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=6.479e^-15)
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_3R_P	<2e-16
In_3R_K	<2e-16
In_3R_Mo	<2e-16

Kruskal-Wallis test

Covariate	χ²	p-value
In_3R_P	15.7696	0.0004
In_3R_K	28.7381	5.7492e-07
In_3R_Mo	12.0421	0.0024

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3333 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	9226136	3R_9226136_DEL [dm3] 3R_13400414_DEL [dm6]	TTAGTTAT	T	1.228e^-6	0.457	INTRON CG9796
3R	17172271	3R_17172271_SNP [dm3] 3R_21346549_SNP [dm6]	G	T	1.511e^-6	0.457	INTRON CG16791	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	18064714	X_18064714_DEL [dm3] X_18170681_DEL [dm6]	AC	A	1.542e^-6	0.457	UTR_3_PRIME Frq1
2R	14285872	2R_14285872_INS [dm3] 2R_18398367_INS [dm6]	A	ACTA	2.120e^-6	0.457	UPSTREAM GstE1 & 1 other INTRON GstE10
3R	25978234	3R_25978234_SNP [dm3] 3R_30152512_SNP [dm6]	G	A	2.484e^-6	0.457	DOWNSTREAM CG11498 INTRON CG15529	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	18065671	X_18065671_SNP [dm3] X_18171638_SNP [dm6]	C	T	2.900e^-6	0.457	UTR_3_PRIME Frq1
2L	10705607	2L_10705607_SNP [dm3] 2L_10705607_SNP [dm6]	C	T	2.974e^-6	0.457	DOWNSTREAM CG6415 INTRON Lip2
2L	10705646	2L_10705646_SNP [dm3] 2L_10705646_SNP [dm6]	C	A	3.694e^-6	0.457	DOWNSTREAM CG6415 INTRON Lip2
3L	10503033	3L_10503033_SNP [dm3] 3L_10509933_SNP [dm6]	G	A	3.969e^-6	0.457	INTRON A2bp1
2L	9396551	2L_9396551_SNP [dm3] 2L_9396551_SNP [dm6]	G	A	4.190e^-6	0.457	DOWNSTREAM CG4438 INTRON Shawl
2L	4209784	2L_4209784_DEL [dm3] 2L_4209784_DEL [dm6]	CC	C	4.363e^-6	0.457	INTRON ft	TF binding site mE1_TFBS_inv
2L	16447926	2L_16447926_SNP [dm3] 2L_16447926_SNP [dm6]	G	A	4.390e^-6	0.457	INTRON CG5888 & 1 other	TF binding site mE1_TFBS_Trl
3R	5145301	3R_5145301_SNP [dm3] 3R_9319579_SNP [dm6]	T	G	4.470e^-6	0.457	INTRON CG8861
3L	5310368	3L_5310368_SNP [dm3] 3L_5317268_SNP [dm6]	A	G	4.660e^-6	0.457	UPSTREAM CR45741 INTERGENIC
2L	10705613	2L_10705613_SNP [dm3] 2L_10705613_SNP [dm6]	A	G	4.812e^-6	0.457	DOWNSTREAM CG6415 INTRON Lip2
3R	18449810	3R_18449810_SNP [dm3] 3R_22624088_SNP [dm6]	T	C	4.897e^-6	0.457	INTRON loco	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA
2L	9588278	2L_9588278_SNP [dm3] 2L_9588278_SNP [dm6]	C	A	5.004e^-6	0.457	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	17579947	3L_17579947_SNP [dm3] 3L_17586847_SNP [dm6]	T	G	5.648e^-6	0.457	INTRON Eip74EF
3L	17764931	3L_17764931_SNP [dm3] 3L_17771831_SNP [dm6]	A	G	5.688e^-6	0.457	INTERGENIC
2L	4207422	2L_4207422_SNP [dm3] 2L_4207422_SNP [dm6]	A	G	5.696e^-6	0.457	SYNONYMOUS_CODING ft	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	10705624	2L_10705624_SNP [dm3] 2L_10705624_SNP [dm6]	C	T	5.735e^-6	0.457	DOWNSTREAM CG6415 INTRON Lip2
2L	4208686	2L_4208686_SNP [dm3] 2L_4208686_SNP [dm6]	G	T	5.955e^-6	0.457	SYNONYMOUS_CODING ft	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	26637072	3R_26637072_SNP [dm3] 3R_30811350_SNP [dm6]	G	A	6.124e^-6	0.457	INTRON cindr
