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=3.632e^-2)
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

2121 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	5505206	3L_5505206_SNP [dm3] 3L_5512106_SNP [dm6]	A	G	1.674e^-7	0.314	DOWNSTREAM Lkr INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_GATAe mE1_TFBS_HSA
3R	15288909	3R_15288909_SNP [dm3] 3R_19463187_SNP [dm6]	A	G	9.813e^-7	0.513	UPSTREAM Dys & 1 other INTRON Dys	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_Kr mE1_TFBS_Trl
X	18534233	X_18534233_SNP [dm3] X_18640200_SNP [dm6]	A	G	1.064e^-6	0.513	SPLICE_SITE_REGION Rip11 INTRON Rip11	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	5158751	3L_5158751_SNP [dm3] 3L_5165651_SNP [dm6]	T	A	1.094e^-6	0.513	INTRON shep
3R	12289893	3R_12289893_SNP [dm3] 3R_16464171_SNP [dm6]	T	A	2.424e^-6	0.825	NON_SYNONYMOUS_CODING CG42232	TF binding site mE1_TFBS_sens
3L	5503669	3L_5503669_SNP [dm3] 3L_5510569_SNP [dm6]	T	C	2.672e^-6	0.825	INTRON CG34342
3R	20727551	3R_20727551_SNP [dm3] 3R_24901829_SNP [dm6]	C	T	3.891e^-6	0.825	SYNONYMOUS_CODING CG10845 INTRON CG13643	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	10031191	3L_10031191_DEL [dm3] 3L_10038091_DEL [dm6]	CA	C	4.094e^-6	0.825	INTRON dpr6
2L	1788747	2L_1788747_SNP [dm3] 2L_1788747_SNP [dm6]	A	C	4.740e^-6	0.825	DOWNSTREAM Gr22d INTERGENIC
2L	1788734	2L_1788734_SNP [dm3] 2L_1788734_SNP [dm6]	C	A	4.759e^-6	0.825	DOWNSTREAM Gr22d INTERGENIC
2L	1788739	2L_1788739_INS [dm3] 2L_1788739_INS [dm6]	T	TT	5.070e^-6	0.825	DOWNSTREAM Gr22d INTERGENIC
3L	1487330	3L_1487330_SNP [dm3] 3L_1487330_SNP [dm6]	T	G	6.458e^-6	0.825	INTRON stet	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_Trl
3L	16130048	3L_16130048_SNP [dm3] 3L_16136948_SNP [dm6]	C	T	6.494e^-6	0.825	SYNONYMOUS_CODING CG5157 DOWNSTREAM CG16838 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	1699738	2L_1699738_SNP [dm3] 2L_1699738_SNP [dm6]	A	C	6.642e^-6	0.825	UTR_3_PRIME chinmo
2L	1699735	2L_1699735_SNP [dm3] 2L_1699735_SNP [dm6]	C	A	6.651e^-6	0.825	UTR_3_PRIME chinmo
2R	9007133	2R_9007133_SNP [dm3] 2R_13119628_SNP [dm6]	A	G	7.233e^-6	0.825	INTRON CG13325
2L	1788750	2L_1788750_SNP [dm3] 2L_1788750_SNP [dm6]	C	T	7.575e^-6	0.825	DOWNSTREAM Gr22d INTERGENIC
3L	5503742	3L_5503742_SNP [dm3] 3L_5510642_SNP [dm6]	G	T	7.946e^-6	0.825	INTRON CG34342
2L	11149818	2L_11149818_SNP [dm3] 2L_11149818_SNP [dm6]	A	T	8.352e^-6	0.825	UPSTREAM Gyc32E INTERGENIC	TF binding site BDTNP1_TFBS_prd
3L	16128605	3L_16128605_SNP [dm3] 3L_16135505_SNP [dm6]	T	G	9.989e^-6	0.835	SYNONYMOUS_CODING CG16838 DOWNSTREAM CG5157
X	12666551	X_12666551_SNP [dm3] X_12772518_SNP [dm6]	A	C	1.066e^-5	0.835	UTR_3_PRIME CG3812 & 1 other
3R	9840450	3R_9840450_SNP [dm3] 3R_14014728_SNP [dm6]	A	C	1.084e^-5	0.835	INTRON rdx	TF binding site BDTNP1_TFBS_dl
X	5324047	X_5324047_SNP [dm3] X_5430014_SNP [dm6]	C	T	1.136e^-5	0.835	UTR_5_PRIME CG15784 UPSTREAM CG15784 DOWNSTREAM CR45517
2L	5445819	2L_5445819_SNP [dm3] 2L_5445819_SNP [dm6]	G	C	1.160e^-5	0.835	INTERGENIC
