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=7.663e^-2)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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_2R_NS	0.0813

Kruskal-Wallis test

Covariate	χ²	p-value
wolba	3.7089	0.0541
In_2L_t	5.7119	0.0575
In_2R_NS	6.9435	0.0311

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1875 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
X	2514417	X_2514417_SNP [dm3] X_2620384_SNP [dm6]	G	T	1.833e^-7	0.182	SYNONYMOUS_CODING Seipin UPSTREAM Tsp3A	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	13754674	2L_13754674_SNP [dm3] 2L_13754674_SNP [dm6]	C	A	1.944e^-7	0.182	DOWNSTREAM CR44846 INTRON CR44846 & 1 other
X	2514292	X_2514292_SNP [dm3] X_2620259_SNP [dm6]	C	A	4.760e^-7	0.187	UTR_5_PRIME Seipin UPSTREAM Tsp3A	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	13754675	2L_13754675_SNP [dm3] 2L_13754675_SNP [dm6]	A	G	4.925e^-7	0.187	DOWNSTREAM CR44846 INTRON CR44846 & 1 other
X	5336457	X_5336457_SNP [dm3] X_5442424_SNP [dm6]	G	A	4.986e^-7	0.187	INTERGENIC
2L	20852414	2L_20852414_SNP [dm3] 2L_20852414_SNP [dm6]	C	A	6.768e^-7	0.207	UPSTREAM twit INTERGENIC	TF binding site mE1_TFBS_cad
X	2514295	X_2514295_SNP [dm3] X_2620262_SNP [dm6]	A	G	7.742e^-7	0.207	START_GAINED Seipin UTR_5_PRIME Seipin UPSTREAM Tsp3A	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	12262931	3L_12262931_SNP [dm3] 3L_12269831_SNP [dm6]	C	A	9.792e^-7	0.229	UTR_3_PRIME Pbgs DOWNSTREAM Pbgs & 1 other
3L	13827221	3L_13827221_DEL [dm3] 3L_13834121_DEL [dm6]	AGA	A	1.344e^-6	0.28	INTERGENIC
X	20722858	X_20722858_SNP [dm3] X_20851831_SNP [dm6]	C	T	1.727e^-6	0.324	INTRON shakB
2R	4324387	2R_4324387_SNP [dm3] 2R_8436882_SNP [dm6]	A	G	2.796e^-6	0.476	UPSTREAM Lcp4 DOWNSTREAM Lcp3 INTERGENIC
3L	14433920	3L_14433920_SNP [dm3] 3L_14440820_SNP [dm6]	T	G	3.045e^-6	0.476	INTRON bbg
2L	3222068	2L_3222068_SNP [dm3] 2L_3222068_SNP [dm6]	T	A	3.501e^-6	0.477	INTERGENIC
2L	17715989	2L_17715989_SNP [dm3] 2L_17715989_SNP [dm6]	C	T	3.560e^-6	0.477	INTRON CadN	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
X	20722902	X_20722902_SNP [dm3] X_20851875_SNP [dm6]	T	A	4.097e^-6	0.512	INTRON shakB
2L	20956300	2L_20956300_SNP [dm3] 2L_20956300_SNP [dm6]	T	C	5.179e^-6	0.607	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	19323680	3R_19323680_INS [dm3] 3R_23497958_INS [dm6]	C	CT	6.360e^-6	0.696	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	25772483	3R_25772483_SNP [dm3] 3R_29946761_SNP [dm6]	G	A	6.685e^-6	0.696	SYNONYMOUS_CODING CG15523	TF binding site mE1_TFBS_cad
X	4831334	X_4831334_SNP [dm3] X_4937301_SNP [dm6]	G	A	7.643e^-6	0.725	INTRON CG44774	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	9705907	2L_9705907_SNP [dm3] 2L_9705907_SNP [dm6]	G	A	7.735e^-6	0.725	START_GAINED CG31710 UTR_5_PRIME CG31710 INTRON pelo	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_cnc mE1_TFBS_HSA mE1_TFBS_Trl
2L	14591926	2L_14591926_SNP [dm3] 2L_14591926_SNP [dm6]	A	T	9.991e^-6	0.856	INTERGENIC
2R	4324019	2R_4324019_SNP [dm3] 2R_8436514_SNP [dm6]	A	T	1.137e^-5	0.856	DOWNSTREAM Lcp3 INTERGENIC
X	12057977	X_12057977_SNP [dm3] X_12163944_SNP [dm6]	C	A	1.183e^-5	0.856	INTRON Ten-a
3L	11448470	3L_11448470_SNP [dm3] 3L_11455370_SNP [dm6]	C	T	1.208e^-5	0.856	INTERGENIC
2L	20846471	2L_20846471_SNP [dm3] 2L_20846471_SNP [dm6]	C	T	1.304e^-5	0.856	INTRON CG31676
2R	15465744	2R_15465744_SNP [dm3] 2R_19578239_SNP [dm6]	T	C	1.336e^-5	0.856	INTRON sm
