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=3.681e^-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
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2546 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
2R	7379626	2R_7379626_SNP [dm3] 2R_11492121_SNP [dm6]	G	A	4.602e^-7	0.404	INTRON inv	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	7229494	3R_7229494_SNP [dm3] 3R_11403772_SNP [dm6]	T	C	6.107e^-7	0.404	UTR_3_PRIME pros
2R	8126340	2R_8126340_SNP [dm3] 2R_12238835_SNP [dm6]	C	A	6.463e^-7	0.404	INTERGENIC
2R	8129610	2R_8129610_SNP [dm3] 2R_12242105_SNP [dm6]	T	C	1.268e^-6	0.444	UPSTREAM CG43316 DOWNSTREAM CG43315 INTERGENIC
3L	1590954	3L_1590954_SNP [dm3] 3L_1590954_SNP [dm6]	C	T	1.383e^-6	0.444	INTRON CG13917
3R	12981451	3R_12981451_SNP [dm3] 3R_17155729_SNP [dm6]	G	A	1.484e^-6	0.444	SYNONYMOUS_CODING Mur89F	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	8115551	2R_8115551_SNP [dm3] 2R_12228046_SNP [dm6]	A	T	1.868e^-6	0.444	INTRON CG8854
2L	760529	2L_760529_SNP [dm3] 2L_760529_SNP [dm6]	T	G	2.474e^-6	0.444	SYNONYMOUS_CODING GABA-B-R3 UTR_3_PRIME GABA-B-R3	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	20224047	3R_20224047_SNP [dm3] 3R_24398325_SNP [dm6]	A	T	2.826e^-6	0.444	UTR_3_PRIME nAChRalpha1
2R	8126227	2R_8126227_SNP [dm3] 2R_12238722_SNP [dm6]	G	A	3.067e^-6	0.444	INTERGENIC
X	9131054	X_9131054_SNP [dm3] X_9237021_SNP [dm6]	C	A	3.149e^-6	0.444	UTR_3_PRIME mxc UPSTREAM mir-4916 & 1 other
3R	19061054	3R_19061054_SNP [dm3] 3R_23235332_SNP [dm6]	G	A	3.263e^-6	0.444	INTRON CG4467
2R	8123411	2R_8123411_DEL [dm3] 2R_12235906_DEL [dm6]	TT	T	3.491e^-6	0.444	INTERGENIC	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	14741100	3R_14741100_SNP [dm3] 3R_18915378_SNP [dm6]	A	T	3.661e^-6	0.444	UTR_5_PRIME Xrp1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Trl
3L	8076676	3L_8076676_SNP [dm3] 3L_8083576_SNP [dm6]	T	C	3.698e^-6	0.444	UPSTREAM CR43974 INTRON Ect4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna
2R	8123410	2R_8123410_SNP [dm3] 2R_12235905_SNP [dm6]	T	G	3.951e^-6	0.444	INTERGENIC	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
2L	4360549	2L_4360549_SNP [dm3] 2L_4360549_SNP [dm6]	C	A	4.164e^-6	0.444	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	760040	2L_760040_SNP [dm3] 2L_760040_SNP [dm6]	T	A	4.334e^-6	0.444	SYNONYMOUS_CODING GABA-B-R3 UTR_3_PRIME GABA-B-R3	TF binding site mE1_TFBS_chinmo
2R	8092654	2R_8092654_SNP [dm3] 2R_12205149_SNP [dm6]	A	T	4.914e^-6	0.444	UPSTREAM CR45276 INTERGENIC
3L	10387324	3L_10387324_SNP [dm3] 3L_10394224_SNP [dm6]	A	C	5.216e^-6	0.444	INTERGENIC
2R	8133866	2R_8133866_SNP [dm3] 2R_12246361_SNP [dm6]	A	C	5.351e^-6	0.444	DOWNSTREAM CR44315 INTERGENIC
2R	8097982	2R_8097982_SNP [dm3] 2R_12210477_SNP [dm6]	T	C	5.497e^-6	0.444	NON_SYNONYMOUS_CODING Sr-CII	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	8163087	2R_8163087_SNP [dm3] 2R_12275582_SNP [dm6]	G	A	5.741e^-6	0.444	UTR_3_PRIME Cam DOWNSTREAM Cam
