DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=4.166e^-12)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	6.0433	0.0487

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1372 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	12710777	3L_12710777_SNP [dm3] 3L_12717677_SNP [dm6]	G	T	7.379e^-7	0.252	INTERGENIC
3L	12710782	3L_12710782_SNP [dm3] 3L_12717682_SNP [dm6]	G	A	7.838e^-7	0.252	INTERGENIC
2R	15159019	2R_15159019_SNP [dm3] 2R_19271514_SNP [dm6]	A	T	1.430e^-6	0.252	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
2R	10621372	2R_10621372_SNP [dm3] 2R_14733867_SNP [dm6]	C	A	1.526e^-6	0.252	INTERGENIC
2R	10715639	2R_10715639_SNP [dm3] 2R_14828134_SNP [dm6]	A	T	1.543e^-6	0.252	INTERGENIC
2R	15158993	2R_15158993_DEL [dm3] 2R_19271488_DEL [dm6]	CA	T	1.708e^-6	0.252	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2R	10705677	2R_10705677_SNP [dm3] 2R_14818172_SNP [dm6]	G	T	1.724e^-6	0.252	NON_SYNONYMOUS_CODING CG10202	TF binding site BDTNP1_TFBS_twi mE1_TFBS_sens
2R	10719564	2R_10719564_SNP [dm3] 2R_14832059_SNP [dm6]	G	A	1.724e^-6	0.252	UPSTREAM CG10205 INTERGENIC
2R	10701426	2R_10701426_SNP [dm3] 2R_14813921_SNP [dm6]	G	A	1.782e^-6	0.252	INTERGENIC	TF binding site mE1_TFBS_Trl
2R	10721948	2R_10721948_SNP [dm3] 2R_14834443_SNP [dm6]	C	A	1.804e^-6	0.252	DOWNSTREAM CG10205 INTERGENIC
2R	10713301	2R_10713301_SNP [dm3] 2R_14825796_SNP [dm6]	T	G	1.816e^-6	0.252	INTERGENIC
2R	10368189	2R_10368189_SNP [dm3] 2R_14480684_SNP [dm6]	G	C	1.829e^-6	0.252	UPSTREAM L INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1
2R	15159014	2R_15159014_SNP [dm3] 2R_19271509_SNP [dm6]	G	T	1.878e^-6	0.252	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
2R	10608747	2R_10608747_SNP [dm3] 2R_14721242_SNP [dm6]	C	T	1.881e^-6	0.252	INTERGENIC	TF binding site mE1_TFBS_inv
2R	15159096	2R_15159096_SNP [dm3] 2R_19271591_SNP [dm6]	G	C	2.198e^-6	0.254	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
2R	10700525	2R_10700525_SNP [dm3] 2R_14813020_SNP [dm6]	G	A	2.246e^-6	0.254	INTERGENIC	regulatory region REDfly_CRMs
2R	13747284	2R_13747284_SNP [dm3] 2R_17859779_SNP [dm6]	C	T	2.414e^-6	0.254	SYNONYMOUS_CODING olf186-F UPSTREAM CG14490
2R	10749489	2R_10749489_SNP [dm3] 2R_14861984_SNP [dm6]	C	T	2.436e^-6	0.254	NON_SYNONYMOUS_CODING Inr-a	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	10608749	2R_10608749_SNP [dm3] 2R_14721244_SNP [dm6]	C	G	5.085e^-6	0.502	INTERGENIC	TF binding site mE1_TFBS_inv
2R	10608696	2R_10608696_SNP [dm3] 2R_14721191_SNP [dm6]	G	A	6.733e^-6	0.631	INTERGENIC
2R	15861441	2R_15861441_SNP [dm3] 2R_19973936_SNP [dm6]	A	G	7.594e^-6	0.67	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	15159007	2R_15159007_SNP [dm3] 2R_19271502_SNP [dm6]	G	A	8.188e^-6	0.67	INTRON rib	enhancer mE1_CBP_Enhancers TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
