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 conformation traits:	20
Number of QTL / associations found:	3,101
Number of chromosomes where QTL / associations are found:	30

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

Chromosomes	Total χ²	df	p-values	FDR ^*	Size of χ²
Chromosome X	2815.68540	29	9e-41	1.928571e-40
Chromosome 1	218.87160	29	4.947403e-31	9.276381e-31
Chromosome 2	2.55420	29	0.998329325823115	9.999994e-01
Chromosome 3	17.95580	29	0.945168	9.999994e-01
Chromosome 4	134.51160	29	1.575537e-15	2.625895e-15
Chromosome 5	2957.47200	29	9e-41	1.928571e-40
Chromosome 6	1418.84580	29	1.080523e-280	3.241569e-279
Chromosome 7	885.05660	29	1.522514e-167	1.141885e-166
Chromosome 8	20.79360	29	0.8665573	9.999994e-01
Chromosome 9	114.87920	29	3.578306e-12	5.367459e-12
Chromosome 10	439.00700	29	8.795557e-75	3.298334e-74
Chromosome 11	2283.36680	29	9e-41	1.928571e-40
Chromosome 12	242.01240	29	1.790556e-35	3.581112e-35
Chromosome 13	17.95580	29	0.945168	9.999994e-01
Chromosome 14	114.87920	29	3.578306e-12	5.367459e-12
Chromosome 15	776.91080	29	8.015333e-145	4.007666e-144
Chromosome 16	39.93580	29	0.08499206	1.158983e-01
Chromosome 17	2.55420	29	0.998329325823115	9.999994e-01
Chromosome 18	134.51160	29	1.575537e-15	2.625895e-15
Chromosome 19	0.51620	29	0.998329325823115	9.999994e-01
Chromosome 20	17.95580	29	0.945168	9.999994e-01
Chromosome 21	65.26940	29	0.0001307322	1.867603e-04
Chromosome 22	398.22020	29	1.706859e-66	5.689530e-66
Chromosome 23	270.15820	29	6.035381e-41	1.646013e-40
Chromosome 24	1013.27340	29	1.355562e-194	2.033343e-193
Chromosome 25	284.81160	29	8.053996e-44	2.416199e-43
Chromosome 26	5.57260	29	0.9999994	9.999994e-01
Chromosome 27	510.51940	29	1.978849e-89	8.480781e-89
Chromosome 28	904.35360	29	1.313525e-171	1.313525e-170
Chromosome 29	776.91080	29	8.015333e-145	4.007666e-144

Chi-squared (χ²) test: Which of the 20 conformation traits are over-represented in the QTLdb

Traits	Total χ²	df	p-values	FDR ^*	Size of χ²
Angularity	43.10706	19	0.001253308	1.671077e-03
Anogenital distance	34.25443	19	0.01714748	1.804998e-02
Body condition score	142.82139	19	5.263114e-21	5.263114e-20
Body form composite index	40.45496	19	0.002850596	3.563245e-03
Bone quality	70.26407	19	8.313422e-08	1.847427e-07
Conformation score	122.24005	19	4.222926e-17	1.689170e-16
Dairy capacity composite index	122.3363	19	4.051032e-17	1.689170e-16
Dairy form	103.5136	19	1.231578e-13	4.105260e-13
Ear length	35.13975	19	0.01343523	1.492803e-02
Ear size	419.87584	19	3.192559e-77	6.385118e-76
Hindquarter proportions	20.71283	19	0.3528832	3.528832e-01
Locomotion	62.58545	19	1.498649e-06	2.997298e-06
Loin strength	37.13175	19	0.00763924	8.987341e-03
Muscularity	57.01379	19	1.137000e-05	1.895000e-05
Presence of horns	86.54013	19	1.352585e-10	3.864529e-10
Rump angle	125.59575	19	9.888037e-18	6.592025e-17
Rump conformation	72.75185	19	3.18922e-08	7.973050e-08
Stature	52.20523	19	6.164002e-05	8.805717e-05
Strength	58.73244	19	6.129623e-06	1.114477e-05
Structural soundness	56.10261	19	1.573272e-05	2.420418e-05

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	=	16885.320600
Number of traits:	20	df	=	551
Number of QTLs:	3,101	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.