3.038467e-73	9.115401e-73
Milk profitability index	85.56325	5	5.735381e-17	6.882457e-17
Milk yield	353.67667	5	2.828095e-74	1.696857e-73
Milking speed	2484.23758	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	=	181603.995900
Number of traits:	6	df	=	145
Number of QTLs:	9,620	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.