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=9.704e^-6)
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_K	0.034698

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	4.8337	0.0279
In_3R_Mo	4.9747	0.0831

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1476 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

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2R	12172163	2R_12172163_SNP [dm3] 2R_16284658_SNP [dm6]	G	T	3.530e^-6	0.991	SPLICE_SITE_REGION CG9068 INTRON CG9068	TF binding site mE1_TFBS_sens
2L	2087424	2L_2087424_SNP [dm3] 2L_2087424_SNP [dm6]	T	A	7.946e^-6	0.991	INTRON dpr3
2R	12172087	2R_12172087_SNP [dm3] 2R_16284582_SNP [dm6]	G	A	9.364e^-6	0.991	SYNONYMOUS_CODING CG9068
2R	10666304	2R_10666304_SNP [dm3] 2R_14778799_SNP [dm6]	G	A	1.197e^-5	0.991	INTRON kn	regulatory region REDfly_CRMs
3R	9536594	3R_9536594_SNP [dm3] 3R_13710872_SNP [dm6]	T	G	1.365e^-5	0.991	UTR_5_PRIME primo-1 UTR_3_PRIME primo-2 UPSTREAM CG31469 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3R	9536596	3R_9536596_SNP [dm3] 3R_13710874_SNP [dm6]	T	C	1.365e^-5	0.991	UTR_5_PRIME primo-1 UTR_3_PRIME primo-2 UPSTREAM CG31469 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3R	9536605	3R_9536605_DEL [dm3] 3R_13710883_DEL [dm6]	GTTC	G	1.365e^-5	0.991	UTR_5_PRIME primo-1 UTR_3_PRIME primo-2 UPSTREAM CG31469 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
3L	1629112	3L_1629112_SNP [dm3] 3L_1629112_SNP [dm6]	G	C	1.489e^-5	0.991	UTR_5_PRIME GC UPSTREAM CG13928	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo
2R	6859900	2R_6859900_SNP [dm3] 2R_10972395_SNP [dm6]	T	C	1.701e^-5	0.991	INTERGENIC	TF binding site mE1_TFBS_inv
2L	14820705	2L_14820705_SNP [dm3] 2L_14820705_SNP [dm6]	C	G	1.806e^-5	0.991	INTERGENIC
2L	14820713	2L_14820713_SNP [dm3] 2L_14820713_SNP [dm6]	T	C	1.806e^-5	0.991	INTERGENIC
2L	14820715	2L_14820715_SNP [dm3] 2L_14820715_SNP [dm6]	C	G	1.806e^-5	0.991	INTERGENIC
2L	14820719	2L_14820719_SNP [dm3] 2L_14820719_SNP [dm6]	A	C	1.806e^-5	0.991	INTERGENIC
2L	14820725	2L_14820725_SNP [dm3] 2L_14820725_SNP [dm6]	T	A	1.806e^-5	0.991	INTERGENIC
3L	9732926	3L_9732926_SNP [dm3] 3L_9739826_SNP [dm6]	T	A	1.929e^-5	0.991	UPSTREAM CG42268 INTRON CG42268	TF binding site mE1_TFBS_cad
3L	9732927	3L_9732927_SNP [dm3] 3L_9739827_SNP [dm6]	T	G	1.929e^-5	0.991	UPSTREAM CG42268 INTRON CG42268	TF binding site mE1_TFBS_cad
2L	21869702	2L_21869702_SNP [dm3] 2L_21869702_SNP [dm6]	A	G	2.052e^-5	0.991	DOWNSTREAM CR44920 EXON CR44917	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	21869710	2L_21869710_SNP [dm3] 2L_21869710_SNP [dm6]	G	A	2.052e^-5	0.991	DOWNSTREAM CR44920 EXON CR44917	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	13101279	3L_13101279_SNP [dm3] 3L_13108179_SNP [dm6]	A	T	2.075e^-5	0.991	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_inv
3L	3876511	3L_3876511_SNP [dm3] 3L_3876511_SNP [dm6]	A	C	2.421e^-5	0.991	INTERGENIC
3R	7113087	3R_7113087_SNP [dm3] 3R_11287365_SNP [dm6]	T	A	2.457e^-5	0.991	EXON CR31386
