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=9.170e^-14)
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	0.05848
In_3R_K	1.139e-11

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	10.7304	0.0047

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2815 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
2R	19285277	2R_19285277_SNP [dm3] 2R_23397754_SNP [dm6]	G	A	6.585e^-7	0.541	SYNONYMOUS_CODING CG3520	TF binding site mE1_TFBS_chinmo
2L	9396702	2L_9396702_SNP [dm3] 2L_9396702_SNP [dm6]	C	T	1.276e^-6	0.541	DOWNSTREAM CG4438 INTRON Shawl
2L	9396551	2L_9396551_SNP [dm3] 2L_9396551_SNP [dm6]	G	A	1.331e^-6	0.541	DOWNSTREAM CG4438 INTRON Shawl
3R	9320040	3R_9320040_SNP [dm3] 3R_13494318_SNP [dm6]	G	A	3.580e^-6	0.541	INTERGENIC
X	8449016	X_8449016_DEL [dm3] X_8554983_DEL [dm6]	TT	T	3.606e^-6	0.541	UTR_3_PRIME Nrg DOWNSTREAM IntS4	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_kn
3R	19919356	3R_19919356_SNP [dm3] 3R_24093634_SNP [dm6]	A	G	3.941e^-6	0.541	INTRON 4EHP	TF binding site mE1_TFBS_HSA
3L	13353723	3L_13353723_SNP [dm3] 3L_13360623_SNP [dm6]	T	A	4.394e^-6	0.541	INTERGENIC
2L	17896790	2L_17896790_SNP [dm3] 2L_17896790_SNP [dm6]	A	T	4.690e^-6	0.541	INTERGENIC
2L	9170893	2L_9170893_SNP [dm3] 2L_9170893_SNP [dm6]	T	C	5.010e^-6	0.541	INTRON tai
3R	22354597	3R_22354597_DEL [dm3] 3R_26528875_DEL [dm6]	GG	G	5.014e^-6	0.541	INTRON plum
2R	18941838	2R_18941838_SNP [dm3] 2R_23054315_SNP [dm6]	T	A	5.046e^-6	0.541	INTERGENIC
3L	5249505	3L_5249505_SNP [dm3] 3L_5256405_SNP [dm6]	C	T	5.320e^-6	0.541	INTRON shep
2R	1349829	2R_1349829_SNP [dm3] 2R_5462324_SNP [dm6]	G	C	5.379e^-6	0.541	INTERGENIC	transposable element FlyBase
3L	4717977	3L_4717977_SNP [dm3] 3L_4717977_SNP [dm6]	C	G	5.492e^-6	0.541	INTRON RhoGEF64C
3L	10503033	3L_10503033_SNP [dm3] 3L_10509933_SNP [dm6]	G	A	5.546e^-6	0.541	INTRON A2bp1
3L	5522754	3L_5522754_SNP [dm3] 3L_5529654_SNP [dm6]	C	T	6.126e^-6	0.541	UPSTREAM Lkr INTERGENIC
2L	9839544	2L_9839544_SNP [dm3] 2L_9839544_SNP [dm6]	T	G	6.249e^-6	0.541	INTRON nAChRalpha6	TF binding site mE1_TFBS_chinmo
3R	18449823	3R_18449823_SNP [dm3] 3R_22624101_SNP [dm6]	A	G	6.437e^-6	0.541	INTRON loco	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA
2R	10584402	2R_10584402_DEL [dm3] 2R_14696897_DEL [dm6]	ATGCAAGCATCATAA...	A	6.666e^-6	0.541	INTRON mspo
2L	17890074	2L_17890074_SNP [dm3] 2L_17890074_SNP [dm6]	C	T	6.672e^-6	0.541	INTERGENIC
3R	26539873	3R_26539873_SNP [dm3] 3R_30714151_SNP [dm6]	A	G	6.739e^-6	0.541	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	10705613	2L_10705613_SNP [dm3] 2L_10705613_SNP [dm6]	A	G	6.804e^-6	0.541	DOWNSTREAM CG6415 INTRON Lip2
3R	19919361	3R_19919361_SNP [dm3] 3R_24093639_SNP [dm6]	C	G	6.833e^-6	0.541	INTRON 4EHP	TF binding site mE1_TFBS_HSA