3R	19059172	3R_19059172_SNP [dm3] 3R_23233450_SNP [dm6]	A	G	6.227e^-6	0.444	SPLICE_SITE_REGION CG4467 INTRON CG4467	TF binding site mE1_TFBS_cad
3R	19059181	3R_19059181_SNP [dm3] 3R_23233459_SNP [dm6]	T	G	6.227e^-6	0.444	INTRON CG4467	TF binding site mE1_TFBS_cad
2R	8166810	2R_8166810_SNP [dm3] 2R_12279305_SNP [dm6]	A	T	6.660e^-6	0.444	UPSTREAM CG42700 DOWNSTREAM Cam INTERGENIC
2R	8092696	2R_8092696_SNP [dm3] 2R_12205191_SNP [dm6]	C	A	6.685e^-6	0.444	UPSTREAM CR45276 INTERGENIC
3L	10294022	3L_10294022_SNP [dm3] 3L_10300922_SNP [dm6]	T	A	6.775e^-6	0.444	INTERGENIC
2L	6982358	2L_6982358_SNP [dm3] 2L_6982358_SNP [dm6]	G	A	7.043e^-6	0.444	SYNONYMOUS_CODING uif	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	13349000	3R_13349000_SNP [dm3] 3R_17523278_SNP [dm6]	G	T	7.109e^-6	0.444	INTERGENIC
3R	19059213	3R_19059213_SNP [dm3] 3R_23233491_SNP [dm6]	A	G	7.415e^-6	0.446	INTRON CG4467	TF binding site mE1_TFBS_cad
2L	15840568	2L_15840568_SNP [dm3] 2L_15840568_SNP [dm6]	C	T	7.603e^-6	0.446	DOWNSTREAM CR45694 INTERGENIC
2L	848395	2L_848395_SNP [dm3] 2L_848395_SNP [dm6]	C	G	8.459e^-6	0.469	INTRON drongo	TF binding site mE1_TFBS_sens
3L	3362268	3L_3362268_SNP [dm3] 3L_3362268_SNP [dm6]	T	G	8.494e^-6	0.469	SYNONYMOUS_CODING kst	TF binding site mE1_TFBS_cad
3R	25119477	3R_25119477_SNP [dm3] 3R_29293755_SNP [dm6]	G	A	8.995e^-6	0.482	UTR_3_PRIME CG14506	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA
2R	8101295	2R_8101295_INS [dm3] 2R_12213790_INS [dm6]	T	TG	9.688e^-6	0.494	UPSTREAM CG13171 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	18621668	3R_18621668_SNP [dm3] 3R_22795946_SNP [dm6]	C	T	1.000e^-5	0.494	INTERGENIC
3R	18621678	3R_18621678_SNP [dm3] 3R_22795956_SNP [dm6]	T	A	1.000e^-5	0.494	INTERGENIC
X	2244201	X_2244201_SNP [dm3] X_2350168_SNP [dm6]	C	A	1.049e^-5	0.496	UPSTREAM ptr INTRON ptr	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	4216726	2R_4216726_SNP [dm3] 2R_8329221_SNP [dm6]	G	A	1.087e^-5	0.496	INTRON pdm3
3R	18621700	3R_18621700_SNP [dm3] 3R_22795978_SNP [dm6]	T	C	1.109e^-5	0.496	INTERGENIC
2R	8122310	2R_8122310_SNP [dm3] 2R_12234805_SNP [dm6]	A	G	1.122e^-5	0.496	UPSTREAM CR44313 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
3R	27274123	3R_27274123_SNP [dm3] 3R_31448401_SNP [dm6]	G	A	1.150e^-5	0.496	INTRON Gprk2
2R	8097803	2R_8097803_SNP [dm3] 2R_12210298_SNP [dm6]	C	T	1.176e^-5	0.496	SYNONYMOUS_CODING Sr-CII	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	8129355	2R_8129355_SNP [dm3] 2R_12241850_SNP [dm6]	A	T	1.189e^-5	0.496	UTR_3_PRIME CG43315 UPSTREAM CG43316 DOWNSTREAM CG43315
2R	9779862	2R_9779862_SNP [dm3] 2R_13892357_SNP [dm6]	T	A	1.240e^-5	0.505	SYNONYMOUS_CODING shot INTRON shot
3L	10293945	3L_10293945_SNP [dm3] 3L_10300845_SNP [dm6]	T	A	1.351e^-5	0.527	INTERGENIC
2R	20266116	2R_20266116_SNP [dm3] 2R_24378593_SNP [dm6]	A	G	1.392e^-5	0.527	NON_SYNONYMOUS_CODING CG13578 DOWNSTREAM mAChR-A	TF binding site mE1_TFBS_chinmo
2R	8108500	2R_8108500_SNP [dm3] 2R_12220995_SNP [dm6]	G	A	1.397e^-5	0.527	INTERGENIC
