QTLdb: entrichment tests

Release 59
(Apr 20, 2026)

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 composition - protein traits:	36
Number of QTL / associations found:	26,408
Number of chromosomes where QTL / associations are found:	30

Chi-squared (χ²) test: are milk composition - protein traits over-represented on some chromosomes?

Chromosomes	Total χ²	df	p-values	FDR ^*	Size of χ²
Chromosome X	21098.89296	29	9e-41	9.310345e-41
Chromosome 1	290.40228	29	6.384429e-45	9.576644e-44
Chromosome 2	3121.36992	29	9e-41	9.310345e-41
Chromosome 3	1050.44832	29	1.864309e-202	5.592927e-201
Chromosome 4	19148.68764	29	9e-41	9.310345e-41
Chromosome 5	12.19284	29	0.9973768	9.973768e-01
Chromosome 6	2132903.17044	29	9e-41	9.310345e-41
Chromosome 7	7571.18124	29	9e-41	9.310345e-41
Chromosome 8	14637.86892	29	9e-41	9.310345e-41
Chromosome 9	14982.41268	29	9e-41	9.310345e-41
Chromosome 10	7257.75732	29	9e-41	9.310345e-41
Chromosome 11	41779.32516	29	9e-41	9.310345e-41
Chromosome 12	18537.98256	29	9e-41	9.310345e-41
Chromosome 13	4090.67604	29	9e-41	9.310345e-41
Chromosome 14	333754.89876	29	9e-41	9.310345e-41
Chromosome 15	3936.93732	29	9e-41	9.310345e-41
Chromosome 16	3962.35584	29	9e-41	9.310345e-41
Chromosome 17	14152.61592	29	9e-41	9.310345e-41
Chromosome 18	16975.38240	29	9e-41	9.310345e-41
Chromosome 19	9551.28780	29	9e-41	9.310345e-41
Chromosome 20	90032.63292	29	9e-41	9.310345e-41
Chromosome 21	18045.67644	29	9e-41	9.310345e-41
Chromosome 22	15280.92612	29	9e-41	9.310345e-41
Chromosome 23	3786.14304	29	9e-41	9.310345e-41
Chromosome 24	17937.17460	29	9e-41	9.310345e-41
Chromosome 25	17452.96596	29	9e-41	9.310345e-41
Chromosome 26	13960.80504	29	9e-41	9.310345e-41
Chromosome 27	26322.41556	29	9e-41	9.310345e-41
Chromosome 28	23205.22272	29	9e-41	9.310345e-41
Chromosome 29	1895.14224	29	9e-41	9.310345e-41

Chi-squared (χ²) test: Which of the 36 milk composition - protein traits are over-represented in the QTLdb

Traits	Total χ²	df	p-values	FDR ^*	Size of χ²
Milk alpha-S1-casein content	65.5189	35	0.00133516	2.403288e-03
Milk alpha-S1-casein percentage	155.29759	35	4.305635e-17	8.611270e-17
Milk alpha-S2-casein percentage	227.94753	35	3.746566e-30	1.037511e-29
Milk alpha-casein content	40.34021	35	0.2459608	3.053306e-01
Milk alpha-casein percentage	42.36915	35	0.1829761	2.352550e-01
Milk alpha-casein to beta-casein ratio	4.51887	35	1	1.000000e+00
Milk alpha-lactalbumin content	8.51585	35	0.9999987	1.000000e+00
Milk alpha-lactalbumin percentage	184.32656	35	3.475455e-22	7.819774e-22
Milk beta-casein content	12.62092	35	0.9998178	1.000000e+00
Milk beta-casein percentage	478.79743	35	2.422084e-79	4.359751e-78
Milk beta-lactoglobulin percentage	2297.03117	35	9e-41	2.700000e-40
Milk beta-lactoglobulin protein content	2385.578	35	9e-41	2.700000e-40
Milk casein content	60.2103	35	0.005078631	7.617947e-03
Milk casein index	155.36364	35	4.194632e-17	8.611270e-17
Milk casein percentage	827.60528	35	3.546999e-151	1.276920e-149
Milk casein yield	63.41714	35	0.002293382	3.752807e-03
Milk delta-9-desaturase content	287.03183	35	2.402346e-41	2.162111e-40
Milk glycosylated kappa-casein percentage	1998.70977	35	9e-41	2.700000e-40
Milk immunoglobulin G content	35.67778	35	0.4363796	5.236555e-01
Milk kappa-casein content	48.06091	35	0.06968158	9.290877e-02
Milk kappa-casein percentage	2839.37464	35	9e-41	2.700000e-40
Milk lactoferrin content	2137.76208	35	9e-41	2.700000e-40
Milk lactoperoxidase content	55.19873	35	0.01622566	2.336495e-02
Milk osteopontin content	4.51887	35	1	1.000000e+00
Milk phosphorylated alpha-S2-casein percentage	447.81305	35	4.316795e-73	5.180154e-72
Milk protein content	61.65652	35	0.003565176	5.580275e-03
Milk protein percentage	5459.5514	35	9e-41	2.700000e-40
Milk protein yield	2387.99521	35	9e-41	2.700000e-40
Milk protein yield persistency	50.20171	35	0.04622594	6.400515e-02
Milk protein-to-fat ratio	77.41011	35	4.840393e-05	9.171271e-05
Milk unglycosylated kappa-casein percentage	2103.35449	35	9e-41	2.700000e-40
Milk urea nitrogen content	193.92952	35	6.533604e-24	1.680070e-23
Milk urea nitrogen yield	190.69338	35	2.504695e-23	6.011268e-23
Milk whey protein content	64.82549	35	0.001598718	2.740659e-03
Milk whey protein percentage	22.303	35	0.9526439	1.000000e+00
Milk whey protein yield	2.25944	35	1	1.000000e+00

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	=	2896734.951000
Number of traits:	36	df	=	1015
Number of QTLs:	26,408	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.