X	5925768	X_5925768_SNP [dm3] X_6031735_SNP [dm6]	A	T	6.998e^-6	0.541	INTERGENIC	silencer mE1_HDAC_PRE
2L	10705646	2L_10705646_SNP [dm3] 2L_10705646_SNP [dm6]	C	A	7.483e^-6	0.541	DOWNSTREAM CG6415 INTRON Lip2
3R	9325710	3R_9325710_DEL [dm3] 3R_13499988_DEL [dm6]	TG	T	7.493e^-6	0.541	INTERGENIC
2L	12397204	2L_12397204_SNP [dm3] 2L_12397204_SNP [dm6]	A	T	7.988e^-6	0.549	UTR_3_PRIME bru-2
2L	10705607	2L_10705607_SNP [dm3] 2L_10705607_SNP [dm6]	C	T	8.194e^-6	0.549	DOWNSTREAM CG6415 INTRON Lip2
3R	5145301	3R_5145301_SNP [dm3] 3R_9319579_SNP [dm6]	T	G	8.665e^-6	0.56	INTRON CG8861
2L	17884043	2L_17884043_SNP [dm3] 2L_17884043_SNP [dm6]	C	T	9.037e^-6	0.562	INTERGENIC
2R	18941876	2R_18941876_SNP [dm3] 2R_23054353_SNP [dm6]	G	A	9.285e^-6	0.562	INTERGENIC
3L	17612801	3L_17612801_SNP [dm3] 3L_17619701_SNP [dm6]	C	T	9.695e^-6	0.568	UPSTREAM Eip74EF DOWNSTREAM CG6259 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
2L	22063003	2L_22063003_INS [dm3] 2L_22063003_INS [dm6]	A	AA	1.067e^-5	0.573	INTERGENIC
2L	17890082	2L_17890082_SNP [dm3] 2L_17890082_SNP [dm6]	A	G	1.073e^-5	0.573	INTERGENIC
3L	15855565	3L_15855565_SNP [dm3] 3L_15862465_SNP [dm6]	C	T	1.127e^-5	0.573	DOWNSTREAM pHCl INTRON pHCl
2R	2774803	2R_2774803_SNP [dm3] 2R_6887298_SNP [dm6]	G	C	1.176e^-5	0.573	NON_SYNONYMOUS_CODING Spn42De
3L	10503135	3L_10503135_SNP [dm3] 3L_10510035_SNP [dm6]	T	C	1.193e^-5	0.573	INTRON A2bp1
3R	7687403	3R_7687403_SNP [dm3] 3R_11861681_SNP [dm6]	A	T	1.200e^-5	0.573	INTRON CG6959
3R	9886639	3R_9886639_DEL [dm3] 3R_14060917_DEL [dm6]	AA	T	1.207e^-5	0.573	INTRON foxo	TF binding site mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA
3R	18526806	3R_18526806_SNP [dm3] 3R_22701084_SNP [dm6]	A	G	1.302e^-5	0.573	UPSTREAM CG6972 DOWNSTREAM Cyp6d4 INTRON CCAP
2R	4577936	2R_4577936_SNP [dm3] 2R_8690431_SNP [dm6]	G	T	1.309e^-5	0.573	INTERGENIC
2L	8060382	2L_8060382_SNP [dm3] 2L_8060382_SNP [dm6]	G	A	1.348e^-5	0.573	SYNONYMOUS_CODING poe
3R	27431292	3R_27431292_SNP [dm3] 3R_31605570_SNP [dm6]	G	T	1.348e^-5	0.573	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
3L	10503050	3L_10503050_SNP [dm3] 3L_10509950_SNP [dm6]	T	C	1.355e^-5	0.573	INTRON A2bp1
3R	9226136	3R_9226136_DEL [dm3] 3R_13400414_DEL [dm6]	TTAGTTAT	T	1.429e^-5	0.573	INTRON CG9796
3L	10503024	3L_10503024_INS [dm3] 3L_10509924_INS [dm6]	G	GCATTT	1.448e^-5	0.573	INTRON A2bp1
X	11003989	X_11003989_DEL [dm3] X_11109956_DEL [dm6]	TCTGCCC	G	1.494e^-5	0.573	INTRON Hsp60	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
3L	17216457	3L_17216457_SNP [dm3] 3L_17223357_SNP [dm6]	T	A	1.540e^-5	0.573	INTRON Rbp6
3L	5740815	3L_5740815_SNP [dm3] 3L_5747715_SNP [dm6]	G	A	1.555e^-5	0.573	UTR_3_PRIME sif
3L	15855570	3L_15855570_SNP [dm3] 3L_15862470_SNP [dm6]	T	A	1.623e^-5	0.573	DOWNSTREAM pHCl INTRON pHCl
2L	16571455	2L_16571455_SNP [dm3] 2L_16571455_SNP [dm6]	G	A	1.635e^-5	0.573	INTRON CG42389