3L	15112978	3L_15112978_SNP [dm3] 3L_15119878_SNP [dm6]	C	A	2.487e^-5	0.991	UTR_3_PRIME CG16959 INTRON Cep135
2R	6859903	2R_6859903_SNP [dm3] 2R_10972398_SNP [dm6]	A	T	2.522e^-5	0.991	INTERGENIC	TF binding site mE1_TFBS_inv
X	15727038	X_15727038_SNP [dm3] X_15833005_SNP [dm6]	A	G	2.558e^-5	0.991	SYNONYMOUS_CODING Chc	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	706375	2L_706375_SNP [dm3] 2L_706375_SNP [dm6]	C	T	2.564e^-5	0.991	SYNONYMOUS_CODING ds	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	22679161	3R_22679161_SNP [dm3] 3R_26853439_SNP [dm6]	C	T	2.797e^-5	0.991	INTRON Lerp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	2087422	2L_2087422_SNP [dm3] 2L_2087422_SNP [dm6]	A	T	2.996e^-5	0.991	INTRON dpr3
2L	14820727	2L_14820727_SNP [dm3] 2L_14820727_SNP [dm6]	C	T	3.020e^-5	0.991	INTERGENIC
2L	14820750	2L_14820750_SNP [dm3] 2L_14820750_SNP [dm6]	G	T	3.023e^-5	0.991	INTERGENIC
3L	9174011	3L_9174011_SNP [dm3] 3L_9180911_SNP [dm6]	G	T	3.061e^-5	0.991	INTRON Rdl
2L	13874993	2L_13874993_SNP [dm3] 2L_13874993_SNP [dm6]	T	G	3.188e^-5	0.991	INTRON CenG1A
2L	2510137	2L_2510137_SNP [dm3] 2L_2510137_SNP [dm6]	C	T	3.392e^-5	0.991	INTERGENIC
2R	13688294	2R_13688294_SNP [dm3] 2R_17800789_SNP [dm6]	T	A	3.393e^-5	0.991	UPSTREAM grh DOWNSTREAM Dhit EXON CR45270	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2R	13688308	2R_13688308_SNP [dm3] 2R_17800803_SNP [dm6]	C	A	3.393e^-5	0.991	UPSTREAM grh DOWNSTREAM Dhit EXON CR45270	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	2087403	2L_2087403_SNP [dm3] 2L_2087403_SNP [dm6]	A	T	3.396e^-5	0.991	INTRON dpr3
2R	9427830	2R_9427830_SNP [dm3] 2R_13540325_SNP [dm6]	G	T	3.473e^-5	0.991	UPSTREAM CG6145 INTRON CG6145	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_Trl
3L	9174015	3L_9174015_SNP [dm3] 3L_9180915_SNP [dm6]	A	T	3.580e^-5	0.991	INTRON Rdl
3L	8637879	3L_8637879_SNP [dm3] 3L_8644779_SNP [dm6]	C	G	3.878e^-5	0.991	DOWNSTREAM CG13305 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	13497643	2R_13497643_SNP [dm3] 2R_17610138_SNP [dm6]	C	T	3.889e^-5	0.991	INTRON CG10936
2L	10967200	2L_10967200_SNP [dm3] 2L_10967200_SNP [dm6]	G	C	4.061e^-5	0.991	UPSTREAM CG33129 INTRON CG33129	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	18431724	X_18431724_SNP [dm3] X_18537691_SNP [dm6]	G	A	4.099e^-5	0.991	INTRON Bx
2L	21869704	2L_21869704_SNP [dm3] 2L_21869704_SNP [dm6]	A	C	4.307e^-5	0.991	DOWNSTREAM CR44920 EXON CR44917	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	12824466	X_12824466_SNP [dm3] X_12930433_SNP [dm6]	A	G	4.357e^-5	0.991	INTRON fne	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	11327471	2L_11327471_SNP [dm3] 2L_11327471_SNP [dm6]	C	T	4.496e^-5	0.991	INTERGENIC
3L	7981437	3L_7981437_SNP [dm3] 3L_7988337_SNP [dm6]	T	A	4.549e^-5	0.991	INTRON nmo	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	13066883	3L_13066883_SNP [dm3] 3L_13073783_SNP [dm6]	C	T	4.582e^-5	0.991	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	12313598	3L_12313598_SNP [dm3] 3L_12320498_SNP [dm6]	G	A	4.654e^-5	0.991	INTERGENIC
