QTLdb: entrichment tests

Release 56
(Apr 24, 2025)

Whole genome analysis for QTL/association enrichment

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 - other traits:	28
Number of QTL / associations found:	2,687
Number of chromosomes where QTL / associations are found:	30

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

Chromosomes	Total χ²	df	p-values	FDR ^*	Size of χ²
Chromosome X	2342.68020	29	9e-41	1.227273e-40
Chromosome 1	2389.82268	29	9e-41	1.227273e-40
Chromosome 2	21203.36344	29	9e-41	1.227273e-40
Chromosome 3	145.40456	29	1.909135e-17	2.290962e-17
Chromosome 4	1469.73036	29	1.550546e-291	4.651638e-290
Chromosome 5	6.14432	29	0.999998	9.999980e-01
Chromosome 6	68890.52100	29	9e-41	1.227273e-40
Chromosome 7	159.20128	29	6.429903e-20	8.386830e-20
Chromosome 8	395.45576	29	6.19247e-66	1.326958e-65
Chromosome 9	373.53092	29	1.660424e-61	3.320848e-61
Chromosome 10	96.46952	29	3.563740e-09	4.112008e-09
Chromosome 11	157.32556	29	1.402962e-19	1.753703e-19
Chromosome 12	66.33340	29	9.460485e-05	1.013623e-04
Chromosome 13	85.79900	29	1.590634e-07	1.767371e-07
Chromosome 14	20557.03972	29	9e-41	1.227273e-40
Chromosome 15	831.28472	29	3.107208e-156	1.165203e-155
Chromosome 16	831.28472	29	3.107208e-156	1.165203e-155
Chromosome 17	677.89428	29	4.055441e-124	1.106029e-123
Chromosome 18	1385.24064	29	1.550854e-273	1.550854e-272
Chromosome 19	799.35604	29	1.572338e-149	5.241127e-149
Chromosome 20	649.09180	29	4.061235e-118	1.015309e-117
Chromosome 21	1223.76408	29	3.382406e-239	2.536804e-238
Chromosome 22	1601.15424	29	9e-41	1.227273e-40
Chromosome 23	1556.72104	29	9e-41	1.227273e-40
Chromosome 24	593.36284	29	1.532857e-106	3.537362e-106
Chromosome 25	3.68508	29	0.998329325823115	9.999980e-01
Chromosome 26	1385.24064	29	1.550854e-273	1.550854e-272
Chromosome 27	930.82164	29	3.465206e-177	1.732603e-176
Chromosome 28	707.32172	29	2.926505e-130	8.779515e-130
Chromosome 29	1000.30588	29	7.457916e-192	4.474750e-191

Chi-squared (χ²) test: Which of the 28 milk composition - other traits are over-represented in the QTLdb

Traits	Total χ²	df	p-values	FDR ^*	Size of χ²
Milk acetone content	69.76978	27	1.209735e-05	1.782767e-05
Milk acidity/alkalinity	66.12335	27	3.936208e-05	5.248277e-05
Milk beta-hydroxybutyrate content	96.34098	27	1.018502e-09	1.584336e-09
Milk calcium content	298.80248	27	1.258408e-47	3.915047e-47
Milk cholesterol content	129.52827	27	2.360896e-15	4.407006e-15
Milk citrate content	64.59593	27	6.388191e-05	8.130425e-05
Milk copper content	66.26314	27	3.764433e-05	5.248277e-05
Milk glycerophosphocholine content	894.82287	27	4.024066e-171	2.816846e-170
Milk glycerophosphocholine to phosphocholine ratio	725.44728	27	1.769602e-135	9.909771e-135
Milk iodine content	97.38317	27	6.895192e-10	1.135679e-09
Milk iron content	378.02662	27	1.462603e-63	5.119110e-63
Milk lactose content	197.49016	27	7.446234e-28	2.084946e-27
Milk lactose yield	60.68489	27	0.0002143767	2.501062e-04
Milk magnesium content	154.01605	27	9.551482e-20	2.057242e-19
Milk manganese content	188.92859	27	3.113491e-26	7.925250e-26
Milk mid-infrared spectra	131.30374	27	1.148429e-15	2.296858e-15
Milk phosphocholine level	62.12693	27	0.0001378844	1.678593e-04
Milk phosphorus content	1255.87622	27	1.095188e-247	3.066526e-246
Milk potassium content	1198.79226	27	1.524038e-235	1.422435e-234
Milk riboflavin content	545.53887	27	5.920319e-98	2.762816e-97
Milk selenium content	420.84006	27	2.803219e-72	1.121288e-71
Milk sodium content	55.75393	27	0.0009232243	1.034011e-03
Milk solids percentage	114.02227	27	1.152507e-12	2.016887e-12
Milk solids yield	28.74555	27	0.3733447	3.871723e-01
Milk vitamin B-12 content	162.66599	27	2.477952e-21	5.781888e-21
Milk zinc content	1222.26661	27	1.551328e-240	2.171859e-239
Non-fat milk solids	32.81486	27	0.2032485	2.188830e-01
Non-fat milk solids percentage	6.7659	27	0.9999733	9.999733e-01

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	=	132515.351080
Number of traits:	28	df	=	783
Number of QTLs:	2,687	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.