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=1.822e^-4)
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

2516 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	16290821	2R_16290821_SNP [dm3] 2R_20403316_SNP [dm6]	C	T	1.360e^-6	0.624	INTERGENIC
2R	14762500	2R_14762500_SNP [dm3] 2R_18874995_SNP [dm6]	A	C	1.380e^-6	0.624	INTERGENIC
3L	23033953	3L_23033953_SNP [dm3] 3L_23040853_SNP [dm6]	T	A	1.509e^-6	0.624	DOWNSTREAM nrm INTERGENIC
3R	10766286	3R_10766286_SNP [dm3] 3R_14940564_SNP [dm6]	G	C	1.984e^-6	0.624	INTERGENIC
2R	17299063	2R_17299063_SNP [dm3] 2R_21411558_SNP [dm6]	A	G	2.098e^-6	0.624	INTRON Sdc
2L	12285953	2L_12285953_SNP [dm3] 2L_12285953_SNP [dm6]	G	T	2.357e^-6	0.624	INTRON aret
2R	14762345	2R_14762345_SNP [dm3] 2R_18874840_SNP [dm6]	C	A	4.005e^-6	0.624	INTERGENIC
3L	8875006	3L_8875006_DEL [dm3] 3L_8881906_DEL [dm6]	CC	C	4.273e^-6	0.624	INTRON dally
3L	996409	3L_996409_SNP [dm3] 3L_996409_SNP [dm6]	T	C	5.442e^-6	0.624	UTR_3_PRIME trio DOWNSTREAM CG12038 & 1 other
2L	9463981	2L_9463981_SNP [dm3] 2L_9463981_SNP [dm6]	A	G	6.240e^-6	0.624	UTR_3_PRIME numb DOWNSTREAM numb
3L	15886584	3L_15886584_SNP [dm3] 3L_15893484_SNP [dm6]	G	A	6.346e^-6	0.624	INTRON pHCl
2L	7812417	2L_7812417_SNP [dm3] 2L_7812417_SNP [dm6]	C	A	6.440e^-6	0.624	INTRON LanB1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	15284967	3L_15284967_SNP [dm3] 3L_15291867_SNP [dm6]	G	C	7.110e^-6	0.624	INTERGENIC
2L	4023666	2L_4023666_SNP [dm3] 2L_4023666_SNP [dm6]	G	A	7.272e^-6	0.624	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	7330950	3L_7330950_SNP [dm3] 3L_7337850_SNP [dm6]	T	C	7.459e^-6	0.624	NON_SYNONYMOUS_CODING eco	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	15240481	3R_15240481_SNP [dm3] 3R_19414759_SNP [dm6]	T	C	7.498e^-6	0.624	INTRON CG31221
3L	4174670	3L_4174670_SNP [dm3] 3L_4174670_SNP [dm6]	G	C	7.806e^-6	0.624	SPLICE_SITE_REGION CG18675 DOWNSTREAM Ero1L & 1 other INTRON CG18675
3L	7221362	3L_7221362_SNP [dm3] 3L_7228262_SNP [dm6]	A	G	8.063e^-6	0.624	INTERGENIC
3R	15240427	3R_15240427_SNP [dm3] 3R_19414705_SNP [dm6]	C	G	8.114e^-6	0.624	INTRON CG31221
3L	15881100	3L_15881100_SNP [dm3] 3L_15888000_SNP [dm6]	A	G	8.367e^-6	0.624	INTRON pHCl
2R	15038134	2R_15038134_SNP [dm3] 2R_19150629_SNP [dm6]	T	A	8.522e^-6	0.624	INTRON ena	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	7331186	3L_7331186_SNP [dm3] 3L_7338086_SNP [dm6]	C	T	9.201e^-6	0.624	NON_SYNONYMOUS_CODING eco	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	8699375	3L_8699375_SNP [dm3] 3L_8706275_SNP [dm6]	C	T	9.770e^-6	0.624	INTERGENIC	TF binding site mE1_TFBS_cad
2R	13946850	2R_13946850_SNP [dm3] 2R_18059345_SNP [dm6]	A	G	1.028e^-5	0.624	UPSTREAM CR45314 INTERGENIC
2R	16173632	2R_16173632_SNP [dm3] 2R_20286127_SNP [dm6]	T	C	1.042e^-5	0.624	SYNONYMOUS_CODING CG16868	TF binding site mE1_TFBS_sens
3L	2392244	3L_2392244_SNP [dm3] 3L_2392244_SNP [dm6]	A	C	1.055e^-5	0.624	INTRON CG45186