3L	14480270	3L_14480270_SNP [dm3] 3L_14487170_SNP [dm6]	A	G	1.439e^-5	0.527	INTRON bbg
2R	8151102	2R_8151102_SNP [dm3] 2R_12263597_SNP [dm6]	C	A	1.472e^-5	0.527	UPSTREAM Cam INTRON Cam
2R	8102309	2R_8102309_INS [dm3] 2R_12214804_INS [dm6]	G	GAGTG	1.516e^-5	0.527	DOWNSTREAM CG13171 INTERGENIC
3L	10710957	3L_10710957_SNP [dm3] 3L_10717857_SNP [dm6]	A	T	1.770e^-5	0.527	INTERGENIC
3R	649406	3R_649406_SNP [dm3] 3R_4823684_SNP [dm6]	G	A	1.780e^-5	0.527	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	754799	3L_754799_SNP [dm3] 3L_754799_SNP [dm6]	T	A	1.785e^-5	0.527	INTRON hng3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	401696	3L_401696_SNP [dm3] 3L_401696_SNP [dm6]	T	G	1.802e^-5	0.527	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	6247716	2R_6247716_SNP [dm3] 2R_10360211_SNP [dm6]	C	G	1.856e^-5	0.527	UPSTREAM CG43396 INTRON CG42732	TF binding site BDTNP1_TFBS_twi
2R	8097882	2R_8097882_SNP [dm3] 2R_12210377_SNP [dm6]	A	G	1.924e^-5	0.527	NON_SYNONYMOUS_CODING Sr-CII	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	8166807	2R_8166807_DEL [dm3] 2R_12279302_DEL [dm6]	AA	A	1.949e^-5	0.527	UPSTREAM CG42700 DOWNSTREAM Cam INTERGENIC
2R	8127327	2R_8127327_SNP [dm3] 2R_12239822_SNP [dm6]	A	T	1.976e^-5	0.527	UPSTREAM CG13170 INTERGENIC
2L	6574979	2L_6574979_SNP [dm3] 2L_6574979_SNP [dm6]	T	A	2.031e^-5	0.527	NON_SYNONYMOUS_CODING CG11319	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	2577043	3L_2577043_SNP [dm3] 3L_2577043_SNP [dm6]	A	C	2.071e^-5	0.527	INTRON msn	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	2244180	X_2244180_SNP [dm3] X_2350147_SNP [dm6]	A	T	2.098e^-5	0.527	UPSTREAM ptr INTRON ptr	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	15840575	2L_15840575_SNP [dm3] 2L_15840575_SNP [dm6]	C	G	2.101e^-5	0.527	DOWNSTREAM CR45694 INTERGENIC
2R	11617898	2R_11617898_SNP [dm3] 2R_15730393_SNP [dm6]	T	C	2.110e^-5	0.527	INTRON CG30089
2R	8156504	2R_8156504_SNP [dm3] 2R_12268999_SNP [dm6]	A	T	2.116e^-5	0.527	INTRON Cam
2L	6594328	2L_6594328_SNP [dm3] 2L_6594328_SNP [dm6]	G	A	2.123e^-5	0.527	INTRON CG11319	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	8092781	2R_8092781_SNP [dm3] 2R_12205276_SNP [dm6]	C	T	2.128e^-5	0.527	UPSTREAM CR45276 INTERGENIC
3L	21813903	3L_21813903_SNP [dm3] 3L_21820803_SNP [dm6]	C	A	2.136e^-5	0.527	INTERGENIC
3L	754844	3L_754844_SNP [dm3] 3L_754844_SNP [dm6]	C	A	2.136e^-5	0.527	INTRON hng3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	19586558	2R_19586558_DEL [dm3] 2R_23699035_DEL [dm6]	TCCATCGCT	T	2.217e^-5	0.527	UTR_3_PRIME CG4091 DOWNSTREAM mRpL43
X	2246568	X_2246568_SNP [dm3] X_2352535_SNP [dm6]	A	T	2.222e^-5	0.527	INTRON ptr	TF binding site mE1_TFBS_sens
2R	8101389	2R_8101389_SNP [dm3] 2R_12213884_SNP [dm6]	A	G	2.278e^-5	0.527	UPSTREAM CG13171 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	8090760	2R_8090760_SNP [dm3] 2R_12203255_SNP [dm6]	C	T	2.295e^-5	0.527	INTERGENIC
