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=1.034e^-7)
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

1605 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	18246158	2R_18246158_SNP [dm3] 2R_22358653_SNP [dm6]	G	A	1.788e^-6	0.95	INTRON Liprin-gamma
X	6388727	X_6388727_SNP [dm3] X_6494694_SNP [dm6]	A	C	2.368e^-6	0.95	INTRON CG42340
2L	6300480	2L_6300480_SNP [dm3] 2L_6300480_SNP [dm6]	G	C	4.650e^-6	0.95	INTRON Ddr
3R	15403647	3R_15403647_SNP [dm3] 3R_19577925_SNP [dm6]	A	C	5.232e^-6	0.95	INTRON Dys
X	2637551	X_2637551_SNP [dm3] X_2743518_SNP [dm6]	G	T	5.357e^-6	0.95	UTR_5_PRIME Syx4 UPSTREAM Syx4 INTRON kirre	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	15403579	3R_15403579_SNP [dm3] 3R_19577857_SNP [dm6]	T	G	5.399e^-6	0.95	INTRON Dys
2R	12286498	2R_12286498_SNP [dm3] 2R_16398993_SNP [dm6]	G	C	5.950e^-6	0.95	UTR_5_PRIME Sema-2b	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	2637365	X_2637365_SNP [dm3] X_2743332_SNP [dm6]	A	T	6.576e^-6	0.95	UPSTREAM Syx4 INTRON kirre & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	15482040	X_15482040_SNP [dm3] X_15588007_SNP [dm6]	C	T	7.611e^-6	0.95	SYNONYMOUS_CODING CG8105 INTRON CG9220	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	13379349	2R_13379349_SNP [dm3] 2R_17491844_SNP [dm6]	G	A	7.681e^-6	0.95	SYNONYMOUS_CODING NT5E-2
2L	11400578	2L_11400578_SNP [dm3] 2L_11400578_SNP [dm6]	A	C	8.268e^-6	0.95	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl
3L	7053130	3L_7053130_DEL [dm3] 3L_7060030_DEL [dm6]	GGG	G	1.168e^-5	0.95	UTR_3_PRIME CG8641
3L	10792374	3L_10792374_SNP [dm3] 3L_10799274_SNP [dm6]	A	T	1.223e^-5	0.95	INTERGENIC
2R	18295192	2R_18295192_SNP [dm3] 2R_22407687_SNP [dm6]	A	C	1.236e^-5	0.95	SYNONYMOUS_CODING CG6044 UPSTREAM ventrally-expressed-protein-D	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	9195161	X_9195161_SNP [dm3] X_9301128_SNP [dm6]	G	A	1.379e^-5	0.95	INTRON lz
3R	22463593	3R_22463593_SNP [dm3] 3R_26637871_SNP [dm6]	A	T	1.455e^-5	0.95	DOWNSTREAM TwdlS INTERGENIC
3R	10059966	3R_10059966_SNP [dm3] 3R_14234244_SNP [dm6]	C	T	1.500e^-5	0.95	INTERGENIC
3L	2352658	3L_2352658_DEL [dm3] 3L_2352658_DEL [dm6]	TGATTGGTC	T	1.502e^-5	0.95	INTERGENIC
X	8790070	X_8790070_SNP [dm3] X_8896037_SNP [dm6]	T	G	1.564e^-5	0.95	INTRON Moe	TF binding site BDTNP1_TFBS_dl
3L	2352687	3L_2352687_SNP [dm3] 3L_2352687_SNP [dm6]	A	T	1.670e^-5	0.95	INTERGENIC
3L	11623255	3L_11623255_INS [dm3] 3L_11630155_INS [dm6]	A	AACCGC	1.682e^-5	0.95	DOWNSTREAM mir-3642 & 1 other INTRON CG18815
2R	2657127	2R_2657127_SNP [dm3] 2R_6769622_SNP [dm6]	C	T	1.709e^-5	0.95	UTR_5_PRIME Epac INTRON Epac
3L	19955520	3L_19955520_SNP [dm3] 3L_19962420_SNP [dm6]	T	C	1.758e^-5	0.95	INTRON Ac76E	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	9791701	2R_9791701_SNP [dm3] 2R_13904196_SNP [dm6]	A	T	1.768e^-5	0.95	INTRON shot	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	8790058	X_8790058_SNP [dm3] X_8896025_SNP [dm6]	T	G	1.836e^-5	0.95	INTRON Moe	TF binding site BDTNP1_TFBS_dl