2R	15864853	2R_15864853_SNP [dm3] 2R_19977348_SNP [dm6]	G	C	8.211e^-6	0.67	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10709770	2R_10709770_SNP [dm3] 2R_14822265_SNP [dm6]	C	T	1.077e^-5	0.822	INTERGENIC
X	6693235	X_6693235_SNP [dm3] X_6799202_SNP [dm6]	C	T	1.169e^-5	0.822	INTRON C3G
2L	6813292	2L_6813292_SNP [dm3] 2L_6813292_SNP [dm6]	G	C	1.188e^-5	0.822	DOWNSTREAM CR44081 INTERGENIC
2R	1049371	2R_1049371_SNP [dm3] 2R_5161866_SNP [dm6]	T	C	1.336e^-5	0.822	INTERGENIC	transposable element FlyBase
2R	10674472	2R_10674472_SNP [dm3] 2R_14786967_SNP [dm6]	A	G	1.371e^-5	0.822	INTRON kn	TF binding site BDTNP1_TFBS_dl
2R	10675354	2R_10675354_SNP [dm3] 2R_14787849_SNP [dm6]	C	A	1.371e^-5	0.822	INTRON kn	TF binding site BDTNP1_TFBS_da
2L	6813096	2L_6813096_SNP [dm3] 2L_6813096_SNP [dm6]	A	C	1.402e^-5	0.822	EXON CR44081
X	16159938	X_16159938_SNP [dm3] X_16265905_SNP [dm6]	T	C	1.411e^-5	0.822	INTRON CG12507
2R	10787579	2R_10787579_SNP [dm3] 2R_14900074_SNP [dm6]	T	C	1.437e^-5	0.822	SYNONYMOUS_CODING Cyp317a1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	10616116	2R_10616116_SNP [dm3] 2R_14728611_SNP [dm6]	G	A	1.447e^-5	0.822	INTERGENIC
2R	14222034	2R_14222034_SNP [dm3] 2R_18334529_SNP [dm6]	A	C	1.552e^-5	0.83	INTRON sbb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	16159941	X_16159941_MNP [dm3] X_16265908_MNP [dm6]	CAT	TTG	1.571e^-5	0.83	INTRON CG12507
2R	10787362	2R_10787362_SNP [dm3] 2R_14899857_SNP [dm6]	T	C	1.605e^-5	0.83	SYNONYMOUS_CODING Cyp317a1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	10787392	2R_10787392_SNP [dm3] 2R_14899887_SNP [dm6]	A	T	1.665e^-5	0.83	SYNONYMOUS_CODING Cyp317a1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	10154268	2R_10154268_SNP [dm3] 2R_14266763_SNP [dm6]	T	C	1.762e^-5	0.83	INTRON CG8547
2R	10721104	2R_10721104_SNP [dm3] 2R_14833599_SNP [dm6]	G	A	1.784e^-5	0.83	NON_SYNONYMOUS_CODING CG10205 UTR_3_PRIME CG10205
2R	10666546	2R_10666546_SNP [dm3] 2R_14779041_SNP [dm6]	T	C	1.804e^-5	0.83	INTRON kn
3L	1845109	3L_1845109_SNP [dm3] 3L_1845109_SNP [dm6]	A	G	1.814e^-5	0.83	INTERGENIC
2L	17888894	2L_17888894_SNP [dm3] 2L_17888894_SNP [dm6]	C	T	1.920e^-5	0.857	INTERGENIC
2L	7270498	2L_7270498_SNP [dm3] 2L_7270498_SNP [dm6]	G	T	1.989e^-5	0.868	INTRON Wnt4
2R	14222022	2R_14222022_SNP [dm3] 2R_18334517_SNP [dm6]	G	A	2.161e^-5	0.921	INTRON sbb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	3372773	2R_3372773_SNP [dm3] 2R_7485268_SNP [dm6]	A	G	2.345e^-5	0.978	SYNONYMOUS_CODING wech	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	10460322	2R_10460322_SNP [dm3] 2R_14572817_SNP [dm6]	C	A	2.421e^-5	0.984	SYNONYMOUS_CODING LamC INTRON ttv
2L	2425224	2L_2425224_SNP [dm3] 2L_2425224_SNP [dm6]	C	T	2.466e^-5	0.984	DOWNSTREAM CG9886 & 1 other INTERGENIC
2R	15863357	2R_15863357_SNP [dm3] 2R_19975852_SNP [dm6]	G	A	2.766e^-5	1	INTERGENIC
2R	10676596	2R_10676596_SNP [dm3] 2R_14789091_SNP [dm6]	G	T	2.866e^-5	1	INTRON kn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	16159947	X_16159947_SNP [dm3] X_16265914_SNP [dm6]	C	T	2.878e^-5	1	INTRON CG12507