2L	12280030	2L_12280030_SNP [dm3] 2L_12280030_SNP [dm6]	C	A	1.151e^-5	0.624	INTRON aret
2L	9463006	2L_9463006_SNP [dm3] 2L_9463006_SNP [dm6]	T	G	1.216e^-5	0.624	UTR_3_PRIME numb
3L	995303	3L_995303_SNP [dm3] 3L_995303_SNP [dm6]	C	T	1.279e^-5	0.624	SYNONYMOUS_CODING CG12038 DOWNSTREAM trio	TF binding site mE1_TFBS_cad
3R	11596080	3R_11596080_SNP [dm3] 3R_15770358_SNP [dm6]	A	T	1.343e^-5	0.624	INTERGENIC
X	11627399	X_11627399_SNP [dm3] X_11733366_SNP [dm6]	T	A	1.396e^-5	0.624	UPSTREAM inaF-B INTRON CG15221 & 1 other
X	11627405	X_11627405_SNP [dm3] X_11733372_SNP [dm6]	G	T	1.431e^-5	0.624	UPSTREAM inaF-B INTRON CG15221 & 1 other
X	11627415	X_11627415_SNP [dm3] X_11733382_SNP [dm6]	C	T	1.483e^-5	0.624	UPSTREAM inaF-B INTRON CG15221 & 1 other
3L	4174699	3L_4174699_SNP [dm3] 3L_4174699_SNP [dm6]	T	C	1.509e^-5	0.624	DOWNSTREAM Ero1L & 1 other INTRON CG18675
2L	17563702	2L_17563702_SNP [dm3] 2L_17563702_SNP [dm6]	G	A	1.528e^-5	0.624	INTERGENIC
3L	7799372	3L_7799372_SNP [dm3] 3L_7806272_SNP [dm6]	T	G	1.546e^-5	0.624	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
3R	14093531	3R_14093531_SNP [dm3] 3R_18267809_SNP [dm6]	G	C	1.551e^-5	0.624	UTR_5_PRIME CG18599	TF binding site mE1_TFBS_run
2L	9551241	2L_9551241_SNP [dm3] 2L_9551241_SNP [dm6]	C	G	1.780e^-5	0.624	UPSTREAM jp INTRON jp
X	6208047	X_6208047_SNP [dm3] X_6314014_SNP [dm6]	T	C	1.801e^-5	0.624	INTRON CG15894
3L	4709865	3L_4709865_SNP [dm3] 3L_4709865_SNP [dm6]	T	C	1.812e^-5	0.624	UTR_5_PRIME CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4709870	3L_4709870_SNP [dm3] 3L_4709870_SNP [dm6]	A	C	1.812e^-5	0.624	UTR_5_PRIME CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	8874976	3L_8874976_MNP [dm3] 3L_8881876_MNP [dm6]	CAT	TGA	1.818e^-5	0.624	INTRON dally
3L	8875004	3L_8875004_SNP [dm3] 3L_8881904_SNP [dm6]	T	C	1.818e^-5	0.624	INTRON dally
X	12990471	X_12990471_SNP [dm3] X_13096438_SNP [dm6]	A	T	2.032e^-5	0.624	UTR_3_PRIME CG43313 DOWNSTREAM CG2200	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	7484924	2L_7484924_SNP [dm3] 2L_7484924_SNP [dm6]	G	C	2.033e^-5	0.624	INTRON Ziz
2R	17092769	2R_17092769_SNP [dm3] 2R_21205264_SNP [dm6]	T	C	2.034e^-5	0.624	SYNONYMOUS_CODING Glycogenin INTRON CG44245
2R	16173290	2R_16173290_SNP [dm3] 2R_20285785_SNP [dm6]	T	C	2.037e^-5	0.624	SYNONYMOUS_CODING CG16868	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	14072021	2R_14072021_SNP [dm3] 2R_18184516_SNP [dm6]	C	T	2.056e^-5	0.624	UTR_3_PRIME CG33958 UPSTREAM CG5721	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	17116102	2R_17116102_SNP [dm3] 2R_21228597_SNP [dm6]	A	G	2.091e^-5	0.624	INTRON ASPP
2R	16173650	2R_16173650_SNP [dm3] 2R_20286145_SNP [dm6]	T	C	2.215e^-5	0.624	SYNONYMOUS_CODING CG16868	TF binding site mE1_TFBS_sens
3R	9738642	3R_9738642_SNP [dm3] 3R_13912920_SNP [dm6]	T	G	2.238e^-5	0.624	INTERGENIC	TF binding site mE1_TFBS_inv
