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 general reproduction parameters traits:	11
Number of QTL / associations found:	10,957
Number of chromosomes where QTL / associations are found:	31

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

Chromosomes	Total χ²	df	p-values	FDR ^*	Size of χ²
Chromosome X	2829195.58405	30	9e-41	9.300000e-41
Chromosome 1	3649.73345	30	9e-41	9.300000e-41
Chromosome 2	3398.43108	30	9e-41	9.300000e-41
Chromosome 3	3522.96186	30	9e-41	9.300000e-41
Chromosome 4	3649.73345	30	9e-41	9.300000e-41
Chromosome 5	904.20088	30	7.97598e-171	2.472554e-169
Chromosome 6	2941.82119	30	9e-41	9.300000e-41
Chromosome 7	3628.44922	30	9e-41	9.300000e-41
Chromosome 8	3628.44922	30	9e-41	9.300000e-41
Chromosome 9	2753.56521	30	9e-41	9.300000e-41
Chromosome 10	3439.69241	30	9e-41	9.300000e-41
Chromosome 11	3564.97009	30	9e-41	9.300000e-41
Chromosome 12	3757.08817	30	9e-41	9.300000e-41
Chromosome 13	3543.93490	30	9e-41	9.300000e-41
Chromosome 14	53.47441	30	0.00525814	5.258140e-03
Chromosome 15	3377.89386	30	9e-41	9.300000e-41
Chromosome 16	3713.95948	30	9e-41	9.300000e-41
Chromosome 17	2661.77142	30	9e-41	9.300000e-41
Chromosome 18	3276.14111	30	9e-41	9.300000e-41
Chromosome 19	3357.41879	30	9e-41	9.300000e-41
Chromosome 20	3439.69241	30	9e-41	9.300000e-41
Chromosome 21	3586.06754	30	9e-41	9.300000e-41
Chromosome 22	3649.73345	30	9e-41	9.300000e-41
Chromosome 23	2571.53369	30	9e-41	9.300000e-41
Chromosome 24	3586.06754	30	9e-41	9.300000e-41
Chromosome 25	3522.96186	30	9e-41	9.300000e-41
Chromosome 26	3713.95948	30	9e-41	9.300000e-41
Chromosome 27	3800.46568	30	9e-41	9.300000e-41
Chromosome 28	3649.73345	30	9e-41	9.300000e-41
Chromosome 29	3628.44922	30	9e-41	9.300000e-41
Chromosome 31	3822.24788	30	9e-41	9.300000e-41

Chi-squared (χ²) test: Which of the 11 general reproduction parameters traits are over-represented in the QTLdb

Traits	Total χ²	df	p-values	FDR ^*	Size of χ²
Birth index	1239.03564	10	5.465651e-260	6.012216e-259
Calf mortality	1146.5628	10	4.823331e-240	2.652832e-239
Calf size	2755.96185	10	9e-41	9.000000e-41
Calving index	2562.72832	10	9e-41	9.000000e-41
Paired testes volume	912.08334	10	1.596775e-189	5.854842e-189
Paired testes weight	643.45547	10	8.522736e-132	2.343752e-131
Perinatal mortality	3655.57612	10	9e-41	9.000000e-41
Reproductive problems	486.98791	10	2.659647e-98	5.851223e-98
Retained placenta	6207.05404	10	9e-41	9.000000e-41
Scrotal circumference	298.36701	10	3.442082e-58	6.310484e-58
Testicular hypoplasia	1505.59781	10	9e-41	9.000000e-41

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.:	31	χ²	=	2926990.186450
Number of traits:	11	df	=	300
Number of QTLs:	10,957	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.