2R	3867405	2R_3867405_SNP [dm3] 2R_7979900_SNP [dm6]	T	A	2.892e^-5	1	SYNONYMOUS_CODING ACC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	20465379	X_20465379_DEL [dm3] X_20594352_DEL [dm6]	GTGCGTGTCCTTGCGTCTGT...	G	2.924e^-5	1	INTRON RunxA
3L	12327923	3L_12327923_SNP [dm3] 3L_12334823_SNP [dm6]	A	G	2.980e^-5	1	SYNONYMOUS_CODING CG32105	TF binding site mE1_TFBS_chinmo
2L	6909521	2L_6909521_SNP [dm3] 2L_6909521_SNP [dm6]	G	A	3.048e^-5	1	SYNONYMOUS_CODING Rat1	TF binding site mE1_TFBS_sens
2R	10366370	2R_10366370_SNP [dm3] 2R_14478865_SNP [dm6]	T	C	3.048e^-5	1	DOWNSTREAM CR44462 INTERGENIC	TF binding site mE1_TFBS_cad
2L	6813219	2L_6813219_DEL [dm3] 2L_6813219_DEL [dm6]	ATGCTACCTCAATCA...	A	3.103e^-5	1	DOWNSTREAM CR44081 INTERGENIC
2R	1006333	2R_1006333_SNP [dm3] 2R_5118828_SNP [dm6]	T	C	3.208e^-5	1	INTRON gus
2R	12198042	2R_12198042_SNP [dm3] 2R_16310537_SNP [dm6]	C	T	3.222e^-5	1	INTRON Nox	TF binding site mE1_TFBS_chinmo
3R	7989751	3R_7989751_SNP [dm3] 3R_12164029_SNP [dm6]	C	T	3.230e^-5	1	NON_SYNONYMOUS_CODING Cpn
2L	18000246	2L_18000246_SNP [dm3] 2L_18000246_SNP [dm6]	A	G	3.244e^-5	1	INTERGENIC
X	18351380	X_18351380_SNP [dm3] X_18457347_SNP [dm6]	T	C	3.268e^-5	1	INTRON CG32547
2R	10666534	2R_10666534_SNP [dm3] 2R_14779029_SNP [dm6]	G	A	3.325e^-5	1	INTRON kn
2L	19806769	2L_19806769_SNP [dm3] 2L_19806769_SNP [dm6]	C	T	3.611e^-5	1	INTRON sick
2R	3373740	2R_3373740_SNP [dm3] 2R_7486235_SNP [dm6]	G	A	3.734e^-5	1	UTR_5_PRIME wech INTRON wech	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	2685245	2L_2685245_SNP [dm3] 2L_2685245_SNP [dm6]	T	C	3.783e^-5	1	INTRON CG31690
2R	15869005	2R_15869005_SNP [dm3] 2R_19981500_SNP [dm6]	T	C	3.948e^-5	1	UPSTREAM CG8654 INTRON CG8654	TF binding site mE1_TFBS_cad
2R	1049533	2R_1049533_SNP [dm3] 2R_5162028_SNP [dm6]	T	C	4.030e^-5	1	INTERGENIC	transposable element FlyBase
2R	14222033	2R_14222033_SNP [dm3] 2R_18334528_SNP [dm6]	T	A	4.090e^-5	1	INTRON sbb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	20465406	X_20465406_DEL [dm3] X_20594379_DEL [dm6]	AGTGGTTAG	A	4.159e^-5	1	INTRON RunxA
2R	10154275	2R_10154275_SNP [dm3] 2R_14266770_SNP [dm6]	A	G	4.184e^-5	1	INTRON CG8547
2L	3792077	2L_3792077_SNP [dm3] 2L_3792077_SNP [dm6]	A	C	4.272e^-5	1	INTRON CG3921
X	11840457	X_11840457_SNP [dm3] X_11946424_SNP [dm6]	G	T	4.282e^-5	1	INTRON cac
2R	15595811	2R_15595811_SNP [dm3] 2R_19708306_SNP [dm6]	C	A	4.320e^-5	1	INTERGENIC
3R	15559644	3R_15559644_SNP [dm3] 3R_19733922_SNP [dm6]	A	C	4.322e^-5	1	INTRON GluClalpha
2L	3986342	2L_3986342_SNP [dm3] 2L_3986342_SNP [dm6]	C	T	4.521e^-5	1	INTRON fred
3L	9462464	3L_9462464_DEL [dm3] 3L_9469364_DEL [dm6]	GTTG	G	4.535e^-5	1	INTRON CG44838	TF binding site BDTNP1_TFBS_dl
