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=3.234e^-13)
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
wolba	0.06403
In_2L_t	0.02707

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.7412	0.0344
In_3R_K	5.3994	0.0672

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2286 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	15055734	3L_15055734_SNP [dm3] 3L_15062634_SNP [dm6]	T	C	1.178e^-7	0.221	UPSTREAM CG13460 & 1 other INTRON Sytbeta
3R	17370221	3R_17370221_SNP [dm3] 3R_21544499_SNP [dm6]	C	A	1.409e^-6	0.56	INTERGENIC	TF binding site BDTNP1_TFBS_prd
3R	10249528	3R_10249528_SNP [dm3] 3R_14423806_SNP [dm6]	A	G	1.487e^-6	0.56	INTRON cv-c
2L	11334482	2L_11334482_INS [dm3] 2L_11334482_INS [dm6]	G	GG	1.504e^-6	0.56	INTERGENIC
3R	17618570	3R_17618570_SNP [dm3] 3R_21792848_SNP [dm6]	A	G	1.597e^-6	0.56	INTRON CASK	TF binding site mE1_TFBS_cad
3L	11142376	3L_11142376_SNP [dm3] 3L_11149276_SNP [dm6]	G	A	1.793e^-6	0.56	DOWNSTREAM CG6216 INTRON CG32082
3L	15881100	3L_15881100_SNP [dm3] 3L_15888000_SNP [dm6]	A	G	3.197e^-6	0.701	INTRON pHCl
3L	4410601	3L_4410601_SNP [dm3] 3L_4410601_SNP [dm6]	T	C	3.791e^-6	0.701	INTRON DOR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3L	4410596	3L_4410596_SNP [dm3] 3L_4410596_SNP [dm6]	T	A	4.376e^-6	0.701	INTRON DOR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3R	24205174	3R_24205174_SNP [dm3] 3R_28379452_SNP [dm6]	A	G	4.387e^-6	0.701	INTERGENIC
3L	4410589	3L_4410589_SNP [dm3] 3L_4410589_SNP [dm6]	T	G	4.412e^-6	0.701	INTRON DOR	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
X	5449728	X_5449728_SNP [dm3] X_5555695_SNP [dm6]	C	A	4.486e^-6	0.701	INTRON Vsx2	TF binding site mE1_TFBS_cnc mE1_TFBS_Kr
3L	15889722	3L_15889722_SNP [dm3] 3L_15896622_SNP [dm6]	A	G	6.207e^-6	0.757	INTRON pHCl
3L	7799372	3L_7799372_SNP [dm3] 3L_7806272_SNP [dm6]	T	G	6.637e^-6	0.757	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
3L	18364980	3L_18364980_SNP [dm3] 3L_18371880_SNP [dm6]	C	T	6.785e^-6	0.757	INTERGENIC
3R	17365836	3R_17365836_SNP [dm3] 3R_21540114_SNP [dm6]	A	T	7.033e^-6	0.757	INTERGENIC
3L	12853414	3L_12853414_SNP [dm3] 3L_12860314_SNP [dm6]	A	G	7.114e^-6	0.757	SYNONYMOUS_CODING CG32107	TF binding site mE1_TFBS_sens
3L	8675181	3L_8675181_SNP [dm3] 3L_8682081_SNP [dm6]	G	A	7.262e^-6	0.757	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
3L	8607436	3L_8607436_SNP [dm3] 3L_8614336_SNP [dm6]	C	T	8.323e^-6	0.794	INTRON CG6282
2L	13539501	2L_13539501_SNP [dm3] 2L_13539501_SNP [dm6]	G	A	9.177e^-6	0.794	INTRON B4
3L	5775282	3L_5775282_SNP [dm3] 3L_5782182_SNP [dm6]	A	C	9.419e^-6	0.794	NON_SYNONYMOUS_CODING PGRP-LD UTR_3_PRIME Pmi
3L	7799375	3L_7799375_SNP [dm3] 3L_7806275_SNP [dm6]	C	T	1.062e^-5	0.794	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
3R	18651406	3R_18651406_SNP [dm3] 3R_22825684_SNP [dm6]	C	T	1.145e^-5	0.794	EXON CR44350
3L	12853276	3L_12853276_SNP [dm3] 3L_12860176_SNP [dm6]	G	A	1.154e^-5	0.794	SYNONYMOUS_CODING CG32107	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	9269114	2R_9269114_SNP [dm3] 2R_13381609_SNP [dm6]	T	G	1.184e^-5	0.794	INTERGENIC
