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=2.043e^-6)
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

Covariate	p-value	Significance
In_2L_t	1.043e-05
In_3R_K	0.05147

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	15.6949	0.0004
In_3R_K	5.2804	0.0713

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1976 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
3R	9381344	3R_9381344_SNP [dm3] 3R_13555622_SNP [dm6]	C	A	4.661e^-7	0.632	INTERGENIC
3R	15854570	3R_15854570_SNP [dm3] 3R_20028848_SNP [dm6]	T	G	8.650e^-7	0.632	UPSTREAM CG4424 DOWNSTREAM trem INTRON CG4854	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_sens
3L	8251891	3L_8251891_SNP [dm3] 3L_8258791_SNP [dm6]	T	A	1.810e^-6	0.632	INTRON Dscam4
3R	9381472	3R_9381472_DEL [dm3] 3R_13555750_DEL [dm6]	GTAGTGAATACTAA...	G	2.500e^-6	0.632	INTERGENIC
2R	20135625	2R_20135625_SNP [dm3] 2R_24248102_SNP [dm6]	G	A	3.195e^-6	0.632	DOWNSTREAM Ir60a INTRON nord
2R	14222340	2R_14222340_SNP [dm3] 2R_18334835_SNP [dm6]	A	G	3.323e^-6	0.632	INTRON sbb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	15854577	3R_15854577_SNP [dm3] 3R_20028855_SNP [dm6]	A	G	3.390e^-6	0.632	UPSTREAM CG4424 DOWNSTREAM trem INTRON CG4854	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_sens
3R	15814105	3R_15814105_SNP [dm3] 3R_19988383_SNP [dm6]	A	G	4.055e^-6	0.632	INTRON Hs6st	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	21791448	3R_21791448_SNP [dm3] 3R_25965726_SNP [dm6]	T	C	4.527e^-6	0.632	SYNONYMOUS_CODING boss	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	13996704	2R_13996704_SNP [dm3] 2R_18109199_SNP [dm6]	A	T	4.663e^-6	0.632	UPSTREAM CG5756 & 1 other INTERGENIC
3R	9395927	3R_9395927_SNP [dm3] 3R_13570205_SNP [dm6]	A	C	4.910e^-6	0.632	INTERGENIC
3R	9381408	3R_9381408_SNP [dm3] 3R_13555686_SNP [dm6]	A	T	4.911e^-6	0.632	INTERGENIC
3L	5489845	3L_5489845_SNP [dm3] 3L_5496745_SNP [dm6]	G	T	5.008e^-6	0.632	DOWNSTREAM blanks INTERGENIC
X	5533616	X_5533616_SNP [dm3] X_5639583_SNP [dm6]	C	T	5.046e^-6	0.632	INTRON CG42492	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	9392385	3R_9392385_DEL [dm3] 3R_13566663_DEL [dm6]	CATACAATGGTTACTTTC...	C	5.241e^-6	0.632	INTERGENIC
2R	8790543	2R_8790543_SNP [dm3] 2R_12903038_SNP [dm6]	C	A	5.394e^-6	0.632	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	15854826	3R_15854826_SNP [dm3] 3R_20029104_SNP [dm6]	T	C	6.506e^-6	0.653	DOWNSTREAM trem INTRON CG4854
3R	9381546	3R_9381546_DEL [dm3] 3R_13555824_DEL [dm6]	TT	T	6.962e^-6	0.653	INTERGENIC
2R	15659776	2R_15659776_SNP [dm3] 2R_19772271_SNP [dm6]	C	T	6.970e^-6	0.653	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	15131224	2L_15131224_SNP [dm3] 2L_15131224_SNP [dm6]	G	C	7.244e^-6	0.653	INTERGENIC
2R	13412097	2R_13412097_SNP [dm3] 2R_17524592_SNP [dm6]	C	T	7.307e^-6	0.653	SPLICE_SITE_REGION Patronin INTRON Patronin	TF binding site mE1_TFBS_cad
3R	15854438	3R_15854438_SNP [dm3] 3R_20028716_SNP [dm6]	A	G	8.047e^-6	0.686	SYNONYMOUS_CODING CG4854 UPSTREAM CG4424 DOWNSTREAM trem	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2L	13022926	2L_13022926_SNP [dm3] 2L_13022926_SNP [dm6]	A	T	8.732e^-6	0.691	UTR_3_PRIME CG9932