2L	18501185	2L_18501185_SNP [dm3] 2L_18501185_SNP [dm6]	A	C	2.267e^-5	0.624	UTR_5_PRIME kon UPSTREAM kon	TF binding site BDTNP1_TFBS_da
3L	14941736	3L_14941736_SNP [dm3] 3L_14948636_SNP [dm6]	G	A	2.289e^-5	0.624	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2R	15205607	2R_15205607_SNP [dm3] 2R_19318102_SNP [dm6]	A	G	2.306e^-5	0.624	SYNONYMOUS_CODING Rgk1
2L	10521817	2L_10521817_SNP [dm3] 2L_10521817_SNP [dm6]	A	T	2.339e^-5	0.624	INTERGENIC
2R	16020141	2R_16020141_SNP [dm3] 2R_20132636_SNP [dm6]	C	T	2.359e^-5	0.624	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	5160017	2L_5160017_SNP [dm3] 2L_5160017_SNP [dm6]	G	T	2.398e^-5	0.624	SYNONYMOUS_CODING Msp300 INTRON Msp300
2R	9143623	2R_9143623_SNP [dm3] 2R_13256118_SNP [dm6]	T	A	2.417e^-5	0.624	UPSTREAM CR44343 & 1 other INTERGENIC
3L	8070513	3L_8070513_SNP [dm3] 3L_8077413_SNP [dm6]	T	A	2.420e^-5	0.624	UTR_5_PRIME Ect4 INTRON Ect4	TF binding site mE1_TFBS_Trl
2R	12008938	2R_12008938_SNP [dm3] 2R_16121433_SNP [dm6]	G	A	2.475e^-5	0.624	SYNONYMOUS_CODING Jhe	TF binding site BDTNP1_TFBS_bcd
2L	16381665	2L_16381665_SNP [dm3] 2L_16381665_SNP [dm6]	T	A	2.487e^-5	0.624	INTERGENIC
3L	15055734	3L_15055734_SNP [dm3] 3L_15062634_SNP [dm6]	T	C	2.490e^-5	0.624	UPSTREAM CG13460 & 1 other INTRON Sytbeta
3L	10757529	3L_10757529_SNP [dm3] 3L_10764429_SNP [dm6]	G	T	2.581e^-5	0.624	INTERGENIC	TF binding site mE1_TFBS_HSA
2L	9551242	2L_9551242_SNP [dm3] 2L_9551242_SNP [dm6]	G	T	2.656e^-5	0.624	UPSTREAM jp INTRON jp
X	14686048	X_14686048_SNP [dm3] X_14792015_SNP [dm6]	A	G	2.659e^-5	0.624	SYNONYMOUS_CODING rut INTRON rut	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	9147190	2R_9147190_SNP [dm3] 2R_13259685_SNP [dm6]	G	A	2.704e^-5	0.624	UPSTREAM CG42319 INTERGENIC
2R	16418053	2R_16418053_SNP [dm3] 2R_20530548_SNP [dm6]	G	T	2.727e^-5	0.624	INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	3532494	X_3532494_SNP [dm3] X_3638461_SNP [dm6]	G	A	2.738e^-5	0.624	INTRON AstA-R1
2L	9463504	2L_9463504_SNP [dm3] 2L_9463504_SNP [dm6]	A	C	2.746e^-5	0.624	UTR_3_PRIME numb DOWNSTREAM numb	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
2R	3576103	2R_3576103_SNP [dm3] 2R_7688598_SNP [dm6]	G	T	2.786e^-5	0.624	INTRON CG1399
2R	10482470	2R_10482470_SNP [dm3] 2R_14594965_SNP [dm6]	C	T	2.835e^-5	0.624	SYNONYMOUS_CODING CG12869 DOWNSTREAM RpI1	TF binding site mE1_TFBS_cad
2R	16175402	2R_16175402_SNP [dm3] 2R_20287897_SNP [dm6]	C	T	2.836e^-5	0.624	NON_SYNONYMOUS_CODING CG34199 UPSTREAM CG16868 DOWNSTREAM Cpr56F
2R	8129610	2R_8129610_SNP [dm3] 2R_12242105_SNP [dm6]	T	C	2.857e^-5	0.624	UPSTREAM CG43316 DOWNSTREAM CG43315 INTERGENIC
3R	1904450	3R_1904450_SNP [dm3] 3R_6078728_SNP [dm6]	C	T	2.861e^-5	0.624	UPSTREAM Or83c INTERGENIC
X	5449728	X_5449728_SNP [dm3] X_5555695_SNP [dm6]	C	A	2.865e^-5	0.624	INTRON Vsx2	TF binding site mE1_TFBS_cnc mE1_TFBS_Kr
