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=7.998e^-21)
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	0.018907
In_2R_NS	<

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	23.7729	6.883e-06
In_2R_NS	10.2197	0.006

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

4358 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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Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	5749736	3R_5749736_SNP [dm3] 3R_9924014_SNP [dm6]	G	T	1.287e^-7	0.075	INTRON Glut4EF
3R	27081378	3R_27081378_SNP [dm3] 3R_31255656_SNP [dm6]	C	A	1.781e^-7	0.075	SYNONYMOUS_CODING spn-F UPSTREAM CG1750	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	5749737	3R_5749737_SNP [dm3] 3R_9924015_SNP [dm6]	T	A	1.842e^-7	0.075	INTRON Glut4EF
2L	5059830	2L_5059830_SNP [dm3] 2L_5059830_SNP [dm6]	G	A	1.919e^-7	0.075	UPSTREAM Rpn11 & 1 other DOWNSTREAM CR45291 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cnc mE1_TFBS_HSA
X	15479915	X_15479915_SNP [dm3] X_15585882_SNP [dm6]	C	T	2.036e^-7	0.075	UTR_3_PRIME CG9220 DOWNSTREAM CG8097	TF binding site mE1_TFBS_cad
3R	24105628	3R_24105628_SNP [dm3] 3R_28279906_SNP [dm6]	C	T	2.662e^-7	0.075	INTERGENIC
2R	18438479	2R_18438479_SNP [dm3] 2R_22550974_SNP [dm6]	C	T	3.198e^-7	0.075	SYNONYMOUS_CODING CG6018 INTRON px	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	10401921	X_10401921_SNP [dm3] X_10507888_SNP [dm6]	T	C	3.359e^-7	0.075	INTRON spri
X	12722153	X_12722153_SNP [dm3] X_12828120_SNP [dm6]	A	C	3.592e^-7	0.075	INTRON Pde9
2L	15337740	2L_15337740_SNP [dm3] 2L_15337740_SNP [dm6]	C	T	4.512e^-7	0.085	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	10091812	3L_10091812_SNP [dm3] 3L_10098712_SNP [dm6]	G	C	5.894e^-7	0.087	UPSTREAM CG42825 DOWNSTREAM CG42826 INTRON dpr6
3L	18730258	3L_18730258_SNP [dm3] 3L_18737158_SNP [dm6]	G	A	6.983e^-7	0.087	INTERGENIC
X	10400173	X_10400173_SNP [dm3] X_10506140_SNP [dm6]	A	G	7.351e^-7	0.087	INTRON spri
2L	12827807	2L_12827807_SNP [dm3] 2L_12827807_SNP [dm6]	C	G	7.431e^-7	0.087	INTERGENIC
2L	15319282	2L_15319282_SNP [dm3] 2L_15319282_SNP [dm6]	A	G	8.575e^-7	0.087	UPSTREAM nht INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	18460323	3L_18460323_SNP [dm3] 3L_18467223_SNP [dm6]	T	C	8.639e^-7	0.087	INTERGENIC
2L	8892181	2L_8892181_SNP [dm3] 2L_8892181_SNP [dm6]	C	T	8.964e^-7	0.087	DOWNSTREAM CG42713 INTERGENIC
3R	24105625	3R_24105625_SNP [dm3] 3R_28279903_SNP [dm6]	A	T	9.015e^-7	0.087	INTERGENIC
2L	8096361	2L_8096361_INS [dm3] 2L_8096361_INS [dm6]	C	CGGTTTTCTTTAAAT...	9.583e^-7	0.087	INTRON Bsg
3L	8463332	3L_8463332_SNP [dm3] 3L_8470232_SNP [dm6]	C	T	9.730e^-7	0.087	INTRON Gug
3R	23853048	3R_23853048_SNP [dm3] 3R_28027326_SNP [dm6]	A	T	1.005e^-6	0.087	INTRON CG34362
3R	14591678	3R_14591678_SNP [dm3] 3R_18765956_SNP [dm6]	G	C	1.089e^-6	0.087	INTRON CG7720
X	17397279	X_17397279_SNP [dm3] X_17503246_SNP [dm6]	T	C	1.256e^-6	0.087	INTRON CG43658	TF binding site BDTNP1_TFBS_twi