2R	12279590	2R_12279590_INS [dm3] 2R_16392085_INS [dm6]	A	AA	4.647e^-5	1	INTRON Sema-2b	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3R	12329056	3R_12329056_SNP [dm3] 3R_16503334_SNP [dm6]	T	G	4.674e^-5	1	INTRON CG42342	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
2L	15976159	2L_15976159_DEL [dm3] 2L_15976159_DEL [dm6]	ACAAG	A	4.682e^-5	1	INTERGENIC
2R	14706594	2R_14706594_DEL [dm3] 2R_18819089_DEL [dm6]	TTG	T	4.823e^-5	1	UPSTREAM Phb2 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	16798884	3L_16798884_SNP [dm3] 3L_16805784_SNP [dm6]	A	T	4.941e^-5	1	INTRON CG9674 & 1 other	TF binding site mE1_TFBS_Trl
3R	15559662	3R_15559662_SNP [dm3] 3R_19733940_SNP [dm6]	A	G	4.954e^-5	1	INTRON GluClalpha
2L	2685254	2L_2685254_SNP [dm3] 2L_2685254_SNP [dm6]	T	C	5.060e^-5	1	INTRON CG31690
2L	2685246	2L_2685246_SNP [dm3] 2L_2685246_SNP [dm6]	A	C	5.122e^-5	1	INTRON CG31690
3L	18295612	3L_18295612_SNP [dm3] 3L_18302512_SNP [dm6]	T	C	5.152e^-5	1	DOWNSTREAM grim INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_Kr
3L	18295639	3L_18295639_SNP [dm3] 3L_18302539_SNP [dm6]	T	A	5.191e^-5	1	DOWNSTREAM grim INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_Kr
2R	10666533	2R_10666533_SNP [dm3] 2R_14779028_SNP [dm6]	G	A	5.262e^-5	1	INTRON kn
2L	2685239	2L_2685239_SNP [dm3] 2L_2685239_SNP [dm6]	A	C	5.303e^-5	1	INTRON CG31690
2L	1260917	2L_1260917_INS [dm3] 2L_1260917_INS [dm6]	A	AA	5.318e^-5	1	INTRON robo3
2R	10608720	2R_10608720_SNP [dm3] 2R_14721215_SNP [dm6]	C	G	5.323e^-5	1	INTERGENIC	TF binding site mE1_TFBS_inv
X	5970814	X_5970814_SNP [dm3] X_6076781_SNP [dm6]	G	A	5.617e^-5	1	SYNONYMOUS_CODING CG4666
3R	10873414	3R_10873414_SNP [dm3] 3R_15047692_SNP [dm6]	C	T	5.679e^-5	1	INTERGENIC
2R	17182549	2R_17182549_SNP [dm3] 2R_21295044_SNP [dm6]	T	G	5.718e^-5	1	SYNONYMOUS_CODING CG9752 UPSTREAM CG42672 DOWNSTREAM RpL29	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
3L	18295617	3L_18295617_SNP [dm3] 3L_18302517_SNP [dm6]	T	A	5.730e^-5	1	DOWNSTREAM grim INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_Kr
2L	3239513	2L_3239513_SNP [dm3] 2L_3239513_SNP [dm6]	T	A	5.732e^-5	1	INTERGENIC
3R	12327632	3R_12327632_SNP [dm3] 3R_16501910_SNP [dm6]	G	A	5.742e^-5	1	UPSTREAM decay & 1 other INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	10341078	2R_10341078_SNP [dm3] 2R_14453573_SNP [dm6]	G	A	5.932e^-5	1	INTRON Oaz	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
X	3277717	X_3277717_SNP [dm3] X_3383684_SNP [dm6]	C	A	6.198e^-5	1	INTRON dm & 1 other
3R	12326543	3R_12326543_SNP [dm3] 3R_16500821_SNP [dm6]	C	T	6.554e^-5	1	SYNONYMOUS_CODING decay	TF binding site mE1_TFBS_cad mE1_TFBS_Trl
2R	15299127	2R_15299127_SNP [dm3] 2R_19411622_SNP [dm6]	A	G	6.571e^-5	1	UPSTREAM hts INTRON hts	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl

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By genomic position
Variant impact
Gene name

Delta_Death.at.48h Experience 5 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results