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 pigmentation traits:	11
Number of QTL / associations found:	275
Number of chromosomes where QTL / associations are found:	21

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

Chromosomes	Total χ²	df	p-values	FDR ^*	Size of χ²
Chromosome 1	122.88760	20	8.303486e-17	1.453110e-16
Chromosome 2	3.04766	20	0.9999953	9.999953e-01
Chromosome 4	122.88760	20	8.303486e-17	1.453110e-16
Chromosome 5	909.48759	20	7.517597e-180	1.578695e-178
Chromosome 6	4713.00764	20	9e-41	6.300000e-40
Chromosome 7	103.40759	20	3.078184e-13	4.617276e-13
Chromosome 9	103.40759	20	3.078184e-13	4.617276e-13
Chromosome 11	122.88760	20	8.303486e-17	1.453110e-16
Chromosome 12	122.88760	20	8.303486e-17	1.453110e-16
Chromosome 13	69.48766	20	2.207748e-07	2.575706e-07
Chromosome 14	122.88760	20	8.303486e-17	1.453110e-16
Chromosome 15	69.48766	20	2.207748e-07	2.575706e-07
Chromosome 16	122.88760	20	8.303486e-17	1.453110e-16
Chromosome 18	42.28763	20	0.002536453	2.803448e-03
Chromosome 19	8.04760	20	0.9915481	9.999953e-01
Chromosome 20	122.88760	20	8.303486e-17	1.453110e-16
Chromosome 21	85.60761	20	4.299899e-10	6.019859e-10
Chromosome 22	3988.20763	20	9e-41	6.300000e-40
Chromosome 24	122.88760	20	8.303486e-17	1.453110e-16
Chromosome 28	69.48766	20	2.207748e-07	2.575706e-07
Chromosome 29	122.88760	20	8.303486e-17	1.453110e-16

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

Traits	Total χ²	df	p-values	FDR ^*	Size of χ²
Coat color	168.59692	10	5.414535e-31	5.955989e-30
Degree of spotting	9.34959	10	0.4992785	6.865079e-01
Eye area pigmentation	48.04338	10	6.094521e-07	1.340795e-06
Eyelid pigmentation	139.80454	10	4.621544e-25	2.541849e-24
Facial pigmentation	80.50328	10	4.000071e-13	1.100020e-12
Hoof pigmentation	34.05182	10	0.000181002	2.844317e-04
Sole pigmentation	1.23932	10	0.999544	9.995440e-01
Teat pigmentation	41.40444	10	9.567446e-06	1.754032e-05
White spotting	93.27772	10	1.196228e-15	4.386169e-15
White spotting on back	1.23932	10	0.999544	9.995440e-01
White spotting on belly	1.23932	10	0.999544	9.995440e-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.:	21	χ²	=	11270.959920
Number of traits:	11	df	=	200
Number of QTLs:	275	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.