X	5324045	X_5324045_SNP [dm3] X_5430012_SNP [dm6]	A	T	1.166e^-5	0.835	START_GAINED CG15784 UTR_5_PRIME CG15784 UPSTREAM CG15784 DOWNSTREAM CR45517
3L	3530703	3L_3530703_SNP [dm3] 3L_3530703_SNP [dm6]	T	C	1.210e^-5	0.835	INTRON Eip63E
3L	12381139	3L_12381139_SNP [dm3] 3L_12388039_SNP [dm6]	A	C	1.246e^-5	0.835	UPSTREAM Ncc69 INTRON Ncc69
3L	12381141	3L_12381141_DEL [dm3] 3L_12388041_DEL [dm6]	AAT	C	1.246e^-5	0.835	UPSTREAM Ncc69 INTRON Ncc69
X	7450403	X_7450403_SNP [dm3] X_7556370_SNP [dm6]	A	T	1.352e^-5	0.861	EXON CR44501	TF binding site BDTNP1_TFBS_da mE1_TFBS_GATAe mE1_TFBS_HSA
2L	8307939	2L_8307939_SNP [dm3] 2L_8307939_SNP [dm6]	G	A	1.377e^-5	0.861	UPSTREAM CG7818 INTRON Ostgamma	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
3L	10188818	3L_10188818_SNP [dm3] 3L_10195718_SNP [dm6]	T	A	1.475e^-5	0.863	INTRON ect
X	5296638	X_5296638_INS [dm3] X_5402605_INS [dm6]	A	ATCAGAACAGA...	1.523e^-5	0.863	UTR_3_PRIME SK INTRON SK
2L	17445031	2L_17445031_SNP [dm3] 2L_17445031_SNP [dm6]	C	G	1.594e^-5	0.863	INTRON dl
2L	16836590	2L_16836590_SNP [dm3] 2L_16836590_SNP [dm6]	T	A	1.725e^-5	0.863	NON_SYNONYMOUS_CODING CG13283	TF binding site mE1_TFBS_sens
2R	9119984	2R_9119984_SNP [dm3] 2R_13232479_SNP [dm6]	C	T	1.761e^-5	0.863	SYNONYMOUS_CODING CG4670 DOWNSTREAM fsd	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
X	6643090	X_6643090_INS [dm3] X_6749057_INS [dm6]	A	ACA	1.776e^-5	0.863	INTRON CG14439
3L	1487360	3L_1487360_SNP [dm3] 3L_1487360_SNP [dm6]	A	G	1.943e^-5	0.863	INTRON stet	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_Trl
2R	4674221	2R_4674221_SNP [dm3] 2R_8786716_SNP [dm6]	C	T	1.977e^-5	0.863	INTERGENIC
3R	12290125	3R_12290125_SNP [dm3] 3R_16464403_SNP [dm6]	C	G	2.011e^-5	0.863	NON_SYNONYMOUS_CODING CG42232	TF binding site mE1_TFBS_inv mE1_TFBS_sens
X	9224573	X_9224573_SNP [dm3] X_9330540_SNP [dm6]	A	C	2.017e^-5	0.863	UPSTREAM CG34450 DOWNSTREAM CG34449 INTRON CG34449
3L	15877326	3L_15877326_SNP [dm3] 3L_15884226_SNP [dm6]	G	T	2.042e^-5	0.863	DOWNSTREAM CR44050 INTRON pHCl
2L	17444982	2L_17444982_SNP [dm3] 2L_17444982_SNP [dm6]	C	G	2.050e^-5	0.863	INTRON dl
3L	12381148	3L_12381148_SNP [dm3] 3L_12388048_SNP [dm6]	G	T	2.058e^-5	0.863	UPSTREAM Ncc69 INTRON Ncc69
2R	12147869	2R_12147869_INS [dm3] 2R_16260364_INS [dm6]	C	CTCC	2.076e^-5	0.863	UPSTREAM CngA INTERGENIC
3R	11861018	3R_11861018_DEL [dm3] 3R_16035296_DEL [dm6]	ACT	A	2.132e^-5	0.863	INTRON pnr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	12289151	3R_12289151_SNP [dm3] 3R_16463429_SNP [dm6]	C	G	2.187e^-5	0.863	SYNONYMOUS_CODING CG42232	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	17600150	2L_17600150_SNP [dm3] 2L_17600150_SNP [dm6]	G	T	2.402e^-5	0.863	INTRON Sytalpha
3L	15877220	3L_15877220_SNP [dm3] 3L_15884120_SNP [dm6]	T	C	2.477e^-5	0.863	DOWNSTREAM CR44050 INTRON pHCl
3R	20727688	3R_20727688_SNP [dm3] 3R_24901966_SNP [dm6]	G	C	2.503e^-5	0.863	SYNONYMOUS_CODING CG10845 INTRON CG13643	TF binding site mE1_TFBS_HSA
3R	10377945	3R_10377945_SNP [dm3] 3R_14552223_SNP [dm6]	G	T	2.534e^-5	0.863	INTRON Pde6