3R	19111230	3R_19111230_SNP [dm3] 3R_23285508_SNP [dm6]	C	T	1.837e^-5	0.95	SYNONYMOUS_CODING CG6763 DOWNSTREAM CG17083	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	8726228	3L_8726228_DEL [dm3] 3L_8733128_DEL [dm6]	TA	T	1.848e^-5	0.95	UTR_3_PRIME Prm DOWNSTREAM Prm & 1 other
3L	15225713	3L_15225713_SNP [dm3] 3L_15232613_SNP [dm6]	A	G	2.028e^-5	0.95	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	14092206	X_14092206_SNP [dm3] X_14198173_SNP [dm6]	C	T	2.079e^-5	0.95	SYNONYMOUS_CODING yl	TF binding site mE1_TFBS_chinmo
3L	15225656	3L_15225656_SNP [dm3] 3L_15232556_SNP [dm6]	T	A	2.176e^-5	0.95	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	7659470	2R_7659470_SNP [dm3] 2R_11771965_SNP [dm6]	C	G	2.228e^-5	0.95	INTRON ths
3R	6379066	3R_6379066_DEL [dm3] 3R_10553344_DEL [dm6]	AA	A	2.238e^-5	0.95	INTRON hth	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	10274174	X_10274174_SNP [dm3] X_10380141_SNP [dm6]	G	A	2.243e^-5	0.95	SYNONYMOUS_CODING CG32681 INTRON CG17841	TF binding site BDTNP1_TFBS_sna
2L	20497335	2L_20497335_SNP [dm3] 2L_20497335_SNP [dm6]	A	G	2.348e^-5	0.95	INTERGENIC
2L	20507465	2L_20507465_SNP [dm3] 2L_20507465_SNP [dm6]	G	T	2.427e^-5	0.95	INTERGENIC
3R	19802857	3R_19802857_SNP [dm3] 3R_23977135_SNP [dm6]	G	A	2.445e^-5	0.95	SYNONYMOUS_CODING CG31140	TF binding site mE1_TFBS_chinmo
3L	557919	3L_557919_SNP [dm3] 3L_557919_SNP [dm6]	A	G	2.473e^-5	0.95	INTRON hipk	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	19955513	3L_19955513_SNP [dm3] 3L_19962413_SNP [dm6]	T	C	2.540e^-5	0.95	INTRON Ac76E	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	12857772	3L_12857772_SNP [dm3] 3L_12864672_SNP [dm6]	C	A	2.577e^-5	0.95	INTERGENIC
X	2577768	X_2577768_SNP [dm3] X_2683735_SNP [dm6]	G	A	2.632e^-5	0.95	UPSTREAM CG2652 EXON CR44470
X	2577786	X_2577786_SNP [dm3] X_2683753_SNP [dm6]	A	G	2.632e^-5	0.95	UPSTREAM CG2652 EXON CR44470
3L	15225651	3L_15225651_SNP [dm3] 3L_15232551_SNP [dm6]	C	T	2.645e^-5	0.95	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12285821	2R_12285821_DEL [dm3] 2R_16398316_DEL [dm6]	AA	A	2.651e^-5	0.95	UPSTREAM Sema-2b INTRON Sema-2b	TF binding site mE1_TFBS_cad
2L	11221916	2L_11221916_SNP [dm3] 2L_11221916_SNP [dm6]	C	T	2.658e^-5	0.95	INTRON ab	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	12857722	3L_12857722_SNP [dm3] 3L_12864622_SNP [dm6]	C	T	2.727e^-5	0.95	INTERGENIC
2L	12181264	2L_12181264_DEL [dm3] 2L_12181264_DEL [dm6]	AATAG	A	2.829e^-5	0.95	INTRON aret
3R	14083815	3R_14083815_SNP [dm3] 3R_18258093_SNP [dm6]	C	T	2.868e^-5	0.95	DOWNSTREAM moi & 1 other INTERGENIC
2L	12181285	2L_12181285_INS [dm3] 2L_12181285_INS [dm6]	C	CGC	2.908e^-5	0.95	INTRON aret
2L	9289912	2L_9289912_SNP [dm3] 2L_9289912_SNP [dm6]	T	C	2.945e^-5	0.95	INTRON Ggamma30A
X	14092242	X_14092242_SNP [dm3] X_14198209_SNP [dm6]	G	A	3.121e^-5	0.95	SYNONYMOUS_CODING yl	TF binding site mE1_TFBS_chinmo
3R	19111269	3R_19111269_SNP [dm3] 3R_23285547_SNP [dm6]	C	T	3.198e^-5	0.95	SYNONYMOUS_CODING CG6763 DOWNSTREAM CG17083	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	6252928	X_6252928_SNP [dm3] X_6358895_SNP [dm6]	C	T	3.272e^-5	0.95	SPLICE_SITE_REGION kdn INTRON kdn	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
