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=1.537e^-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

2569 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	19164428	2R_19164428_SNP [dm3] 2R_23276905_SNP [dm6]	T	G	1.698e^-7	0.318	INTERGENIC
3R	10766286	3R_10766286_SNP [dm3] 3R_14940564_SNP [dm6]	G	C	5.652e^-7	0.385	INTERGENIC
2R	19164453	2R_19164453_SNP [dm3] 2R_23276930_SNP [dm6]	C	T	7.194e^-7	0.385	INTERGENIC
2R	17299063	2R_17299063_SNP [dm3] 2R_21411558_SNP [dm6]	A	G	8.208e^-7	0.385	INTRON Sdc
2R	17809823	2R_17809823_SNP [dm3] 2R_21922318_SNP [dm6]	C	T	2.389e^-6	0.658	INTRON Fili
2L	9463006	2L_9463006_SNP [dm3] 2L_9463006_SNP [dm6]	T	G	2.669e^-6	0.658	UTR_3_PRIME numb
3L	23033953	3L_23033953_SNP [dm3] 3L_23040853_SNP [dm6]	T	A	2.947e^-6	0.658	DOWNSTREAM nrm INTERGENIC
3R	23990088	3R_23990088_DEL [dm3] 3R_28164366_DEL [dm6]	CGCC	C	3.175e^-6	0.658	INTRON CG34354
3L	7454914	3L_7454914_SNP [dm3] 3L_7461814_SNP [dm6]	G	A	3.494e^-6	0.658	INTERGENIC
3L	15284967	3L_15284967_SNP [dm3] 3L_15291867_SNP [dm6]	G	C	3.627e^-6	0.658	INTERGENIC
2L	9463981	2L_9463981_SNP [dm3] 2L_9463981_SNP [dm6]	A	G	4.222e^-6	0.658	UTR_3_PRIME numb DOWNSTREAM numb
3L	730003	3L_730003_SNP [dm3] 3L_730003_SNP [dm6]	C	G	4.566e^-6	0.658	INTERGENIC	TF binding site mE1_TFBS_inv
2R	16098791	2R_16098791_SNP [dm3] 2R_20211286_SNP [dm6]	A	C	6.032e^-6	0.658	DOWNSTREAM CG16894 INTERGENIC
2R	9929328	2R_9929328_SNP [dm3] 2R_14041823_SNP [dm6]	A	T	6.154e^-6	0.658	INTRON mam	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA
2R	10171323	2R_10171323_SNP [dm3] 2R_14283818_SNP [dm6]	A	G	6.240e^-6	0.658	INTRON Ih
X	3293411	X_3293411_SNP [dm3] X_3399378_SNP [dm6]	G	C	6.289e^-6	0.658	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	10171279	2R_10171279_SNP [dm3] 2R_14283774_SNP [dm6]	C	T	6.299e^-6	0.658	INTRON Ih
X	8618518	X_8618518_SNP [dm3] X_8724485_SNP [dm6]	A	T	6.346e^-6	0.658	UPSTREAM CR43297 INTERGENIC
X	8618588	X_8618588_SNP [dm3] X_8724555_SNP [dm6]	T	C	6.711e^-6	0.658	UPSTREAM CR43297 INTERGENIC
2R	16290821	2R_16290821_SNP [dm3] 2R_20403316_SNP [dm6]	C	T	7.957e^-6	0.658	INTERGENIC
X	8618591	X_8618591_SNP [dm3] X_8724558_SNP [dm6]	G	A	9.145e^-6	0.658	UPSTREAM CR43297 INTERGENIC
2R	12008938	2R_12008938_SNP [dm3] 2R_16121433_SNP [dm6]	G	A	9.362e^-6	0.658	SYNONYMOUS_CODING Jhe	TF binding site BDTNP1_TFBS_bcd
3L	15608171	3L_15608171_SNP [dm3] 3L_15615071_SNP [dm6]	G	A	9.906e^-6	0.658	INTRON comm3
X	16153547	X_16153547_SNP [dm3] X_16259514_SNP [dm6]	G	A	1.055e^-5	0.658	INTERGENIC
2L	9463504	2L_9463504_SNP [dm3] 2L_9463504_SNP [dm6]	A	C	1.065e^-5	0.658	UTR_3_PRIME numb DOWNSTREAM numb	TF binding site mE1_TFBS_HSA mE1_TFBS_kn
3L	2392244	3L_2392244_SNP [dm3] 3L_2392244_SNP [dm6]	A	C	1.075e^-5	0.658	INTRON CG45186