3R	4960462	3R_4960462_SNP [dm3] 3R_9134740_SNP [dm6]	T	C	2.601e^-5	0.863	INTRON pum
2L	8128425	2L_8128425_DEL [dm3] 2L_8128425_DEL [dm6]	TTC	T	2.620e^-5	0.863	INTRON CG8668	TF binding site BDTNP1_TFBS_dl
3R	22621765	3R_22621765_SNP [dm3] 3R_26796043_SNP [dm6]	G	A	2.778e^-5	0.863	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
2L	7773946	2L_7773946_SNP [dm3] 2L_7773946_SNP [dm6]	A	C	2.799e^-5	0.863	INTRON CG7191
3R	15876004	3R_15876004_SNP [dm3] 3R_20050282_SNP [dm6]	G	C	2.804e^-5	0.863	INTRON CG17193
X	15181879	X_15181879_SNP [dm3] X_15287846_SNP [dm6]	T	C	2.823e^-5	0.863	INTERGENIC
3L	1198152	3L_1198152_SNP [dm3] 3L_1198152_SNP [dm6]	C	T	2.946e^-5	0.863	SYNONYMOUS_CODING Aplip1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	9223510	X_9223510_SNP [dm3] X_9329477_SNP [dm6]	G	A	2.978e^-5	0.863	SYNONYMOUS_CODING CG34450 INTRON CG34449
3R	3230915	3R_3230915_SNP [dm3] 3R_7405193_SNP [dm6]	C	T	3.069e^-5	0.863	INTERGENIC
3R	16606144	3R_16606144_SNP [dm3] 3R_20780422_SNP [dm6]	G	T	3.100e^-5	0.863	UTR_5_PRIME Syp INTRON Syp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	20727509	3R_20727509_SNP [dm3] 3R_24901787_SNP [dm6]	T	C	3.173e^-5	0.863	NON_SYNONYMOUS_CODING CG10845 INTRON CG13643	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	5324048	X_5324048_SNP [dm3] X_5430015_SNP [dm6]	T	C	3.195e^-5	0.863	UTR_5_PRIME CG15784 UPSTREAM CG15784 DOWNSTREAM CR45517
2R	16770898	2R_16770898_SNP [dm3] 2R_20883393_SNP [dm6]	G	C	3.273e^-5	0.863	DOWNSTREAM otp & 1 other INTERGENIC
2R	17149229	2R_17149229_SNP [dm3] 2R_21261724_SNP [dm6]	A	G	3.332e^-5	0.863	INTRON Rgk3
2R	17001589	2R_17001589_SNP [dm3] 2R_21114084_SNP [dm6]	T	G	3.336e^-5	0.863	INTRON ktub
3R	10570162	3R_10570162_SNP [dm3] 3R_14744440_SNP [dm6]	A	G	3.401e^-5	0.863	INTRON jvl
X	6975832	X_6975832_INS [dm3] X_7081799_INS [dm6]	C	CT	3.411e^-5	0.863	INTRON Sxl
3R	8946395	3R_8946395_SNP [dm3] 3R_13120673_SNP [dm6]	C	A	3.437e^-5	0.863	INTRON timeout
X	16319043	X_16319043_SNP [dm3] X_16425010_SNP [dm6]	G	A	3.450e^-5	0.863	INTRON hang	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	9224569	X_9224569_INS [dm3] X_9330536_INS [dm6]	C	CTTTGTGTGTAGGAC...	3.558e^-5	0.863	UPSTREAM CG34450 DOWNSTREAM CG34449 INTRON CG34449
3R	12289607	3R_12289607_SNP [dm3] 3R_16463885_SNP [dm6]	A	G	3.597e^-5	0.863	SYNONYMOUS_CODING CG42232	TF binding site mE1_TFBS_sens
3R	5694576	3R_5694576_SNP [dm3] 3R_9868854_SNP [dm6]	T	A	3.645e^-5	0.863	UPSTREAM Teh1 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_ttk
3L	8435914	3L_8435914_SNP [dm3] 3L_8442814_SNP [dm6]	A	T	3.822e^-5	0.863	UPSTREAM Unr DOWNSTREAM CG6983 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	8653142	3L_8653142_SNP [dm3] 3L_8660042_SNP [dm6]	G	C	3.907e^-5	0.863	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	19912084	3R_19912084_SNP [dm3] 3R_24086362_SNP [dm6]	T	A	3.924e^-5	0.863	INTRON 4EHP
2L	12389210	2L_12389210_SNP [dm3] 2L_12389210_SNP [dm6]	C	T	4.106e^-5	0.863	SYNONYMOUS_CODING bru-2 UTR_3_PRIME bru-2	TF binding site mE1_TFBS_sbb
3R	19912085	3R_19912085_SNP [dm3] 3R_24086363_SNP [dm6]	T	G	4.160e^-5	0.863	INTRON 4EHP