3R	13377631	3R_13377631_SNP [dm3] 3R_17551909_SNP [dm6]	T	C	8.837e^-6	0.691	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9384896	3R_9384896_SNP [dm3] 3R_13559174_SNP [dm6]	C	T	9.989e^-6	0.723	INTERGENIC
2L	13022818	2L_13022818_SNP [dm3] 2L_13022818_SNP [dm6]	G	T	1.002e^-5	0.723	UTR_3_PRIME CG9932
2R	14219961	2R_14219961_SNP [dm3] 2R_18332456_SNP [dm6]	T	C	1.093e^-5	0.759	INTRON sbb	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_run
X	20157145	X_20157145_SNP [dm3] X_20286118_SNP [dm6]	A	T	1.204e^-5	0.761	INTERGENIC
2R	14227634	2R_14227634_INS [dm3] 2R_18340129_INS [dm6]	C	CC	1.222e^-5	0.761	INTRON sbb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	12620366	2L_12620366_SNP [dm3] 2L_12620366_SNP [dm6]	C	G	1.227e^-5	0.761	INTRON Ref2 & 1 other	TF binding site mE1_TFBS_sens
3L	1197403	3L_1197403_SNP [dm3] 3L_1197403_SNP [dm6]	G	A	1.258e^-5	0.761	INTRON Aplip1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11848993	3L_11848993_SNP [dm3] 3L_11855893_SNP [dm6]	T	A	1.390e^-5	0.764	INTRON CG44837
X	4463826	X_4463826_SNP [dm3] X_4569793_SNP [dm6]	G	T	1.535e^-5	0.764	INTRON CR32773	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
3L	321414	3L_321414_SNP [dm3] 3L_321414_SNP [dm6]	T	G	1.570e^-5	0.764	INTRON CG32344	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_slp1 BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	5021150	2L_5021150_SNP [dm3] 2L_5021150_SNP [dm6]	G	A	1.596e^-5	0.764	INTRON vkg
2L	1971254	2L_1971254_SNP [dm3] 2L_1971254_SNP [dm6]	T	G	1.610e^-5	0.764	UPSTREAM erm INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	1971291	2L_1971291_DEL [dm3] 2L_1971291_DEL [dm6]	AC	A	1.610e^-5	0.764	UPSTREAM erm INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	8616485	2R_8616485_SNP [dm3] 2R_12728980_SNP [dm6]	C	G	1.629e^-5	0.764	INTRON CG42663
2R	8536569	2R_8536569_SNP [dm3] 2R_12649064_SNP [dm6]	T	C	1.631e^-5	0.764	UPSTREAM CG8785 INTERGENIC
3R	820886	3R_820886_SNP [dm3] 3R_4995164_SNP [dm6]	G	C	1.638e^-5	0.764	INTRON CG2022	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
2R	6218177	2R_6218177_SNP [dm3] 2R_10330672_SNP [dm6]	C	T	1.670e^-5	0.764	INTRON CG42732	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	821025	3R_821025_SNP [dm3] 3R_4995303_SNP [dm6]	T	C	1.715e^-5	0.766	INTRON CG2022	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	5063371	3L_5063371_SNP [dm3] 3L_5063371_SNP [dm6]	G	A	1.770e^-5	0.767	INTRON Con
2L	1971337	2L_1971337_SNP [dm3] 2L_1971337_SNP [dm6]	C	T	1.799e^-5	0.767	UPSTREAM erm INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	8762613	2L_8762613_SNP [dm3] 2L_8762613_SNP [dm6]	C	G	1.951e^-5	0.777	INTERGENIC
3R	13377664	3R_13377664_SNP [dm3] 3R_17551942_SNP [dm6]	T	G	1.973e^-5	0.777	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	975294	3L_975294_SNP [dm3] 3L_975294_SNP [dm6]	A	C	1.976e^-5	0.777	INTRON Glut1