2L	12296926	2L_12296926_SNP [dm3] 2L_12296926_SNP [dm6]	C	T	6.699e^-6	0.457	INTRON aret
3R	26637079	3R_26637079_SNP [dm3] 3R_30811357_SNP [dm6]	G	C	6.783e^-6	0.457	INTRON cindr
2R	10605253	2R_10605253_SNP [dm3] 2R_14717748_SNP [dm6]	C	A	6.881e^-6	0.457	INTERGENIC
3L	17026609	3L_17026609_SNP [dm3] 3L_17033509_SNP [dm6]	T	C	6.993e^-6	0.457	UPSTREAM CR45756 EXON CR43250	TF binding site BDTNP1_TFBS_dl
X	10306399	X_10306399_DEL [dm3] X_10412366_DEL [dm6]	TT	T	7.660e^-6	0.457	UTR_3_PRIME CG32683
2R	14098751	2R_14098751_INS [dm3] 2R_18211246_INS [dm6]	G	GG	7.718e^-6	0.457	DOWNSTREAM CR45147 INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	16312668	3R_16312668_SNP [dm3] 3R_20486946_SNP [dm6]	G	T	7.907e^-6	0.457	UPSTREAM CR44401 INTERGENIC
3R	9226284	3R_9226284_SNP [dm3] 3R_13400562_SNP [dm6]	G	C	7.910e^-6	0.457	INTRON CG9796
3R	26539873	3R_26539873_SNP [dm3] 3R_30714151_SNP [dm6]	A	G	8.135e^-6	0.457	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	13734487	3L_13734487_SNP [dm3] 3L_13741387_SNP [dm6]	C	A	8.514e^-6	0.457	INTRON bru-3
3L	19380842	3L_19380842_SNP [dm3] 3L_19387742_SNP [dm6]	C	A	8.975e^-6	0.457	NON_SYNONYMOUS_CODING ms_3_76Ba INTRON CG32206
3L	17580000	3L_17580000_SNP [dm3] 3L_17586900_SNP [dm6]	T	A	9.417e^-6	0.457	INTRON Eip74EF
2L	12296927	2L_12296927_SNP [dm3] 2L_12296927_SNP [dm6]	A	G	9.455e^-6	0.457	INTRON aret
3L	17580001	3L_17580001_SNP [dm3] 3L_17586901_SNP [dm6]	T	A	9.532e^-6	0.457	INTRON Eip74EF
3R	18531080	3R_18531080_SNP [dm3] 3R_22705358_SNP [dm6]	C	A	9.688e^-6	0.457	INTRON CG13842
3R	18512253	3R_18512253_SNP [dm3] 3R_22686531_SNP [dm6]	T	C	9.735e^-6	0.457	UPSTREAM CG17625 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA
3L	10503194	3L_10503194_SNP [dm3] 3L_10510094_SNP [dm6]	G	A	9.745e^-6	0.457	INTRON A2bp1
3R	24486343	3R_24486343_SNP [dm3] 3R_28660621_SNP [dm6]	G	T	1.108e^-5	0.467	INTERGENIC
2R	13857300	2R_13857300_SNP [dm3] 2R_17969795_SNP [dm6]	G	A	1.125e^-5	0.467	INTERGENIC
3R	18526806	3R_18526806_SNP [dm3] 3R_22701084_SNP [dm6]	A	G	1.135e^-5	0.467	UPSTREAM CG6972 DOWNSTREAM Cyp6d4 INTRON CCAP
2L	11080476	2L_11080476_SNP [dm3] 2L_11080476_SNP [dm6]	A	G	1.160e^-5	0.467	INTRON AstC
3R	13508769	3R_13508769_SNP [dm3] 3R_17683047_SNP [dm6]	T	C	1.163e^-5	0.467	SYNONYMOUS_CODING CG7655 UPSTREAM alt DOWNSTREAM CG31251	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_sens
3R	9743756	3R_9743756_SNP [dm3] 3R_13918034_SNP [dm6]	G	A	1.169e^-5	0.467	INTERGENIC
3R	18449737	3R_18449737_SNP [dm3] 3R_22624015_SNP [dm6]	A	T	1.189e^-5	0.467	INTRON loco	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA
3L	17579990	3L_17579990_MNP [dm3] 3L_17586890_MNP [dm6]	AAA	TGC	1.194e^-5	0.467	INTRON Eip74EF
3L	13739552	3L_13739552_SNP [dm3] 3L_13746452_SNP [dm6]	T	C	1.226e^-5	0.469	INTRON bru-3