3L	8875006	3L_8875006_DEL [dm3] 3L_8881906_DEL [dm6]	CC	C	1.087e^-5	0.658	INTRON dally
3R	15833329	3R_15833329_SNP [dm3] 3R_20007607_SNP [dm6]	T	C	1.115e^-5	0.658	INTRON Hs6st	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
2R	16099782	2R_16099782_SNP [dm3] 2R_20212277_SNP [dm6]	T	A	1.128e^-5	0.658	NON_SYNONYMOUS_CODING CG16894
2L	18478945	2L_18478945_SNP [dm3] 2L_18478945_SNP [dm6]	C	T	1.128e^-5	0.658	INTRON CG10283
3L	15883966	3L_15883966_SNP [dm3] 3L_15890866_SNP [dm6]	A	G	1.189e^-5	0.658	INTRON pHCl
3R	3098275	3R_3098275_SNP [dm3] 3R_7272553_SNP [dm6]	C	A	1.264e^-5	0.658	DOWNSTREAM rn & 1 other INTERGENIC
X	3293395	X_3293395_SNP [dm3] X_3399362_SNP [dm6]	A	C	1.471e^-5	0.658	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	3293399	X_3293399_MNP [dm3] X_3399366_MNP [dm6]	TAA	CTT	1.471e^-5	0.658	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	3293404	X_3293404_SNP [dm3] X_3399371_SNP [dm6]	A	G	1.471e^-5	0.658	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	3293428	X_3293428_SNP [dm3] X_3399395_SNP [dm6]	A	T	1.486e^-5	0.658	INTRON CR44999 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	8351860	2L_8351860_SNP [dm3] 2L_8351860_SNP [dm6]	G	A	1.517e^-5	0.658	UPSTREAM Mur29B DOWNSTREAM CG7778 INTERGENIC
2L	12280030	2L_12280030_SNP [dm3] 2L_12280030_SNP [dm6]	C	A	1.527e^-5	0.658	INTRON aret
X	11519769	X_11519769_SNP [dm3] X_11625736_SNP [dm6]	A	G	1.541e^-5	0.658	INTRON Ptp10D
2L	8700458	2L_8700458_SNP [dm3] 2L_8700458_SNP [dm6]	G	A	1.543e^-5	0.658	UPSTREAM Hnf4 INTRON Hnf4
3L	11587955	3L_11587955_SNP [dm3] 3L_11594855_SNP [dm6]	G	A	1.553e^-5	0.658	INTERGENIC
2R	10171349	2R_10171349_SNP [dm3] 2R_14283844_SNP [dm6]	G	C	1.580e^-5	0.658	INTRON Ih	TF binding site mE1_TFBS_cad
3L	15608156	3L_15608156_SNP [dm3] 3L_15615056_SNP [dm6]	T	C	1.594e^-5	0.658	INTRON comm3
X	8618759	X_8618759_SNP [dm3] X_8724726_SNP [dm6]	A	G	1.653e^-5	0.658	EXON CR43297
3L	11588003	3L_11588003_SNP [dm3] 3L_11594903_SNP [dm6]	T	A	1.679e^-5	0.658	INTERGENIC
3L	21288769	3L_21288769_SNP [dm3] 3L_21295669_SNP [dm6]	T	C	1.768e^-5	0.658	SYNONYMOUS_CODING Cpr78Cb
X	11519841	X_11519841_SNP [dm3] X_11625808_SNP [dm6]	A	T	1.809e^-5	0.658	INTRON Ptp10D
2L	17225478	2L_17225478_SNP [dm3] 2L_17225478_SNP [dm6]	A	G	1.831e^-5	0.658	INTRON beat-IIIc
2R	17427710	2R_17427710_SNP [dm3] 2R_21540205_SNP [dm6]	G	A	1.885e^-5	0.658	UPSTREAM CG33226 INTRON Egfr & 1 other	TF binding site mE1_TFBS_D mE1_TFBS_HSA
X	11519937	X_11519937_SNP [dm3] X_11625904_SNP [dm6]	C	T	1.898e^-5	0.658	INTRON Ptp10D
3L	3824237	3L_3824237_SNP [dm3] 3L_3824237_SNP [dm6]	T	A	1.974e^-5	0.658	INTRON enc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	16101472	2R_16101472_SNP [dm3] 2R_20213967_SNP [dm6]	A	G	1.978e^-5	0.658	INTERGENIC