2R	8554001	2R_8554001_SNP [dm3] 2R_12666496_SNP [dm6]	C	A	1.669e^-5	0.573	UPSTREAM nemy INTRON nemy	TF binding site mE1_TFBS_bab1
2R	3812654	2R_3812654_SNP [dm3] 2R_7925149_SNP [dm6]	A	T	1.722e^-5	0.573	UPSTREAM Kdm4A INTERGENIC	TF binding site BDTNP1_TFBS_prd
2L	11871932	2L_11871932_SNP [dm3] 2L_11871932_SNP [dm6]	T	C	1.726e^-5	0.573	INTRON Pde1c
2R	17070153	2R_17070153_SNP [dm3] 2R_21182648_SNP [dm6]	T	C	1.734e^-5	0.573	UPSTREAM tRNA:G3:57BCb & 1 other DOWNSTREAM tRNA:CR30209 & 1 other INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	25978234	3R_25978234_SNP [dm3] 3R_30152512_SNP [dm6]	G	A	1.751e^-5	0.573	DOWNSTREAM CG11498 INTRON CG15529	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	9099916	3R_9099916_SNP [dm3] 3R_13274194_SNP [dm6]	C	G	1.759e^-5	0.573	INTERGENIC
X	12377374	X_12377374_SNP [dm3] X_12483341_SNP [dm6]	C	T	1.771e^-5	0.573	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	9128501	2R_9128501_SNP [dm3] 2R_13240996_SNP [dm6]	A	G	1.852e^-5	0.585	UTR_3_PRIME GstE14	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	9295709	3R_9295709_SNP [dm3] 3R_13469987_SNP [dm6]	A	T	1.895e^-5	0.585	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	10605253	2R_10605253_SNP [dm3] 2R_14717748_SNP [dm6]	C	A	1.910e^-5	0.585	INTERGENIC
3L	14692391	3L_14692391_SNP [dm3] 3L_14699291_SNP [dm6]	G	A	1.962e^-5	0.585	NON_SYNONYMOUS_CODING CG17177 UPSTREAM CG17177 INTRON ome
X	18065671	X_18065671_SNP [dm3] X_18171638_SNP [dm6]	C	T	1.982e^-5	0.585	UTR_3_PRIME Frq1
3R	19919315	3R_19919315_SNP [dm3] 3R_24093593_SNP [dm6]	G	A	2.050e^-5	0.585	INTRON 4EHP	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	10503022	3L_10503022_SNP [dm3] 3L_10509922_SNP [dm6]	A	T	2.091e^-5	0.585	INTRON A2bp1
3L	13353696	3L_13353696_SNP [dm3] 3L_13360596_SNP [dm6]	T	A	2.098e^-5	0.585	INTERGENIC
2L	10721693	2L_10721693_SNP [dm3] 2L_10721693_SNP [dm6]	C	A	2.102e^-5	0.585	INTERGENIC
3L	747152	3L_747152_SNP [dm3] 3L_747152_SNP [dm6]	T	A	2.132e^-5	0.585	INTRON hng3	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	9099940	3R_9099940_SNP [dm3] 3R_13274218_SNP [dm6]	T	C	2.151e^-5	0.585	INTERGENIC
2R	6263633	2R_6263633_SNP [dm3] 2R_10376128_SNP [dm6]	T	G	2.208e^-5	0.592	DOWNSTREAM Ir47b & 1 other INTRON CG42732
2L	10705633	2L_10705633_SNP [dm3] 2L_10705633_SNP [dm6]	T	C	2.272e^-5	0.6	DOWNSTREAM CG6415 INTRON Lip2
3R	24508657	3R_24508657_SNP [dm3] 3R_28682935_SNP [dm6]	G	A	2.341e^-5	0.6	INTRON CG9990	TF binding site BDTNP1_TFBS_z
3R	19919338	3R_19919338_SNP [dm3] 3R_24093616_SNP [dm6]	A	C	2.401e^-5	0.6	INTRON 4EHP	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	9172081	2L_9172081_SNP [dm3] 2L_9172081_SNP [dm6]	G	A	2.474e^-5	0.6	INTRON tai
3L	16954178	3L_16954178_SNP [dm3] 3L_16961078_SNP [dm6]	C	T	2.478e^-5	0.6	INTRON Nc73EF