2L	10705633	2L_10705633_SNP [dm3] 2L_10705633_SNP [dm6]	T	C	1.272e^-5	0.472	DOWNSTREAM CG6415 INTRON Lip2
2R	16043078	2R_16043078_SNP [dm3] 2R_20155573_SNP [dm6]	G	A	1.318e^-5	0.472	INTERGENIC
3R	7876398	3R_7876398_SNP [dm3] 3R_12050676_SNP [dm6]	G	A	1.370e^-5	0.472	INTERGENIC
3R	16766433	3R_16766433_SNP [dm3] 3R_20940711_SNP [dm6]	T	A	1.398e^-5	0.472	INTRON CG31191
2R	14285319	2R_14285319_SNP [dm3] 2R_18397814_SNP [dm6]	G	A	1.430e^-5	0.472	UPSTREAM GstE1 & 1 other INTRON GstE10
3R	18449823	3R_18449823_SNP [dm3] 3R_22624101_SNP [dm6]	A	G	1.432e^-5	0.472	INTRON loco	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA
3L	10503136	3L_10503136_SNP [dm3] 3L_10510036_SNP [dm6]	C	A	1.438e^-5	0.472	INTRON A2bp1
3R	5144251	3R_5144251_SNP [dm3] 3R_9318529_SNP [dm6]	G	A	1.472e^-5	0.472	INTRON CG8861
X	18065437	X_18065437_SNP [dm3] X_18171404_SNP [dm6]	C	T	1.485e^-5	0.472	UTR_3_PRIME Frq1
2R	19484911	2R_19484911_SNP [dm3] 2R_23597388_SNP [dm6]	T	C	1.514e^-5	0.472	SYNONYMOUS_CODING apt
3R	9226183	3R_9226183_SNP [dm3] 3R_13400461_SNP [dm6]	T	A	1.548e^-5	0.472	INTRON CG9796
3L	5642397	3L_5642397_SNP [dm3] 3L_5649297_SNP [dm6]	T	A	1.558e^-5	0.472	UTR_3_PRIME Blimp-1 DOWNSTREAM Blimp-1
3L	12298375	3L_12298375_SNP [dm3] 3L_12305275_SNP [dm6]	A	G	1.561e^-5	0.472	INTERGENIC
3R	9226756	3R_9226756_SNP [dm3] 3R_13401034_SNP [dm6]	C	A	1.610e^-5	0.472	INTRON CG9796	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	11171980	3R_11171980_DEL [dm3] 3R_15346258_DEL [dm6]	GCT	G	1.628e^-5	0.472	UTR_5_PRIME CG31301 UPSTREAM Surf4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	2578804	3L_2578804_SNP [dm3] 3L_2578804_SNP [dm6]	A	G	1.665e^-5	0.472	INTRON msn	TF binding site BDTNP1_TFBS_twi
3L	10503135	3L_10503135_SNP [dm3] 3L_10510035_SNP [dm6]	T	C	1.671e^-5	0.472	INTRON A2bp1
3R	9890857	3R_9890857_SNP [dm3] 3R_14065135_SNP [dm6]	A	G	1.713e^-5	0.472	INTRON foxo	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	18376258	X_18376258_INS [dm3] X_18482225_INS [dm6]	A	ACACA	1.772e^-5	0.472	INTRON Hayan	TF binding site mE1_TFBS_inv
2L	17896790	2L_17896790_SNP [dm3] 2L_17896790_SNP [dm6]	A	T	1.817e^-5	0.472	INTERGENIC
2L	13264333	2L_13264333_SNP [dm3] 2L_13264333_SNP [dm6]	A	G	1.829e^-5	0.472	DOWNSTREAM CG31848 INTRON CG44085
3R	27431292	3R_27431292_SNP [dm3] 3R_31605570_SNP [dm6]	G	T	1.856e^-5	0.472	INTRON CycG	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
2R	19285277	2R_19285277_SNP [dm3] 2R_23397754_SNP [dm6]	G	A	1.907e^-5	0.472	SYNONYMOUS_CODING CG3520	TF binding site mE1_TFBS_chinmo
3L	13735365	3L_13735365_SNP [dm3] 3L_13742265_SNP [dm6]	A	G	1.965e^-5	0.472	INTRON bru-3
3R	23947382	3R_23947382_DEL [dm3] 3R_28121660_DEL [dm6]	AA	A	1.976e^-5	0.472	INTERGENIC
2L	16552621	2L_16552621_SNP [dm3] 2L_16552621_SNP [dm6]	G	T	1.976e^-5	0.472	INTRON CG42389
2R	9215028	2R_9215028_SNP [dm3] 2R_13327523_SNP [dm6]	A	G	2.014e^-5	0.472	INTERGENIC