X	8418184	X_8418184_SNP [dm3] X_8524151_SNP [dm6]	T	A	1.202e^-5	0.794	INTRON Nrg	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	15886584	3L_15886584_SNP [dm3] 3L_15893484_SNP [dm6]	G	A	1.210e^-5	0.794	INTRON pHCl
2R	8294112	2R_8294112_SNP [dm3] 2R_12406607_SNP [dm6]	T	C	1.253e^-5	0.794	UTR_3_PRIME Cpr49Af DOWNSTREAM Cpr49Af
2R	14762500	2R_14762500_SNP [dm3] 2R_18874995_SNP [dm6]	A	C	1.254e^-5	0.794	INTERGENIC
3L	12853279	3L_12853279_SNP [dm3] 3L_12860179_SNP [dm6]	A	G	1.326e^-5	0.794	SYNONYMOUS_CODING CG32107	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	8634391	3L_8634391_SNP [dm3] 3L_8641291_SNP [dm6]	T	A	1.377e^-5	0.794	INTRON Cpr66D
3R	17618547	3R_17618547_SNP [dm3] 3R_21792825_SNP [dm6]	C	A	1.662e^-5	0.794	INTRON CASK	TF binding site mE1_TFBS_cad
X	8466240	X_8466240_SNP [dm3] X_8572207_SNP [dm6]	G	A	1.686e^-5	0.794	SYNONYMOUS_CODING spirit	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7799352	3L_7799352_SNP [dm3] 3L_7806252_SNP [dm6]	C	T	1.688e^-5	0.794	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
3L	7799380	3L_7799380_SNP [dm3] 3L_7806280_SNP [dm6]	G	A	1.691e^-5	0.794	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
X	3426860	X_3426860_SNP [dm3] X_3532827_SNP [dm6]	T	G	1.722e^-5	0.794	INTRON CG32791
X	11051264	X_11051264_SNP [dm3] X_11157231_SNP [dm6]	G	A	1.755e^-5	0.794	SYNONYMOUS_CODING CG32668 INTRON Dlic	TF binding site mE1_TFBS_sens
2R	12637185	2R_12637185_SNP [dm3] 2R_16749680_SNP [dm6]	G	A	1.794e^-5	0.794	UPSTREAM Acp53C14b DOWNSTREAM Acp53Ea INTERGENIC
3L	23033953	3L_23033953_SNP [dm3] 3L_23040853_SNP [dm6]	T	A	1.944e^-5	0.794	DOWNSTREAM nrm INTERGENIC
2R	6058050	2R_6058050_SNP [dm3] 2R_10170545_SNP [dm6]	C	T	2.080e^-5	0.794	INTRON KCNQ
2L	7812417	2L_7812417_SNP [dm3] 2L_7812417_SNP [dm6]	C	A	2.246e^-5	0.794	INTRON LanB1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	17055258	3R_17055258_SNP [dm3] 3R_21229536_SNP [dm6]	T	G	2.290e^-5	0.794	DOWNSTREAM e & 1 other INTERGENIC
3R	5366433	3R_5366433_SNP [dm3] 3R_9540711_SNP [dm6]	A	T	2.290e^-5	0.794	SYNONYMOUS_CODING mura	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	10597846	2R_10597846_INS [dm3] 2R_14710341_INS [dm6]	A	AA	2.315e^-5	0.794	INTRON mspo
3R	9882385	3R_9882385_DEL [dm3] 3R_14056663_DEL [dm6]	ATAG	T	2.344e^-5	0.794	UPSTREAM foxo INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	1414405	3L_1414405_SNP [dm3] 3L_1414405_SNP [dm6]	C	T	2.350e^-5	0.794	INTRON Ptp61F	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
X	6323115	X_6323115_SNP [dm3] X_6429082_SNP [dm6]	T	G	2.395e^-5	0.794	INTRON CG42340
2L	7813951	2L_7813951_SNP [dm3] 2L_7813951_SNP [dm6]	T	C	2.452e^-5	0.794	UPSTREAM LanB1 INTRON LanB1
3L	7799586	3L_7799586_SNP [dm3] 3L_7806486_SNP [dm6]	G	C	2.552e^-5	0.794	INTRON CG32369	TF binding site mE1_TFBS_Trl
3L	14134595	3L_14134595_DEL [dm3] 3L_14141495_DEL [dm6]	AAA	A	2.578e^-5	0.794	INTERGENIC	regulatory region REDfly_CRMs