3R	16606324	3R_16606324_SNP [dm3] 3R_20780602_SNP [dm6]	G	A	4.164e^-5	0.863	UTR_5_PRIME Syp INTRON Syp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	13938753	3R_13938753_SNP [dm3] 3R_18113031_SNP [dm6]	G	A	4.241e^-5	0.863	INTRON sr
3L	7921250	3L_7921250_SNP [dm3] 3L_7928150_SNP [dm6]	C	A	4.304e^-5	0.863	INTRON syd	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	12664941	2L_12664941_SNP [dm3] 2L_12664941_SNP [dm6]	C	T	4.344e^-5	0.863	INTRON pdm2	TF binding site mE1_TFBS_cad
3L	4418431	3L_4418431_SNP [dm3] 3L_4418431_SNP [dm6]	C	T	4.401e^-5	0.863	NON_SYNONYMOUS_CODING DOR UPSTREAM DOR
3R	15160447	3R_15160447_SNP [dm3] 3R_19334725_SNP [dm6]	A	G	4.456e^-5	0.863	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad
3L	13402211	3L_13402211_SNP [dm3] 3L_13409111_SNP [dm6]	A	G	4.475e^-5	0.863	INTERGENIC	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_HSA mE1_TFBS_sens
3R	13794833	3R_13794833_SNP [dm3] 3R_17969111_SNP [dm6]	A	G	4.535e^-5	0.863	INTRON cpo
2L	6464258	2L_6464258_SNP [dm3] 2L_6464258_SNP [dm6]	T	A	4.538e^-5	0.863	INTRON CG16947	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	11860762	3R_11860762_SNP [dm3] 3R_16035040_SNP [dm6]	C	T	4.542e^-5	0.863	UTR_5_PRIME pnr INTRON pnr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll mE1_TFBS_cad mE1_TFBS_HSA
X	9224651	X_9224651_INS [dm3] X_9330618_INS [dm6]	C	CATTCCTCAATTAC...	4.563e^-5	0.863	UPSTREAM CG34450 DOWNSTREAM CG34449 INTRON CG34449
2L	7076274	2L_7076274_SNP [dm3] 2L_7076274_SNP [dm6]	A	G	4.599e^-5	0.863	INTRON Pvf2	TF binding site mE1_TFBS_cad
X	12817512	X_12817512_SNP [dm3] X_12923479_SNP [dm6]	C	T	4.753e^-5	0.863	INTRON fne
3L	8653144	3L_8653144_SNP [dm3] 3L_8660044_SNP [dm6]	C	T	4.939e^-5	0.863	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	19912068	3R_19912068_DEL [dm3] 3R_24086346_DEL [dm6]	ACTTTAGTGAT...	G	5.042e^-5	0.863	INTRON 4EHP
2L	19915192	2L_19915192_SNP [dm3] 2L_19915192_SNP [dm6]	T	C	5.067e^-5	0.863	INTRON sick	TF binding site mE1_TFBS_bab1
3L	1487399	3L_1487399_SNP [dm3] 3L_1487399_SNP [dm6]	T	A	5.085e^-5	0.863	INTRON stet	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	12381145	3L_12381145_SNP [dm3] 3L_12388045_SNP [dm6]	G	C	5.098e^-5	0.863	UPSTREAM Ncc69 INTRON Ncc69
2R	16523692	2R_16523692_SNP [dm3] 2R_20636187_SNP [dm6]	G	T	5.169e^-5	0.863	UPSTREAM CG13436 INTRON rig
3R	5694594	3R_5694594_SNP [dm3] 3R_9868872_SNP [dm6]	A	T	5.199e^-5	0.863	UPSTREAM Teh1 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_ttk
3L	12381120	3L_12381120_SNP [dm3] 3L_12388020_SNP [dm6]	C	T	5.223e^-5	0.863	UPSTREAM Ncc69 INTRON Ncc69
X	9224592	X_9224592_SNP [dm3] X_9330559_SNP [dm6]	T	C	5.294e^-5	0.863	UPSTREAM CG34450 DOWNSTREAM CG34449 INTRON CG34449
3L	18332296	3L_18332296_MNP [dm3] 3L_18339196_MNP [dm6]	GTA	TGG	5.364e^-5	0.863	INTERGENIC	TF binding site mE1_TFBS_cad

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Phenotype distribution and association to known covariates

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GWAS results