2L	10705624	2L_10705624_SNP [dm3] 2L_10705624_SNP [dm6]	C	T	2.581e^-5	0.6	DOWNSTREAM CG6415 INTRON Lip2
3R	19919350	3R_19919350_SNP [dm3] 3R_24093628_SNP [dm6]	A	G	2.593e^-5	0.6	INTRON 4EHP	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	12564163	3R_12564163_SNP [dm3] 3R_16738441_SNP [dm6]	A	G	2.597e^-5	0.6	INTERGENIC	TF binding site mE1_TFBS_cad
3L	10503194	3L_10503194_SNP [dm3] 3L_10510094_SNP [dm6]	G	A	2.601e^-5	0.6	INTRON A2bp1
3L	8330183	3L_8330183_SNP [dm3] 3L_8337083_SNP [dm6]	A	C	2.605e^-5	0.6	INTRON Cpr66Cb
2L	12397211	2L_12397211_SNP [dm3] 2L_12397211_SNP [dm6]	C	A	2.625e^-5	0.6	UTR_3_PRIME bru-2
3L	783346	3L_783346_INS [dm3] 3L_783346_INS [dm6]	C	CGC	2.639e^-5	0.6	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	5530365	2R_5530365_SNP [dm3] 2R_9642860_SNP [dm6]	A	T	2.666e^-5	0.6	INTRON Mmp2
3R	12718689	3R_12718689_SNP [dm3] 3R_16892967_SNP [dm6]	C	A	2.693e^-5	0.6	UPSTREAM iab-8 INTRON iab-8 EXON CR43617	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13353416	3L_13353416_SNP [dm3] 3L_13360316_SNP [dm6]	A	C	2.719e^-5	0.6	INTERGENIC
3L	13353778	3L_13353778_SNP [dm3] 3L_13360678_SNP [dm6]	C	A	2.850e^-5	0.602	INTERGENIC
3L	5252865	3L_5252865_SNP [dm3] 3L_5259765_SNP [dm6]	T	C	2.870e^-5	0.602	INTRON shep
3L	5642397	3L_5642397_SNP [dm3] 3L_5649297_SNP [dm6]	T	A	2.887e^-5	0.602	UTR_3_PRIME Blimp-1 DOWNSTREAM Blimp-1
2L	21793557	2L_21793557_SNP [dm3] 2L_21793557_SNP [dm6]	G	T	2.894e^-5	0.602	INTRON CG31612	TF binding site BDTNP1_TFBS_z
3L	8026140	3L_8026140_SNP [dm3] 3L_8033040_SNP [dm6]	T	C	2.924e^-5	0.602	INTRON nmo
X	11003998	X_11003998_INS [dm3] X_11109965_INS [dm6]	G	GCTCTTGG	2.977e^-5	0.602	INTRON Hsp60	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo
3L	10503136	3L_10503136_SNP [dm3] 3L_10510036_SNP [dm6]	C	A	2.986e^-5	0.602	INTRON A2bp1
3R	9312331	3R_9312331_INS [dm3] 3R_13486609_INS [dm6]	T	TT	2.987e^-5	0.602	INTERGENIC
3R	10420289	3R_10420289_SNP [dm3] 3R_14594567_SNP [dm6]	A	T	3.064e^-5	0.603	INTRON stumps	regulatory region REDfly_CRMs
2R	11521580	2R_11521580_SNP [dm3] 2R_15634075_SNP [dm6]	C	T	3.082e^-5	0.603	INTRON CG42524
3L	12310472	3L_12310472_SNP [dm3] 3L_12317372_SNP [dm6]	C	G	3.138e^-5	0.603	INTERGENIC
3R	25315206	3R_25315206_SNP [dm3] 3R_29489484_SNP [dm6]	A	C	3.177e^-5	0.603	UTR_5_PRIME CG2006 UPSTREAM CG2321	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	13857300	2R_13857300_SNP [dm3] 2R_17969795_SNP [dm6]	G	A	3.254e^-5	0.603	INTERGENIC
3R	12718931	3R_12718931_SNP [dm3] 3R_16893209_SNP [dm6]	T	G	3.270e^-5	0.603	INTRON iab-8 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	23947382	3R_23947382_DEL [dm3] 3R_28121660_DEL [dm6]	AA	A	3.288e^-5	0.603	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

TotalVariants_3L phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results