3R	23337364	3R_23337364_SNP [dm3] 3R_27511642_SNP [dm6]	C	G	2.602e^-5	0.794	INTERGENIC
2L	4523664	2L_4523664_SNP [dm3] 2L_4523664_SNP [dm6]	A	C	2.617e^-5	0.794	INTRON dp
2R	10956731	2R_10956731_SNP [dm3] 2R_15069226_SNP [dm6]	C	T	2.677e^-5	0.794	INTERGENIC
3L	450240	3L_450240_SNP [dm3] 3L_450240_SNP [dm6]	T	C	2.720e^-5	0.794	INTRON klar
3R	18651445	3R_18651445_SNP [dm3] 3R_22825723_SNP [dm6]	G	A	2.739e^-5	0.794	EXON CR44350
3L	7330950	3L_7330950_SNP [dm3] 3L_7337850_SNP [dm6]	T	C	2.784e^-5	0.794	NON_SYNONYMOUS_CODING eco	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	4523681	2L_4523681_SNP [dm3] 2L_4523681_SNP [dm6]	G	A	2.860e^-5	0.794	INTRON dp
3L	1738266	3L_1738266_SNP [dm3] 3L_1738266_SNP [dm6]	A	T	2.943e^-5	0.794	UPSTREAM Gk & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_hb
3L	9819590	3L_9819590_SNP [dm3] 3L_9826490_SNP [dm6]	A	C	3.014e^-5	0.794	SYNONYMOUS_CODING CG43897 INTRON CG43897
3L	9566611	3L_9566611_SNP [dm3] 3L_9573511_SNP [dm6]	A	C	3.066e^-5	0.794	INTRON CG42673
3R	24194442	3R_24194442_SNP [dm3] 3R_28368720_SNP [dm6]	C	T	3.147e^-5	0.794	INTERGENIC
3L	11924188	3L_11924188_SNP [dm3] 3L_11931088_SNP [dm6]	T	C	3.171e^-5	0.794	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	9819557	3L_9819557_SNP [dm3] 3L_9826457_SNP [dm6]	C	A	3.176e^-5	0.794	SYNONYMOUS_CODING CG43897 INTRON CG43897
3R	18651398	3R_18651398_SNP [dm3] 3R_22825676_SNP [dm6]	C	T	3.177e^-5	0.794	EXON CR44350
3R	17618513	3R_17618513_SNP [dm3] 3R_21792791_SNP [dm6]	A	C	3.196e^-5	0.794	INTRON CASK	TF binding site mE1_TFBS_cad
X	17243971	X_17243971_SNP [dm3] X_17349938_SNP [dm6]	C	T	3.349e^-5	0.794	INTERGENIC
3L	9627046	3L_9627046_SNP [dm3] 3L_9633946_SNP [dm6]	G	A	3.600e^-5	0.794	INTRON fry	TF binding site mE1_TFBS_cad
3R	19703870	3R_19703870_SNP [dm3] 3R_23878148_SNP [dm6]	A	G	3.613e^-5	0.794	INTRON Pli
2R	14762345	2R_14762345_SNP [dm3] 2R_18874840_SNP [dm6]	C	A	3.623e^-5	0.794	INTERGENIC
3L	15889772	3L_15889772_SNP [dm3] 3L_15896672_SNP [dm6]	G	A	3.716e^-5	0.794	INTRON pHCl
3R	21279810	3R_21279810_INS [dm3] 3R_25454088_INS [dm6]	G	GCACTTATAAGTGTAAG...	3.729e^-5	0.794	INTRON Fur1
3L	7799176	3L_7799176_SNP [dm3] 3L_7806076_SNP [dm6]	T	C	3.738e^-5	0.794	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
3L	5774228	3L_5774228_SNP [dm3] 3L_5781128_SNP [dm6]	C	T	3.775e^-5	0.794	START_GAINED PGRP-LD UTR_5_PRIME PGRP-LD UTR_3_PRIME Pmi UPSTREAM PGRP-LD & 1 other INTRON PGRP-LD & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	7331186	3L_7331186_SNP [dm3] 3L_7338086_SNP [dm6]	C	T	3.816e^-5	0.794	NON_SYNONYMOUS_CODING eco	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	7719578	2R_7719578_SNP [dm3] 2R_11832073_SNP [dm6]	A	G	3.825e^-5	0.794	INTRON Sobp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	18370650	2R_18370650_SNP [dm3] 2R_22483145_SNP [dm6]	T	G	3.869e^-5	0.794	UPSTREAM CG4554 DOWNSTREAM CG4752 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	14762153	2R_14762153_SNP [dm3] 2R_18874648_SNP [dm6]	C	A	3.920e^-5	0.794	INTERGENIC