X	16707826	X_16707826_SNP [dm3] X_16813793_SNP [dm6]	T	C	1.258e^-6	0.087	INTRON CG4829
2L	8891353	2L_8891353_SNP [dm3] 2L_8891353_SNP [dm6]	T	G	1.262e^-6	0.087	UPSTREAM CG42713 INTERGENIC
3R	16107120	3R_16107120_SNP [dm3] 3R_20281398_SNP [dm6]	A	G	1.292e^-6	0.087	INTRON cic
3L	1719544	3L_1719544_SNP [dm3] 3L_1719544_SNP [dm6]	C	A	1.369e^-6	0.087	SYNONYMOUS_CODING drpr INTRON drpr	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	13020068	2L_13020068_DEL [dm3] 2L_13020068_DEL [dm6]	AAA	A	1.399e^-6	0.087	UPSTREAM CG9934 INTRON A16	TF binding site mE1_TFBS_cad
2L	8895468	2L_8895468_SNP [dm3] 2L_8895468_SNP [dm6]	A	T	1.419e^-6	0.087	INTERGENIC
X	12722117	X_12722117_SNP [dm3] X_12828084_SNP [dm6]	A	G	1.459e^-6	0.087	INTRON Pde9
3R	24105586	3R_24105586_SNP [dm3] 3R_28279864_SNP [dm6]	T	G	1.470e^-6	0.087	INTERGENIC
2L	17869516	2L_17869516_SNP [dm3] 2L_17869516_SNP [dm6]	T	A	1.481e^-6	0.087	INTRON CadN2
3R	14591888	3R_14591888_SNP [dm3] 3R_18766166_SNP [dm6]	C	T	1.535e^-6	0.087	INTRON CG7720
2L	8096349	2L_8096349_DEL [dm3] 2L_8096349_DEL [dm6]	CCACAGGAGA	T	1.662e^-6	0.089	INTRON Bsg
3L	8606061	3L_8606061_SNP [dm3] 3L_8612961_SNP [dm6]	C	T	1.701e^-6	0.089	INTRON CG6282
X	15579895	X_15579895_SNP [dm3] X_15685862_SNP [dm6]	A	T	1.706e^-6	0.089	NON_SYNONYMOUS_CODING CG15599	TF binding site BDTNP1_TFBS_prd mE1_TFBS_sens
2L	12840644	2L_12840644_SNP [dm3] 2L_12840644_SNP [dm6]	A	C	1.788e^-6	0.091	UPSTREAM CR44970 & 1 other INTERGENIC
3R	23852615	3R_23852615_SNP [dm3] 3R_28026893_SNP [dm6]	C	T	1.876e^-6	0.092	INTRON CG34362
2L	15319467	2L_15319467_SNP [dm3] 2L_15319467_SNP [dm6]	A	G	1.916e^-6	0.092	UPSTREAM nht INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
X	8829226	X_8829226_SNP [dm3] X_8935193_SNP [dm6]	T	C	2.004e^-6	0.094	INTRON rdgA
3R	24105631	3R_24105631_SNP [dm3] 3R_28279909_SNP [dm6]	T	C	2.078e^-6	0.094	INTERGENIC
2L	12824513	2L_12824513_SNP [dm3] 2L_12824513_SNP [dm6]	C	A	2.098e^-6	0.094	INTERGENIC
2L	12840689	2L_12840689_SNP [dm3] 2L_12840689_SNP [dm6]	A	T	2.167e^-6	0.095	UPSTREAM CR44970 & 1 other INTERGENIC
X	7480202	X_7480202_SNP [dm3] X_7586169_SNP [dm6]	A	G	2.392e^-6	0.097	UPSTREAM CG12689 INTERGENIC	regulatory region REDfly_CRMs
X	7407114	X_7407114_SNP [dm3] X_7513081_SNP [dm6]	T	G	2.400e^-6	0.097	INTRON CG32719
X	11243109	X_11243109_SNP [dm3] X_11349076_SNP [dm6]	A	C	2.437e^-6	0.097	UTR_5_PRIME CG1738 UPSTREAM CG11752 DOWNSTREAM CG11756	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	5059841	2L_5059841_SNP [dm3] 2L_5059841_SNP [dm6]	T	C	2.480e^-6	0.097	UPSTREAM Rpn11 & 1 other DOWNSTREAM CR45291 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cnc mE1_TFBS_HSA
2L	15319340	2L_15319340_SNP [dm3] 2L_15319340_SNP [dm6]	A	G	2.505e^-6	0.097	UPSTREAM nht INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
X	12671635	X_12671635_SNP [dm3] X_12777602_SNP [dm6]	G	C	2.549e^-6	0.097	INTRON CG32647