X	14685801	X_14685801_SNP [dm3] X_14791768_SNP [dm6]	C	T	2.932e^-5	0.624	NON_SYNONYMOUS_CODING rut INTRON rut	TF binding site mE1_TFBS_chinmo
3L	7799375	3L_7799375_SNP [dm3] 3L_7806275_SNP [dm6]	C	T	2.991e^-5	0.624	INTRON CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
X	17923393	X_17923393_SNP [dm3] X_18029360_SNP [dm6]	G	T	2.996e^-5	0.624	INTRON Sh
X	8957546	X_8957546_SNP [dm3] X_9063513_SNP [dm6]	A	T	3.002e^-5	0.624	INTRON CG15365
2L	9551237	2L_9551237_SNP [dm3] 2L_9551237_SNP [dm6]	A	C	3.028e^-5	0.624	UPSTREAM jp INTRON jp
3R	14196704	3R_14196704_SNP [dm3] 3R_18370982_SNP [dm6]	C	T	3.064e^-5	0.624	INTRON gl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	13838051	2R_13838051_SNP [dm3] 2R_17950546_SNP [dm6]	T	A	3.185e^-5	0.624	INTERGENIC
3L	12851980	3L_12851980_SNP [dm3] 3L_12858880_SNP [dm6]	G	A	3.189e^-5	0.624	SYNONYMOUS_CODING CG32107
2R	17809823	2R_17809823_SNP [dm3] 2R_21922318_SNP [dm6]	C	T	3.191e^-5	0.624	INTRON Fili
X	16153547	X_16153547_SNP [dm3] X_16259514_SNP [dm6]	G	A	3.262e^-5	0.624	INTERGENIC
3L	9424248	3L_9424248_SNP [dm3] 3L_9431148_SNP [dm6]	A	G	3.265e^-5	0.624	SYNONYMOUS_CODING MTF-1 UTR_5_PRIME MTF-1 INTRON MTF-1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3R	10766469	3R_10766469_SNP [dm3] 3R_14940747_SNP [dm6]	A	T	3.313e^-5	0.624	INTERGENIC
3R	10766223	3R_10766223_SNP [dm3] 3R_14940501_SNP [dm6]	C	A	3.317e^-5	0.624	INTERGENIC
2R	11764104	2R_11764104_SNP [dm3] 2R_15876599_SNP [dm6]	G	T	3.338e^-5	0.624	INTRON sli	TF binding site BDTNP1_TFBS_da
2R	16101472	2R_16101472_SNP [dm3] 2R_20213967_SNP [dm6]	A	G	3.389e^-5	0.624	INTERGENIC
2R	14340002	2R_14340002_SNP [dm3] 2R_18452497_SNP [dm6]	C	T	3.394e^-5	0.624	SYNONYMOUS_CODING CG5190 DOWNSTREAM CG17669	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	2477618	X_2477618_SNP [dm3] X_2583585_SNP [dm6]	C	G	3.424e^-5	0.624	SYNONYMOUS_CODING CG13759 DOWNSTREAM CG13760	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	9460876	2L_9460876_SNP [dm3] 2L_9460876_SNP [dm6]	C	A	3.535e^-5	0.624	INTRON numb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	995306	3L_995306_SNP [dm3] 3L_995306_SNP [dm6]	A	C	3.663e^-5	0.624	SYNONYMOUS_CODING CG12038 DOWNSTREAM trio	TF binding site mE1_TFBS_cad
2R	9146522	2R_9146522_SNP [dm3] 2R_13259017_SNP [dm6]	C	G	3.698e^-5	0.624	DOWNSTREAM CG10799 INTERGENIC
2L	9464032	2L_9464032_SNP [dm3] 2L_9464032_SNP [dm6]	G	A	3.702e^-5	0.624	UTR_3_PRIME numb DOWNSTREAM numb
3L	2392197	3L_2392197_SNP [dm3] 3L_2392197_SNP [dm6]	C	A	3.719e^-5	0.624	INTRON CG45186
3L	15284947	3L_15284947_SNP [dm3] 3L_15291847_SNP [dm6]	C	A	3.724e^-5	0.624	INTERGENIC
2R	19164428	2R_19164428_SNP [dm3] 2R_23276905_SNP [dm6]	T	G	3.728e^-5	0.624	INTERGENIC
X	17243971	X_17243971_SNP [dm3] X_17349938_SNP [dm6]	C	T	3.730e^-5	0.624	INTERGENIC

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By genomic position
Variant impact
Gene name

idx_Surv_cum_MeHg phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results