2L	6300342	2L_6300342_SNP [dm3] 2L_6300342_SNP [dm6]	A	C	3.304e^-5	0.95	INTRON Ddr
3L	12789935	3L_12789935_DEL [dm3] 3L_12796835_DEL [dm6]	TTGT	T	3.381e^-5	0.95	DOWNSTREAM CG42709 INTRON Atg1
2R	14323526	2R_14323526_SNP [dm3] 2R_18436021_SNP [dm6]	T	C	3.546e^-5	0.95	INTRON CG30118	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	18295204	2R_18295204_SNP [dm3] 2R_22407699_SNP [dm6]	A	C	3.629e^-5	0.95	SYNONYMOUS_CODING CG6044 UPSTREAM ventrally-expressed-protein-D	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	15483515	X_15483515_SNP [dm3] X_15589482_SNP [dm6]	T	C	3.703e^-5	0.95	DOWNSTREAM CG8105 INTRON CG9220
2L	11229843	2L_11229843_SNP [dm3] 2L_11229843_SNP [dm6]	T	G	3.813e^-5	0.95	INTRON ab
2R	10366628	2R_10366628_SNP [dm3] 2R_14479123_SNP [dm6]	G	A	3.839e^-5	0.95	INTERGENIC
2L	18204549	2L_18204549_SNP [dm3] 2L_18204549_SNP [dm6]	G	A	3.942e^-5	0.95	SYNONYMOUS_CODING CG42750	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
2L	18204558	2L_18204558_SNP [dm3] 2L_18204558_SNP [dm6]	G	A	3.942e^-5	0.95	SYNONYMOUS_CODING CG42750	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
2L	20505758	2L_20505758_SNP [dm3] 2L_20505758_SNP [dm6]	G	A	4.004e^-5	0.95	INTERGENIC
3R	16402725	3R_16402725_SNP [dm3] 3R_20577003_SNP [dm6]	A	G	4.010e^-5	0.95	UTR_5_PRIME TFAM UPSTREAM CG5412	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	5212035	2L_5212035_SNP [dm3] 2L_5212035_SNP [dm6]	T	C	4.138e^-5	0.95	SYNONYMOUS_CODING Cyp28d1 DOWNSTREAM CG7742
3L	18740968	3L_18740968_SNP [dm3] 3L_18747868_SNP [dm6]	T	G	4.162e^-5	0.95	SYNONYMOUS_CODING Nufip UPSTREAM Atg3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	3763932	2L_3763932_SNP [dm3] 2L_3763932_SNP [dm6]	A	G	4.169e^-5	0.95	SYNONYMOUS_CODING CG43707	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	3763946	2L_3763946_SNP [dm3] 2L_3763946_SNP [dm6]	T	G	4.169e^-5	0.95	NON_SYNONYMOUS_CODING CG43707	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	14092248	X_14092248_SNP [dm3] X_14198215_SNP [dm6]	T	A	4.201e^-5	0.95	SYNONYMOUS_CODING yl	TF binding site mE1_TFBS_chinmo
X	9042834	X_9042834_SNP [dm3] X_9148801_SNP [dm6]	G	A	4.272e^-5	0.95	NON_SYNONYMOUS_CODING fh UPSTREAM dalao DOWNSTREAM CG7065	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3R	16403328	3R_16403328_SNP [dm3] 3R_20577606_SNP [dm6]	G	A	4.309e^-5	0.95	UPSTREAM TFAM DOWNSTREAM EloB INTRON CG5412	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	16403335	3R_16403335_SNP [dm3] 3R_20577613_SNP [dm6]	C	T	4.309e^-5	0.95	UPSTREAM TFAM DOWNSTREAM EloB INTRON CG5412	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	16402912	3R_16402912_SNP [dm3] 3R_20577190_SNP [dm6]	A	G	4.496e^-5	0.95	NON_SYNONYMOUS_CODING CG5412 UPSTREAM TFAM	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	18740964	3L_18740964_SNP [dm3] 3L_18747864_SNP [dm6]	A	C	4.674e^-5	0.95	NON_SYNONYMOUS_CODING Nufip UPSTREAM Atg3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	18741382	3L_18741382_SNP [dm3] 3L_18748282_SNP [dm6]	G	A	4.674e^-5	0.95	SYNONYMOUS_CODING Nufip UPSTREAM Atg3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