3L	21995881	3L_21995881_SNP [dm3] 3L_22002781_SNP [dm6]	G	A	1.997e^-5	0.658	INTERGENIC
3L	19017086	3L_19017086_SNP [dm3] 3L_19023986_SNP [dm6]	C	T	2.048e^-5	0.658	INTRON nkd	TF binding site mE1_TFBS_sbb
2R	18579313	2R_18579313_SNP [dm3] 2R_22691808_SNP [dm6]	G	A	2.053e^-5	0.658	DOWNSTREAM robo EXON CR44764	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	11519750	X_11519750_SNP [dm3] X_11625717_SNP [dm6]	C	G	2.079e^-5	0.658	INTRON Ptp10D
3L	21292727	3L_21292727_SNP [dm3] 3L_21299627_SNP [dm6]	C	G	2.082e^-5	0.658	UPSTREAM Cpr78Cc DOWNSTREAM CG43702 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna
3L	15284947	3L_15284947_SNP [dm3] 3L_15291847_SNP [dm6]	C	A	2.090e^-5	0.658	INTERGENIC
2L	18478949	2L_18478949_SNP [dm3] 2L_18478949_SNP [dm6]	T	A	2.301e^-5	0.658	INTRON CG10283
3L	12507342	3L_12507342_SNP [dm3] 3L_12514242_SNP [dm6]	G	T	2.320e^-5	0.658	UPSTREAM tral DOWNSTREAM CR45168 INTRON sti	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2L	9463848	2L_9463848_SNP [dm3] 2L_9463848_SNP [dm6]	T	A	2.433e^-5	0.658	UTR_3_PRIME numb DOWNSTREAM numb	TF binding site mE1_TFBS_kn
3R	15242745	3R_15242745_SNP [dm3] 3R_19417023_SNP [dm6]	A	C	2.476e^-5	0.658	INTRON CG31221
3R	15242808	3R_15242808_SNP [dm3] 3R_19417086_SNP [dm6]	T	C	2.518e^-5	0.658	INTRON CG31221
2L	16592080	2L_16592080_SNP [dm3] 2L_16592080_SNP [dm6]	A	G	2.524e^-5	0.658	INTRON CG42389	TF binding site mE1_TFBS_cad
2R	20910216	2R_20910216_DEL [dm3] 2R_25022693_DEL [dm6]	TCCGCAATTCATACGGAGTA...	T	2.586e^-5	0.658	INTRON uzip	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	996409	3L_996409_SNP [dm3] 3L_996409_SNP [dm6]	T	C	2.611e^-5	0.658	UTR_3_PRIME trio DOWNSTREAM CG12038 & 1 other
2R	21060294	2R_21060294_SNP [dm3] 2R_25172771_SNP [dm6]	A	T	2.621e^-5	0.658	UPSTREAM Sfp60F DOWNSTREAM PebII INTERGENIC
2R	17315103	2R_17315103_SNP [dm3] 2R_21427598_SNP [dm6]	G	C	2.698e^-5	0.658	INTRON Sdc
3R	5804235	3R_5804235_SNP [dm3] 3R_9978513_SNP [dm6]	C	T	2.722e^-5	0.658	INTRON Glut4EF
3L	1250879	3L_1250879_SNP [dm3] 3L_1250879_SNP [dm6]	G	A	2.766e^-5	0.658	START_LOST CG9129 DOWNSTREAM Sac1	TF binding site mE1_TFBS_cad
2R	10482470	2R_10482470_SNP [dm3] 2R_14594965_SNP [dm6]	C	T	2.834e^-5	0.658	SYNONYMOUS_CODING CG12869 DOWNSTREAM RpI1	TF binding site mE1_TFBS_cad
X	17243819	X_17243819_SNP [dm3] X_17349786_SNP [dm6]	A	T	2.887e^-5	0.658	INTERGENIC
3R	11187358	3R_11187358_SNP [dm3] 3R_15361636_SNP [dm6]	T	A	2.892e^-5	0.658	UTR_5_PRIME ldlCp UPSTREAM Trax	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	9464032	2L_9464032_SNP [dm3] 2L_9464032_SNP [dm6]	G	A	2.906e^-5	0.658	UTR_3_PRIME numb DOWNSTREAM numb
2L	15359234	2L_15359234_SNP [dm3] 2L_15359234_SNP [dm6]	C	G	2.952e^-5	0.658	INTERGENIC
3R	15240481	3R_15240481_SNP [dm3] 3R_19414759_SNP [dm6]	T	C	2.960e^-5	0.658	INTRON CG31221