3L	10503120	3L_10503120_SNP [dm3] 3L_10510020_SNP [dm6]	A	G	2.037e^-5	0.472	INTRON A2bp1
X	11517464	X_11517464_SNP [dm3] X_11623431_SNP [dm6]	G	A	2.096e^-5	0.472	INTRON Ptp10D	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	18065438	X_18065438_SNP [dm3] X_18171405_SNP [dm6]	C	T	2.110e^-5	0.472	UTR_3_PRIME Frq1
3R	10699979	3R_10699979_SNP [dm3] 3R_14874257_SNP [dm6]	T	G	2.110e^-5	0.472	UPSTREAM btsz INTRON btsz
3R	10420289	3R_10420289_SNP [dm3] 3R_14594567_SNP [dm6]	A	T	2.115e^-5	0.472	INTRON stumps	regulatory region REDfly_CRMs
3R	16766421	3R_16766421_SNP [dm3] 3R_20940699_SNP [dm6]	T	A	2.138e^-5	0.472	INTRON CG31191
2L	12297009	2L_12297009_SNP [dm3] 2L_12297009_SNP [dm6]	A	C	2.161e^-5	0.472	INTRON aret
3R	9226941	3R_9226941_SNP [dm3] 3R_13401219_SNP [dm6]	G	T	2.178e^-5	0.472	INTRON CG9796	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	4707265	2L_4707265_SNP [dm3] 2L_4707265_SNP [dm6]	G	T	2.179e^-5	0.472	INTRON CG34351
3L	10503325	3L_10503325_SNP [dm3] 3L_10510225_SNP [dm6]	T	C	2.186e^-5	0.472	INTRON A2bp1
3L	10503024	3L_10503024_INS [dm3] 3L_10509924_INS [dm6]	G	GCATTT	2.190e^-5	0.472	INTRON A2bp1
3L	4318147	3L_4318147_SNP [dm3] 3L_4318147_SNP [dm6]	G	T	2.229e^-5	0.475	NON_SYNONYMOUS_CODING Claspin UPSTREAM CG32250	TF binding site mE1_TFBS_HSA
3R	11682316	3R_11682316_SNP [dm3] 3R_15856594_SNP [dm6]	A	T	2.257e^-5	0.476	INTRON Hmt-1	TF binding site mE1_TFBS_sens
2L	1552225	2L_1552225_SNP [dm3] 2L_1552225_SNP [dm6]	A	G	2.430e^-5	0.479	INTERGENIC
2L	21793557	2L_21793557_SNP [dm3] 2L_21793557_SNP [dm6]	G	T	2.435e^-5	0.479	INTRON CG31612	TF binding site BDTNP1_TFBS_z
3L	6379351	3L_6379351_SNP [dm3] 3L_6386251_SNP [dm6]	A	C	2.456e^-5	0.479	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
2L	14105058	2L_14105058_MNP [dm3] 2L_14105058_MNP [dm6]	TCA	GTC	2.494e^-5	0.479	INTRON CG16879	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	14285336	2R_14285336_SNP [dm3] 2R_18397831_SNP [dm6]	T	C	2.506e^-5	0.479	UPSTREAM GstE1 & 1 other INTRON GstE10
2L	9412519	2L_9412519_SNP [dm3] 2L_9412519_SNP [dm6]	G	A	2.520e^-5	0.479	INTRON Shawl
2R	18603310	2R_18603310_SNP [dm3] 2R_22715805_SNP [dm6]	T	C	2.544e^-5	0.479	SYNONYMOUS_CODING CG30268	TF binding site BDTNP1_TFBS_twi
2R	14285859	2R_14285859_SNP [dm3] 2R_18398354_SNP [dm6]	C	T	2.568e^-5	0.479	UPSTREAM GstE1 & 1 other INTRON GstE10
2R	14285889	2R_14285889_SNP [dm3] 2R_18398384_SNP [dm6]	A	G	2.579e^-5	0.479	UPSTREAM GstE1 & 1 other INTRON GstE10
2R	20173697	2R_20173697_SNP [dm3] 2R_24286174_SNP [dm6]	C	T	2.719e^-5	0.479	INTRON nvy	TF binding site mE1_TFBS_chinmo
2L	17489659	2L_17489659_SNP [dm3] 2L_17489659_SNP [dm6]	C	A	2.724e^-5	0.479	INTRON qua	TF binding site mE1_TFBS_cad

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Missing results

By genomic position
Variant impact
Gene name

TotalVariants_3R phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results