3L	10362687	3L_10362687_SNP [dm3] 3L_10369587_SNP [dm6]	G	T	1.989e^-5	0.777	INTERGENIC
3R	26105331	3R_26105331_SNP [dm3] 3R_30279609_SNP [dm6]	T	C	2.081e^-5	0.784	SYNONYMOUS_CODING hdc	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	15235046	3L_15235046_SNP [dm3] 3L_15241946_SNP [dm6]	G	A	2.163e^-5	0.784	UTR_3_PRIME Tollo	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	12282353	2L_12282353_SNP [dm3] 2L_12282353_SNP [dm6]	A	G	2.165e^-5	0.784	INTRON aret
3R	3553491	3R_3553491_SNP [dm3] 3R_7727769_SNP [dm6]	C	G	2.207e^-5	0.784	INTERGENIC
3L	7011895	3L_7011895_SNP [dm3] 3L_7018795_SNP [dm6]	C	G	2.215e^-5	0.784	INTRON Mp
2R	13416712	2R_13416712_SNP [dm3] 2R_17529207_SNP [dm6]	G	T	2.603e^-5	0.857	INTRON Patronin
3L	3920699	3L_3920699_SNP [dm3] 3L_3920699_SNP [dm6]	G	A	2.622e^-5	0.857	INTRON Eip63F-1
3L	7251571	3L_7251571_SNP [dm3] 3L_7258471_SNP [dm6]	C	A	2.633e^-5	0.857	INTRON CG14830
3L	5161079	3L_5161079_SNP [dm3] 3L_5167979_SNP [dm6]	C	T	2.715e^-5	0.857	INTRON shep
3R	8235840	3R_8235840_SNP [dm3] 3R_12410118_SNP [dm6]	T	C	2.815e^-5	0.857	INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
3R	15462287	3R_15462287_SNP [dm3] 3R_19636565_SNP [dm6]	C	T	2.864e^-5	0.857	NON_SYNONYMOUS_CODING subdued DOWNSTREAM CG34138
X	19014571	X_19014571_SNP [dm3] X_19120538_SNP [dm6]	T	G	2.979e^-5	0.857	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	8928584	2R_8928584_SNP [dm3] 2R_13041079_SNP [dm6]	T	A	3.018e^-5	0.857	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2R	18261619	2R_18261619_SNP [dm3] 2R_22374114_SNP [dm6]	T	A	3.150e^-5	0.857	UPSTREAM Rtf1 INTRON CR44759	TF binding site BDTNP1_TFBS_dl
X	19014638	X_19014638_SNP [dm3] X_19120605_SNP [dm6]	T	C	3.244e^-5	0.857	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	15462650	3R_15462650_SNP [dm3] 3R_19636928_SNP [dm6]	A	C	3.247e^-5	0.857	SYNONYMOUS_CODING subdued
3R	15807723	3R_15807723_SNP [dm3] 3R_19982001_SNP [dm6]	C	A	3.277e^-5	0.857	INTRON Hs6st
3R	15854306	3R_15854306_SNP [dm3] 3R_20028584_SNP [dm6]	C	G	3.344e^-5	0.857	NON_SYNONYMOUS_CODING CG4854 UPSTREAM CG4424 DOWNSTREAM trem	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	19824457	2L_19824457_DEL [dm3] 2L_19824457_DEL [dm6]	TGGCCAAGAATTTACTGAAT...	T	3.385e^-5	0.857	INTRON sick
3L	8310063	3L_8310063_SNP [dm3] 3L_8316963_SNP [dm6]	C	T	3.415e^-5	0.857	INTERGENIC
2L	1298809	2L_1298809_INS [dm3] 2L_1298809_INS [dm6]	T	TT	3.446e^-5	0.857	INTERGENIC
3L	8880121	3L_8880121_SNP [dm3] 3L_8887021_SNP [dm6]	A	G	3.539e^-5	0.857	INTRON dally
2L	15466197	2L_15466197_DEL [dm3] 2L_15466197_DEL [dm6]	ATTA	A	3.564e^-5	0.857	INTERGENIC
3L	12486417	3L_12486417_DEL [dm3] 3L_12493317_DEL [dm6]	AAATTCTATTGCACAGGTTG...	A	3.573e^-5	0.857	INTRON CG10657 EXON CR45682	TF binding site mE1_TFBS_cad
3L	9824671	3L_9824671_SNP [dm3] 3L_9831571_SNP [dm6]	T	C	3.604e^-5	0.857	INTRON CG43897	TF binding site mE1_TFBS_cad
3L	4952007	3L_4952007_SNP [dm3] 3L_4952007_SNP [dm6]	A	G	3.669e^-5	0.857	INTRON Con	TF binding site mE1_TFBS_chinmo
3R	15466053	3R_15466053_SNP [dm3] 3R_19640331_SNP [dm6]	G	T	3.676e^-5	0.857	INTRON subdued