2L	5688038	2L_5688038_SNP [dm3] 2L_5688038_SNP [dm6]	T	G	4.736e^-5	0.95	INTERGENIC
3R	11276825	3R_11276825_DEL [dm3] 3R_15451103_DEL [dm6]	AAT	G	4.835e^-5	0.95	INTRON AdamTS-A
3L	18740925	3L_18740925_SNP [dm3] 3L_18747825_SNP [dm6]	C	T	5.086e^-5	0.95	NON_SYNONYMOUS_CODING Nufip UPSTREAM Atg3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3L	4628381	3L_4628381_SNP [dm3] 3L_4628381_SNP [dm6]	C	T	5.210e^-5	0.95	SYNONYMOUS_CODING Rpd3	TF binding site mE1_TFBS_sens
2L	12181451	2L_12181451_SNP [dm3] 2L_12181451_SNP [dm6]	T	C	5.494e^-5	0.95	INTRON aret
3R	16403106	3R_16403106_SNP [dm3] 3R_20577384_SNP [dm6]	G	C	5.544e^-5	0.95	SYNONYMOUS_CODING CG5412 UPSTREAM TFAM DOWNSTREAM EloB	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	19955581	3L_19955581_SNP [dm3] 3L_19962481_SNP [dm6]	G	T	5.667e^-5	0.95	INTRON Ac76E	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	2691996	2R_2691996_SNP [dm3] 2R_6804491_SNP [dm6]	A	G	5.703e^-5	0.95	INTERGENIC
2R	10912819	2R_10912819_SNP [dm3] 2R_15025314_SNP [dm6]	T	C	5.857e^-5	0.95	UPSTREAM Obp51a INTRON hbs EXON CR45256	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	10059958	3R_10059958_SNP [dm3] 3R_14234236_SNP [dm6]	C	A	5.905e^-5	0.95	INTERGENIC
2L	12145818	2L_12145818_SNP [dm3] 2L_12145818_SNP [dm6]	A	T	6.120e^-5	0.95	INTRON CG31760
3L	7876642	3L_7876642_SNP [dm3] 3L_7883542_SNP [dm6]	C	T	6.280e^-5	0.95	INTRON CG32365
3L	7876645	3L_7876645_SNP [dm3] 3L_7883545_SNP [dm6]	T	A	6.280e^-5	0.95	INTRON CG32365
X	15460011	X_15460011_SNP [dm3] X_15565978_SNP [dm6]	T	A	6.333e^-5	0.95	INTERGENIC
2L	9418526	2L_9418526_SNP [dm3] 2L_9418526_SNP [dm6]	G	A	6.471e^-5	0.95	INTRON Mco1
3L	8810411	3L_8810411_SNP [dm3] 3L_8817311_SNP [dm6]	A	T	6.474e^-5	0.95	INTERGENIC
2R	11554255	2R_11554255_SNP [dm3] 2R_15666750_SNP [dm6]	A	G	6.562e^-5	0.95	INTRON fus	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
3R	4564929	3R_4564929_SNP [dm3] 3R_8739207_SNP [dm6]	A	C	6.603e^-5	0.95	INTRON CG9801	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2L	10050351	2L_10050351_SNP [dm3] 2L_10050351_SNP [dm6]	T	C	6.816e^-5	0.95	SYNONYMOUS_CODING CG33301	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	23652168	3R_23652168_SNP [dm3] 3R_27826446_SNP [dm6]	G	T	6.885e^-5	0.95	INTRON CG34353	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
2L	1449079	2L_1449079_SNP [dm3] 2L_1449079_SNP [dm6]	C	T	6.963e^-5	0.95	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	7270406	2L_7270406_INS [dm3] 2L_7270406_INS [dm6]	A	ATATGCACTAAAATAAA...	7.047e^-5	0.95	INTRON Wnt4
2L	7270418	2L_7270418_SNP [dm3] 2L_7270418_SNP [dm6]	A	C	7.047e^-5	0.95	INTRON Wnt4
2L	7270546	2L_7270546_SNP [dm3] 2L_7270546_SNP [dm6]	A	T	7.047e^-5	0.95	INTRON Wnt4
2R	5344714	2R_5344714_SNP [dm3] 2R_9457209_SNP [dm6]	A	G	7.047e^-5	0.95	UPSTREAM Camta INTRON Camta
2R	2663922	2R_2663922_SNP [dm3] 2R_6776417_SNP [dm6]	C	T	7.088e^-5	0.95	UTR_5_PRIME Epac INTRON Epac	TF binding site mE1_TFBS_cad

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By genomic position
Variant impact
Gene name

pc_MB_Beta_Normal phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results