X	11519899	X_11519899_DEL [dm3] X_11625866_DEL [dm6]	GG	G	2.984e^-5	0.658	INTRON Ptp10D
3L	11587976	3L_11587976_SNP [dm3] 3L_11594876_SNP [dm6]	C	G	2.984e^-5	0.658	INTERGENIC
3L	8462387	3L_8462387_SNP [dm3] 3L_8469287_SNP [dm6]	T	C	2.986e^-5	0.658	INTRON Gug	TF binding site BDTNP1_TFBS_twi
2R	17974312	2R_17974312_SNP [dm3] 2R_22086807_SNP [dm6]	G	A	3.034e^-5	0.658	SYNONYMOUS_CODING CG13502 INTRON CG13502
2R	15035166	2R_15035166_SNP [dm3] 2R_19147661_SNP [dm6]	T	G	3.112e^-5	0.658	INTRON ena	TF binding site mE1_TFBS_HSA
3L	1250838	3L_1250838_SNP [dm3] 3L_1250838_SNP [dm6]	A	G	3.187e^-5	0.658	UTR_5_PRIME CG9129 DOWNSTREAM Sac1	TF binding site mE1_TFBS_cad
2R	8933808	2R_8933808_SNP [dm3] 2R_13046303_SNP [dm6]	C	G	3.193e^-5	0.658	UTR_3_PRIME CG13323 DOWNSTREAM CG13323
2R	19940705	2R_19940705_SNP [dm3] 2R_24053182_SNP [dm6]	T	C	3.222e^-5	0.658	DOWNSTREAM sei INTRON ppk29
2R	3576103	2R_3576103_SNP [dm3] 2R_7688598_SNP [dm6]	G	T	3.273e^-5	0.658	INTRON CG1399
X	11519775	X_11519775_INS [dm3] X_11625742_INS [dm6]	C	CATAC	3.369e^-5	0.658	INTRON Ptp10D
3L	9424141	3L_9424141_SNP [dm3] 3L_9431041_SNP [dm6]	A	G	3.401e^-5	0.658	NON_SYNONYMOUS_CODING MTF-1 START_GAINED MTF-1 UTR_5_PRIME MTF-1 INTRON MTF-1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
X	8618739	X_8618739_SNP [dm3] X_8724706_SNP [dm6]	A	G	3.487e^-5	0.658	EXON CR43297
2R	20905916	2R_20905916_DEL [dm3] 2R_25018393_DEL [dm6]	AGTGGCCTGGCCATTAATTA...	A	3.496e^-5	0.658	INTRON uzip	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	11187373	3R_11187373_SNP [dm3] 3R_15361651_SNP [dm6]	C	A	3.550e^-5	0.658	UTR_5_PRIME ldlCp UPSTREAM Trax	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	13838051	2R_13838051_SNP [dm3] 2R_17950546_SNP [dm6]	T	A	3.566e^-5	0.658	INTERGENIC
3L	2285397	3L_2285397_SNP [dm3] 3L_2285397_SNP [dm6]	G	C	3.598e^-5	0.658	INTRON MsR2
3R	15240427	3R_15240427_SNP [dm3] 3R_19414705_SNP [dm6]	C	G	3.629e^-5	0.658	INTRON CG31221
X	11519749	X_11519749_SNP [dm3] X_11625716_SNP [dm6]	T	C	3.672e^-5	0.658	INTRON Ptp10D
3R	14686520	3R_14686520_SNP [dm3] 3R_18860798_SNP [dm6]	C	G	3.713e^-5	0.658	INTERGENIC
3L	11588042	3L_11588042_SNP [dm3] 3L_11594942_SNP [dm6]	G	A	3.734e^-5	0.658	INTERGENIC
3L	2285238	3L_2285238_SNP [dm3] 3L_2285238_SNP [dm6]	G	T	3.752e^-5	0.658	INTRON MsR2
3L	8874976	3L_8874976_MNP [dm3] 3L_8881876_MNP [dm6]	CAT	TGA	3.775e^-5	0.658	INTRON dally
3L	8875004	3L_8875004_SNP [dm3] 3L_8881904_SNP [dm6]	T	C	3.775e^-5	0.658	INTRON dally
3L	13869735	3L_13869735_SNP [dm3] 3L_13876635_SNP [dm6]	A	G	3.835e^-5	0.658	INTRON dysc

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By genomic position
Variant impact
Gene name

idx_Surv_5MeHg phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results