2R	6082595	2R_6082595_SNP [dm3] 2R_10195090_SNP [dm6]	T	C	3.732e^-5	0.857	INTERGENIC
3R	10183644	3R_10183644_SNP [dm3] 3R_14357922_SNP [dm6]	C	T	3.804e^-5	0.857	DOWNSTREAM CG31320 INTRON NK7.1
3L	2381180	3L_2381180_SNP [dm3] 3L_2381180_SNP [dm6]	G	C	3.846e^-5	0.857	INTRON CG45186
3R	15462495	3R_15462495_SNP [dm3] 3R_19636773_SNP [dm6]	T	A	3.856e^-5	0.857	DOWNSTREAM CG34138 INTRON subdued
3R	23460878	3R_23460878_SNP [dm3] 3R_27635156_SNP [dm6]	C	T	4.020e^-5	0.857	DOWNSTREAM Tusp INTRON CG5611	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	4979552	3L_4979552_SNP [dm3] 3L_4979552_SNP [dm6]	C	T	4.036e^-5	0.857	DOWNSTREAM CG17030 INTRON Con	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9377665	3R_9377665_SNP [dm3] 3R_13551943_SNP [dm6]	G	A	4.040e^-5	0.857	INTERGENIC
X	4463893	X_4463893_SNP [dm3] X_4569860_SNP [dm6]	T	G	4.065e^-5	0.857	INTRON CR32773	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_sens
2R	6082599	2R_6082599_SNP [dm3] 2R_10195094_SNP [dm6]	A	T	4.072e^-5	0.857	INTERGENIC
3L	5432759	3L_5432759_INS [dm3] 3L_5439659_INS [dm6]	A	AA	4.089e^-5	0.857	UTR_3_PRIME CG34391
2R	6082598	2R_6082598_SNP [dm3] 2R_10195093_SNP [dm6]	G	T	4.099e^-5	0.857	INTERGENIC
2L	14145344	2L_14145344_SNP [dm3] 2L_14145344_SNP [dm6]	A	G	4.139e^-5	0.857	INTRON CG17341
2R	13728961	2R_13728961_SNP [dm3] 2R_17841456_SNP [dm6]	T	C	4.299e^-5	0.857	UTR_3_PRIME grh DOWNSTREAM grh
3L	5063397	3L_5063397_SNP [dm3] 3L_5063397_SNP [dm6]	T	C	4.316e^-5	0.857	INTRON Con
2R	8699501	2R_8699501_SNP [dm3] 2R_12811996_SNP [dm6]	G	T	4.371e^-5	0.857	INTERGENIC
X	16065065	X_16065065_DEL [dm3] X_16171032_DEL [dm6]	AACTGTATCTGTGCGCA...	A	4.372e^-5	0.857	INTERGENIC
3R	26745266	3R_26745266_SNP [dm3] 3R_30919544_SNP [dm6]	T	G	4.386e^-5	0.857	INTRON Ptx1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	13556507	3R_13556507_SNP [dm3] 3R_17730785_SNP [dm6]	A	G	4.389e^-5	0.857	SYNONYMOUS_CODING Lgr1
3L	5759701	3L_5759701_SNP [dm3] 3L_5766601_SNP [dm6]	T	C	4.427e^-5	0.857	SYNONYMOUS_CODING Txl UPSTREAM CG10576 DOWNSTREAM Ppat-Dpck	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
2R	18260231	2R_18260231_SNP [dm3] 2R_22372726_SNP [dm6]	A	G	4.464e^-5	0.857	DOWNSTREAM CR44759 INTRON Liprin-gamma	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	8386486	3L_8386486_SNP [dm3] 3L_8393386_SNP [dm6]	G	C	4.495e^-5	0.857	SYNONYMOUS_CODING Jon66Cii	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	17595842	3L_17595842_DEL [dm3] 3L_17602742_DEL [dm6]	TT	T	4.506e^-5	0.857	UTR_5_PRIME Eip74EF
3L	8384729	3L_8384729_SNP [dm3] 3L_8391629_SNP [dm6]	C	A	4.634e^-5	0.857	SYNONYMOUS_CODING Jon66Ci DOWNSTREAM ImpE1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	8235851	3R_8235851_SNP [dm3] 3R_12410129_SNP [dm6]	A	G	4.658e^-5	0.857	INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
3R	9389752	3R_9389752_DEL [dm3] 3R_13564030_DEL [dm6]	CC	C	4.712e^-5	0.857	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_6_C26_1 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results