2L	14820708	2L_14820708_SNP [dm3] 2L_14820708_SNP [dm6]	T	A	4.684e^-5	0.991	INTERGENIC
2L	13987314	2L_13987314_SNP [dm3] 2L_13987314_SNP [dm6]	T	C	4.885e^-5	0.991	INTRON rk
3L	7420860	3L_7420860_SNP [dm3] 3L_7427760_SNP [dm6]	G	A	4.885e^-5	0.991	INTRON CG42458
2L	21869688	2L_21869688_SNP [dm3] 2L_21869688_SNP [dm6]	C	T	4.977e^-5	0.991	DOWNSTREAM CR44920 EXON CR44917	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	15727078	X_15727078_SNP [dm3] X_15833045_SNP [dm6]	G	A	5.012e^-5	0.991	SYNONYMOUS_CODING Chc	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	18431639	X_18431639_SNP [dm3] X_18537606_SNP [dm6]	C	T	5.101e^-5	0.991	INTRON Bx
X	18431697	X_18431697_SNP [dm3] X_18537664_SNP [dm6]	A	T	5.123e^-5	0.991	INTRON Bx
2L	2087437	2L_2087437_SNP [dm3] 2L_2087437_SNP [dm6]	G	A	5.189e^-5	0.991	INTRON dpr3
2L	2087373	2L_2087373_SNP [dm3] 2L_2087373_SNP [dm6]	A	G	5.233e^-5	0.991	INTRON dpr3
2L	15865753	2L_15865753_SNP [dm3] 2L_15865753_SNP [dm6]	T	A	5.286e^-5	0.991	UPSTREAM CG42792 INTERGENIC
3R	7113085	3R_7113085_SNP [dm3] 3R_11287363_SNP [dm6]	T	A	5.301e^-5	0.991	EXON CR31386
3L	15109465	3L_15109465_SNP [dm3] 3L_15116365_SNP [dm6]	G	A	5.356e^-5	0.991	UTR_3_PRIME CG13458 UPSTREAM Cep135	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
X	10085133	X_10085133_SNP [dm3] X_10191100_SNP [dm6]	G	C	5.465e^-5	0.991	NON_SYNONYMOUS_CODING CG43902 INTRON CR44894
3L	16660789	3L_16660789_SNP [dm3] 3L_16667689_SNP [dm6]	A	T	5.482e^-5	0.991	UTR_5_PRIME Galphaf	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
X	6005925	X_6005925_SNP [dm3] X_6111892_SNP [dm6]	T	A	5.616e^-5	0.991	INTRON Ca-alpha1T	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	17125028	2R_17125028_SNP [dm3] 2R_21237523_SNP [dm6]	T	G	5.942e^-5	0.991	INTRON ASPP
2L	20558100	2L_20558100_SNP [dm3] 2L_20558100_SNP [dm6]	A	T	5.953e^-5	0.991	INTERGENIC
2R	9630469	2R_9630469_SNP [dm3] 2R_13742964_SNP [dm6]	G	T	6.138e^-5	0.991	INTRON fas
3R	7461708	3R_7461708_SNP [dm3] 3R_11635986_SNP [dm6]	G	T	6.179e^-5	0.991	INTRON Csk	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	10018329	3L_10018329_SNP [dm3] 3L_10025229_SNP [dm6]	G	C	6.187e^-5	0.991	INTRON dpr6
2L	5487017	2L_5487017_DEL [dm3] 2L_5487017_DEL [dm6]	ATG	C	6.385e^-5	0.991	EXON CR45287
2L	5487022	2L_5487022_SNP [dm3] 2L_5487022_SNP [dm6]	G	T	6.385e^-5	0.991	EXON CR45287
2L	3081780	2L_3081780_SNP [dm3] 2L_3081780_SNP [dm6]	T	C	6.468e^-5	0.991	INTRON toc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	20591036	3L_20591036_SNP [dm3] 3L_20597936_SNP [dm6]	G	T	6.766e^-5	0.991	UTR_3_PRIME knrl
3L	18311535	3L_18311535_SNP [dm3] 3L_18318435_SNP [dm6]	A	T	6.865e^-5	0.991	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	11132873	3L_11132873_SNP [dm3] 3L_11139773_SNP [dm6]	G	C	6.993e^-5	0.991	INTRON CG32082
2R	12172171	2R_12172171_SNP [dm3] 2R_16284666_SNP [dm6]	T	A	7.036e^-5	0.991	INTRON CG9068	TF binding site mE1_TFBS_sens