2R	16489867	2R_16489867_SNP [dm3] 2R_20602362_SNP [dm6]	A	C	2.629e^-6	0.097	UPSTREAM bl INTRON bl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2L	15337302	2L_15337302_SNP [dm3] 2L_15337302_SNP [dm6]	G	C	2.634e^-6	0.097	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	10420231	2L_10420231_SNP [dm3] 2L_10420231_SNP [dm6]	A	C	2.851e^-6	0.103	DOWNSTREAM pie INTRON RfC3	TF binding site mE1_TFBS_ttk
2L	15349755	2L_15349755_SNP [dm3] 2L_15349755_SNP [dm6]	A	C	2.973e^-6	0.105	INTERGENIC
X	12332193	X_12332193_SNP [dm3] X_12438160_SNP [dm6]	C	A	3.070e^-6	0.105	INTRON Pkcdelta
3R	5140182	3R_5140182_SNP [dm3] 3R_9314460_SNP [dm6]	G	T	3.157e^-6	0.105	INTRON CG8861
3R	16104869	3R_16104869_SNP [dm3] 3R_20279147_SNP [dm6]	A	T	3.166e^-6	0.105	INTRON cic
3R	810200	3R_810200_INS [dm3] 3R_4984478_INS [dm6]	A	ACA	3.321e^-6	0.105	UPSTREAM CG14662 DOWNSTREAM CR43424 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
2L	15338050	2L_15338050_SNP [dm3] 2L_15338050_SNP [dm6]	T	A	3.381e^-6	0.105	INTERGENIC	TF binding site mE1_TFBS_cad
3R	16107125	3R_16107125_SNP [dm3] 3R_20281403_SNP [dm6]	T	G	3.404e^-6	0.105	INTRON cic
3R	16107134	3R_16107134_SNP [dm3] 3R_20281412_SNP [dm6]	G	T	3.407e^-6	0.105	INTRON cic
3R	16107135	3R_16107135_SNP [dm3] 3R_20281413_SNP [dm6]	C	G	3.428e^-6	0.105	INTRON cic
2L	12188129	2L_12188129_SNP [dm3] 2L_12188129_SNP [dm6]	C	A	3.790e^-6	0.113	INTRON aret
3R	5410565	3R_5410565_SNP [dm3] 3R_9584843_SNP [dm6]	G	T	3.815e^-6	0.113	INTRON CG8301	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	9868764	X_9868764_SNP [dm3] X_9974731_SNP [dm6]	G	A	4.146e^-6	0.113	INTRON CG43386
3R	16107154	3R_16107154_SNP [dm3] 3R_20281432_SNP [dm6]	A	T	4.156e^-6	0.113	INTRON cic
2L	15319276	2L_15319276_SNP [dm3] 2L_15319276_SNP [dm6]	G	A	4.164e^-6	0.113	UPSTREAM nht INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	12824096	2L_12824096_SNP [dm3] 2L_12824096_SNP [dm6]	A	G	4.217e^-6	0.113	INTERGENIC
3R	11594071	3R_11594071_SNP [dm3] 3R_15768349_SNP [dm6]	T	C	4.320e^-6	0.113	UPSTREAM CG5623 INTERGENIC
2L	5971092	2L_5971092_SNP [dm3] 2L_5971092_SNP [dm6]	C	T	4.374e^-6	0.113	UPSTREAM CR43465 DOWNSTREAM Ucp4B INTERGENIC	TF binding site mE1_TFBS_cad
2L	8096077	2L_8096077_SNP [dm3] 2L_8096077_SNP [dm6]	T	A	4.513e^-6	0.113	INTRON Bsg
2L	17867777	2L_17867777_SNP [dm3] 2L_17867777_SNP [dm6]	C	A	4.601e^-6	0.113	INTRON CadN2
2L	18676857	2L_18676857_SNP [dm3] 2L_18676857_SNP [dm6]	A	G	4.661e^-6	0.113	NON_SYNONYMOUS_CODING Mst36Fa UPSTREAM CG31751	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2L	8096039	2L_8096039_SNP [dm3] 2L_8096039_SNP [dm6]	G	C	4.668e^-6	0.113	INTRON Bsg
3L	2570088	3L_2570088_SNP [dm3] 3L_2570088_SNP [dm6]	C	T	4.694e^-6	0.113	INTRON msn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	16107155	3R_16107155_SNP [dm3] 3R_20281433_SNP [dm6]	G	T	4.707e^-6	0.113	INTRON cic
2L	12841291	2L_12841291_SNP [dm3] 2L_12841291_SNP [dm6]	A	T	4.752e^-6	0.113	UPSTREAM CR44971 EXON CR44970