X	2477618	X_2477618_SNP [dm3] X_2583585_SNP [dm6]	C	G	3.938e^-5	0.794	SYNONYMOUS_CODING CG13759 DOWNSTREAM CG13760	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	9627055	3L_9627055_SNP [dm3] 3L_9633955_SNP [dm6]	G	A	3.966e^-5	0.794	INTRON fry	TF binding site mE1_TFBS_cad
3L	14372394	3L_14372394_SNP [dm3] 3L_14379294_SNP [dm6]	C	T	4.042e^-5	0.794	INTERGENIC
3L	14941736	3L_14941736_SNP [dm3] 3L_14948636_SNP [dm6]	G	A	4.080e^-5	0.794	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
3R	17055240	3R_17055240_SNP [dm3] 3R_21229518_SNP [dm6]	A	C	4.097e^-5	0.794	DOWNSTREAM e & 1 other INTERGENIC
3L	9824838	3L_9824838_SNP [dm3] 3L_9831738_SNP [dm6]	A	T	4.282e^-5	0.794	INTRON CG43897
2R	14303689	2R_14303689_SNP [dm3] 2R_18416184_SNP [dm6]	C	T	4.358e^-5	0.794	SYNONYMOUS_CODING Dp1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	7812421	2L_7812421_SNP [dm3] 2L_7812421_SNP [dm6]	A	G	4.399e^-5	0.794	INTRON LanB1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	20682224	2L_20682224_DEL [dm3] 2L_20682224_DEL [dm6]	ATATA	A	4.445e^-5	0.794	UPSTREAM CG2617 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	15250918	3R_15250918_SNP [dm3] 3R_19425196_SNP [dm6]	T	A	4.470e^-5	0.794	UTR_5_PRIME CG3517 INTRON CG31221	TF binding site mE1_TFBS_cad
X	5449785	X_5449785_SNP [dm3] X_5555752_SNP [dm6]	G	A	4.607e^-5	0.794	INTRON Vsx2	TF binding site mE1_TFBS_Kr
2L	13702736	2L_13702736_SNP [dm3] 2L_13702736_SNP [dm6]	C	T	4.655e^-5	0.794	INTRON CG31814
3L	9819560	3L_9819560_SNP [dm3] 3L_9826460_SNP [dm6]	A	C	4.761e^-5	0.794	SYNONYMOUS_CODING CG43897 INTRON CG43897
X	11051435	X_11051435_SNP [dm3] X_11157402_SNP [dm6]	C	T	4.779e^-5	0.794	SYNONYMOUS_CODING CG32668 INTRON Dlic	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	11051447	X_11051447_SNP [dm3] X_11157414_SNP [dm6]	G	A	4.779e^-5	0.794	SYNONYMOUS_CODING CG32668 INTRON Dlic	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	11051474	X_11051474_SNP [dm3] X_11157441_SNP [dm6]	G	A	4.779e^-5	0.794	SYNONYMOUS_CODING CG32668 INTRON Dlic	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	14093531	3R_14093531_SNP [dm3] 3R_18267809_SNP [dm6]	G	C	4.824e^-5	0.794	UTR_5_PRIME CG18599	TF binding site mE1_TFBS_run
2L	3236091	2L_3236091_SNP [dm3] 2L_3236091_SNP [dm6]	A	C	4.830e^-5	0.794	INTERGENIC
3L	9566619	3L_9566619_SNP [dm3] 3L_9573519_SNP [dm6]	G	T	4.903e^-5	0.794	INTRON CG42673
2L	9157681	2L_9157681_SNP [dm3] 2L_9157681_SNP [dm6]	A	G	4.905e^-5	0.794	INTRON CG32982	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	12653896	2R_12653896_SNP [dm3] 2R_16766391_SNP [dm6]	C	T	4.938e^-5	0.794	UPSTREAM CG5348 & 2 others INTRON unc-104
2L	2430940	2L_2430940_SNP [dm3] 2L_2430940_SNP [dm6]	T	C	4.968e^-5	0.794	INTRON dpp
3L	11924175	3L_11924175_DEL [dm3] 3L_11931075_DEL [dm6]	TT	T	5.037e^-5	0.794	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

pc_Surv_MeHg_10 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results