2R	8096216	2R_8096216_SNP [dm3] 2R_12208711_SNP [dm6]	G	A	2.305e^-5	0.527	DOWNSTREAM Sr-CII INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_gt BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	8101314	2R_8101314_SNP [dm3] 2R_12213809_SNP [dm6]	T	C	2.312e^-5	0.527	UPSTREAM CG13171 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	26087300	3R_26087300_SNP [dm3] 3R_30261578_SNP [dm6]	T	C	2.315e^-5	0.527	INTERGENIC	TF binding site mE1_TFBS_Kr
3R	19063757	3R_19063757_SNP [dm3] 3R_23238035_SNP [dm6]	T	A	2.349e^-5	0.527	INTRON CG4467
2R	8158540	2R_8158540_SNP [dm3] 2R_12271035_SNP [dm6]	G	T	2.364e^-5	0.527	INTRON Cam
3L	6022449	3L_6022449_SNP [dm3] 3L_6029349_SNP [dm6]	C	T	2.368e^-5	0.527	INTERGENIC
2R	8089970	2R_8089970_SNP [dm3] 2R_12202465_SNP [dm6]	A	G	2.404e^-5	0.527	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	20704889	3L_20704889_SNP [dm3] 3L_20711789_SNP [dm6]	T	A	2.405e^-5	0.527	INTERGENIC	TF binding site mE1_TFBS_bab1
X	8807740	X_8807740_SNP [dm3] X_8913707_SNP [dm6]	C	G	2.453e^-5	0.527	INTRON rdgA
3L	5932662	3L_5932662_DEL [dm3] 3L_5939562_DEL [dm6]	TA	T	2.476e^-5	0.527	INTRON CG33993
2R	8101325	2R_8101325_SNP [dm3] 2R_12213820_SNP [dm6]	T	C	2.503e^-5	0.527	UPSTREAM CG13171 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	8090555	2R_8090555_DEL [dm3] 2R_12203050_DEL [dm6]	AAAA	A	2.518e^-5	0.527	INTERGENIC
X	8807732	X_8807732_INS [dm3] X_8913699_INS [dm6]	T	TGT	2.528e^-5	0.527	INTRON rdgA
2R	8113999	2R_8113999_SNP [dm3] 2R_12226494_SNP [dm6]	C	G	2.569e^-5	0.527	UTR_5_PRIME CG8854 INTRON CG8854	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	8097753	2R_8097753_SNP [dm3] 2R_12210248_SNP [dm6]	C	T	2.604e^-5	0.527	INTRON Sr-CII	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	3362307	3L_3362307_SNP [dm3] 3L_3362307_SNP [dm6]	G	C	2.605e^-5	0.527	SYNONYMOUS_CODING kst	TF binding site mE1_TFBS_cad
2R	8090744	2R_8090744_SNP [dm3] 2R_12203239_SNP [dm6]	A	G	2.624e^-5	0.527	INTERGENIC
3L	497296	3L_497296_SNP [dm3] 3L_497296_SNP [dm6]	A	T	2.657e^-5	0.527	INTRON klar
2R	8090624	2R_8090624_SNP [dm3] 2R_12203119_SNP [dm6]	G	A	2.666e^-5	0.527	INTERGENIC
2L	4360550	2L_4360550_SNP [dm3] 2L_4360550_SNP [dm6]	C	A	2.755e^-5	0.527	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	21805234	2L_21805234_SNP [dm3] 2L_21805234_SNP [dm6]	G	A	2.761e^-5	0.527	INTERGENIC
2R	8092783	2R_8092783_SNP [dm3] 2R_12205278_SNP [dm6]	G	T	2.771e^-5	0.527	UPSTREAM CR45276 INTERGENIC
2R	8163976	2R_8163976_SNP [dm3] 2R_12276471_SNP [dm6]	C	A	2.777e^-5	0.527	UTR_3_PRIME Cam
3R	518661	3R_518661_DEL [dm3] 3R_4692939_DEL [dm6]	TAA	T	2.789e^-5	0.527	INTRON CG43427
3L	754847	3L_754847_INS [dm3] 3L_754847_INS [dm6]	A	ATCATTAAGCATAGTTTCAG...	2.807e^-5	0.527	INTRON hng3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	8113441	2R_8113441_SNP [dm3] 2R_12225936_SNP [dm6]	C	T	2.809e^-5	0.527	SYNONYMOUS_CODING CG8854	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_NI_34 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results