2L	15319295	2L_15319295_SNP [dm3] 2L_15319295_SNP [dm6]	T	C	4.797e^-6	0.113	UPSTREAM nht INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	14419590	2L_14419590_SNP [dm3] 2L_14419590_SNP [dm6]	T	C	4.813e^-6	0.113	INTERGENIC
2L	18672643	2L_18672643_SNP [dm3] 2L_18672643_SNP [dm6]	T	A	4.907e^-6	0.113	NON_SYNONYMOUS_CODING CG43339 DOWNSTREAM Mst36Fb
X	12239910	X_12239910_SNP [dm3] X_12345877_SNP [dm6]	C	T	4.928e^-6	0.113	INTERGENIC
3L	18460309	3L_18460309_SNP [dm3] 3L_18467209_SNP [dm6]	A	G	4.941e^-6	0.113	INTERGENIC
X	9547791	X_9547791_SNP [dm3] X_9653758_SNP [dm6]	T	G	4.952e^-6	0.113	INTRON l_1_G0232
3R	5919522	3R_5919522_SNP [dm3] 3R_10093800_SNP [dm6]	T	C	5.193e^-6	0.115	EXON CR43459	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	6099928	2L_6099928_SNP [dm3] 2L_6099928_SNP [dm6]	C	T	5.208e^-6	0.115	UPSTREAM CG9175 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	25882076	3R_25882076_SNP [dm3] 3R_30056354_SNP [dm6]	G	T	5.233e^-6	0.115	NON_SYNONYMOUS_CODING CG15526 UPSTREAM CG7950 & 2 others	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
3R	23853050	3R_23853050_SNP [dm3] 3R_28027328_SNP [dm6]	T	A	5.321e^-6	0.116	INTRON CG34362
3R	16104879	3R_16104879_SNP [dm3] 3R_20279157_SNP [dm6]	A	G	5.485e^-6	0.117	INTRON cic
2L	5074881	2L_5074881_SNP [dm3] 2L_5074881_SNP [dm6]	A	G	5.571e^-6	0.117	INTRON pgant5
3R	810190	3R_810190_INS [dm3] 3R_4984468_INS [dm6]	T	TG	5.649e^-6	0.117	UPSTREAM CG14662 DOWNSTREAM CR43424 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
3L	3492624	3L_3492624_SNP [dm3] 3L_3492624_SNP [dm6]	C	A	5.677e^-6	0.117	INTRON CG42324
X	11237150	X_11237150_INS [dm3] X_11343117_INS [dm6]	T	TT	5.685e^-6	0.117	INTRON CG34348
2L	12446288	2L_12446288_SNP [dm3] 2L_12446288_SNP [dm6]	C	T	5.764e^-6	0.117	UTR_3_PRIME CG5421 UPSTREAM Oatp33Ea	TF binding site BDTNP1_TFBS_da
X	12722141	X_12722141_SNP [dm3] X_12828108_SNP [dm6]	C	T	5.817e^-6	0.117	INTRON Pde9
X	15711445	X_15711445_SNP [dm3] X_15817412_SNP [dm6]	G	A	5.987e^-6	0.117	UPSTREAM sd INTRON sd	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA
3L	13072190	3L_13072190_SNP [dm3] 3L_13079090_SNP [dm6]	A	T	5.995e^-6	0.117	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
3R	26373786	3R_26373786_SNP [dm3] 3R_30548064_SNP [dm6]	A	G	6.015e^-6	0.117	INTRON tmod
3L	16334434	3L_16334434_SNP [dm3] 3L_16341334_SNP [dm6]	A	C	6.058e^-6	0.117	SYNONYMOUS_CODING CG4998	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	13140901	X_13140901_SNP [dm3] X_13246868_SNP [dm6]	T	G	6.455e^-6	0.122	INTRON mew	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_inv
2L	10693487	2L_10693487_SNP [dm3] 2L_10693487_SNP [dm6]	T	C	6.616e^-6	0.122	NON_SYNONYMOUS_CODING CG17108	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3R	857561	3R_857561_SNP [dm3] 3R_5031839_SNP [dm6]	A	C	6.620e^-6	0.122	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

pc_SegregVariants_2R phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results