2L	6933655	2L_6933655_SNP [dm3] 2L_6933655_SNP [dm6]	C	G	7.147e^-5	0.991	SYNONYMOUS_CODING CG18304	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	9732929	3L_9732929_INS [dm3] 3L_9739829_INS [dm6]	A	AAACTTCTAACACTT...	7.147e^-5	0.991	UPSTREAM CG42268 INTRON CG42268	TF binding site mE1_TFBS_cad
2R	8823035	2R_8823035_SNP [dm3] 2R_12935530_SNP [dm6]	G	T	7.578e^-5	0.991	INTRON CG13322	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3L	12020064	3L_12020064_SNP [dm3] 3L_12026964_SNP [dm6]	G	C	7.610e^-5	0.991	UPSTREAM CR43994 INTRON rols
2R	14152597	2R_14152597_SNP [dm3] 2R_18265092_SNP [dm6]	T	A	7.755e^-5	0.991	INTERGENIC
2L	10044419	2L_10044419_INS [dm3] 2L_10044419_INS [dm6]	C	CAGCGGAAAAAA...	7.968e^-5	0.991	INTERGENIC
2L	14823391	2L_14823391_SNP [dm3] 2L_14823391_SNP [dm6]	A	T	7.987e^-5	0.991	INTERGENIC
3L	16822690	3L_16822690_SNP [dm3] 3L_16829590_SNP [dm6]	T	C	8.110e^-5	0.991	UPSTREAM CG13024 INTERGENIC	TF binding site mE1_TFBS_HSA
2L	9192021	2L_9192021_SNP [dm3] 2L_9192021_SNP [dm6]	T	A	8.351e^-5	0.991	INTRON tai
3L	5186875	3L_5186875_SNP [dm3] 3L_5193775_SNP [dm6]	T	A	8.363e^-5	0.991	INTRON shep
3L	4529033	3L_4529033_SNP [dm3] 3L_4529033_SNP [dm6]	C	G	8.658e^-5	0.991	INTRON Tie
3L	9732935	3L_9732935_SNP [dm3] 3L_9739835_SNP [dm6]	A	G	8.741e^-5	0.991	UPSTREAM CG42268 INTRON CG42268	TF binding site mE1_TFBS_cad
3R	11106790	3R_11106790_SNP [dm3] 3R_15281068_SNP [dm6]	G	T	8.778e^-5	0.991	UPSTREAM Tm1 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
X	16932491	X_16932491_SNP [dm3] X_17038458_SNP [dm6]	C	T	8.937e^-5	0.991	INTRON CG45002
X	10085137	X_10085137_SNP [dm3] X_10191104_SNP [dm6]	G	A	9.029e^-5	0.991	SYNONYMOUS_CODING CG43902 INTRON CR44894
3L	7420876	3L_7420876_SNP [dm3] 3L_7427776_SNP [dm6]	A	G	9.071e^-5	0.991	INTRON CG42458
3L	18311546	3L_18311546_SNP [dm3] 3L_18318446_SNP [dm6]	C	T	9.084e^-5	0.991	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	2087442	2L_2087442_SNP [dm3] 2L_2087442_SNP [dm6]	T	G	9.085e^-5	0.991	INTRON dpr3
2L	2387973	2L_2387973_SNP [dm3] 2L_2387973_SNP [dm6]	A	G	9.541e^-5	0.991	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	1631148	3L_1631148_SNP [dm3] 3L_1631148_SNP [dm6]	C	T	9.596e^-5	0.991	UTR_3_PRIME nSyb DOWNSTREAM nSyb
X	16776036	X_16776036_SNP [dm3] X_16882003_SNP [dm6]	T	C	9.737e^-5	0.991	SYNONYMOUS_CODING CG4872 DOWNSTREAM CG9104	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2L	20951888	2L_20951888_SNP [dm3] 2L_20951888_SNP [dm6]	G	T	9.754e^-5	0.991	INTERGENIC
2L	20951898	2L_20951898_SNP [dm3] 2L_20951898_SNP [dm6]	A	C	9.754e^-5	0.991	INTERGENIC
X	16938971	X_16938971_SNP [dm3] X_17044938_SNP [dm6]	G	A	9.921e^-5	0.991	INTRON CG45002
3R	3142113	3R_3142113_SNP [dm3] 3R_7316391_SNP [dm6]	C	T	1.030e^-4	0.991	SYNONYMOUS_CODING CG10029
2R	12161954	2R_12161954_SNP [dm3] 2R_16274449_SNP [dm6]	A	G	1.042e^-4	0.991	NON_SYNONYMOUS_CODING CG33017

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By genomic position
Variant impact
Gene name

mn_TAG_Glycerol phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results