2L	6826035	2L_6826035_SNP [dm3] 2L_6826035_SNP [dm6]	T	A	1.352e^-5	0.856	INTRON sens-2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3L	12263000	3L_12263000_SNP [dm3] 3L_12269900_SNP [dm6]	C	A	1.359e^-5	0.856	UTR_3_PRIME Pbgs DOWNSTREAM Pbgs & 1 other
2R	14490269	2R_14490269_SNP [dm3] 2R_18602764_SNP [dm6]	G	T	1.402e^-5	0.856	INTRON GEFmeso
X	21204018	X_21204018_INS [dm3] X_21332991_INS [dm6]	T	TT	1.470e^-5	0.856	UTR_3_PRIME tty INTRON tty	TF binding site mE1_TFBS_cad
2R	4324047	2R_4324047_SNP [dm3] 2R_8436542_SNP [dm6]	T	A	1.518e^-5	0.856	DOWNSTREAM Lcp3 INTERGENIC
X	2514075	X_2514075_SNP [dm3] X_2620042_SNP [dm6]	G	C	1.540e^-5	0.856	UTR_5_PRIME Seipin UPSTREAM Tsp3A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
2R	13234305	2R_13234305_SNP [dm3] 2R_17346800_SNP [dm6]	G	C	1.560e^-5	0.856	INTRON mbl
3L	2377147	3L_2377147_SNP [dm3] 3L_2377147_SNP [dm6]	C	T	1.561e^-5	0.856	SYNONYMOUS_CODING CG15877 UPSTREAM CG45186 DOWNSTREAM CG9004	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_hkb mE1_TFBS_HSA
X	9321217	X_9321217_SNP [dm3] X_9427184_SNP [dm6]	T	A	1.599e^-5	0.856	INTRON mgl
X	9321206	X_9321206_SNP [dm3] X_9427173_SNP [dm6]	T	A	1.647e^-5	0.858	INTRON mgl
X	20723084	X_20723084_SNP [dm3] X_20852057_SNP [dm6]	G	T	1.783e^-5	0.877	INTRON shakB
2R	3178527	2R_3178527_SNP [dm3] 2R_7291022_SNP [dm6]	T	A	1.831e^-5	0.877	INTRON pwn	TF binding site mE1_TFBS_cad
2L	15381290	2L_15381290_SNP [dm3] 2L_15381290_SNP [dm6]	G	T	1.871e^-5	0.877	INTERGENIC
X	20860324	X_20860324_SNP [dm3] X_20989297_SNP [dm6]	T	A	1.904e^-5	0.877	INTERGENIC
2L	18486222	2L_18486222_DEL [dm3] 2L_18486222_DEL [dm6]	TTCCAAAAGATT...	T	1.936e^-5	0.877	INTRON CG10176	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA
3L	13853684	3L_13853684_SNP [dm3] 3L_13860584_SNP [dm6]	G	T	1.965e^-5	0.877	UTR_3_PRIME CG8745 DOWNSTREAM Hml	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2R	4324394	2R_4324394_SNP [dm3] 2R_8436889_SNP [dm6]	C	T	2.072e^-5	0.89	UPSTREAM Lcp4 DOWNSTREAM Lcp3 INTERGENIC
2R	3240066	2R_3240066_SNP [dm3] 2R_7352561_SNP [dm6]	A	G	2.108e^-5	0.89	INTRON Dscam1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	6570851	2R_6570851_SNP [dm3] 2R_10683346_SNP [dm6]	T	C	2.136e^-5	0.89	INTRON stan	TF binding site BDTNP1_TFBS_dl
2L	17319029	2L_17319029_SNP [dm3] 2L_17319029_SNP [dm6]	G	C	2.208e^-5	0.9	DOWNSTREAM CR45696 INTERGENIC
X	11939987	X_11939987_SNP [dm3] X_12045954_SNP [dm6]	C	T	2.316e^-5	0.9	INTRON CR43960 & 1 other
3R	12947547	3R_12947547_SNP [dm3] 3R_17121825_SNP [dm6]	A	G	2.363e^-5	0.9	UTR_3_PRIME CG42779 INTRON cher	TF binding site mE1_TFBS_inv
2R	14077331	2R_14077331_SNP [dm3] 2R_18189826_SNP [dm6]	T	G	2.420e^-5	0.9	DOWNSTREAM CG14500 INTRON CG33958
3R	20355955	3R_20355955_SNP [dm3] 3R_24530233_SNP [dm6]	C	A	2.511e^-5	0.9	UPSTREAM ana1 DOWNSTREAM CG6607 INTRON CG13623	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad
X	21893008	X_21893008_SNP [dm3] X_22491172_SNP [dm6]	A	T	2.544e^-5	0.9	UPSTREAM l_1_G0196 & 1 other INTRON l_1_G0196
X	11658627	X_11658627_SNP [dm3] X_11764594_SNP [dm6]	C	T	2.623e^-5	0.9	UPSTREAM CG9360 INTRON m	TF binding site mE1_TFBS_cnc
2R	16648581	2R_16648581_SNP [dm3] 2R_20761076_SNP [dm6]	T	C	2.681e^-5	0.9	INTERGENIC
3L	6560960	3L_6560960_SNP [dm3] 3L_6567860_SNP [dm6]	A	G	2.681e^-5	0.9	SYNONYMOUS_CODING jv INTRON CG18769	TF binding site mE1_TFBS_HSA
2R	4321121	2R_4321121_SNP [dm3] 2R_8433616_SNP [dm6]	A	T	2.795e^-5	0.9	UPSTREAM Lcp1Psi DOWNSTREAM Lcp2 INTERGENIC
3R	23854220	3R_23854220_SNP [dm3] 3R_28028498_SNP [dm6]	A	T	2.820e^-5	0.9	INTRON CG34362
2L	6826022	2L_6826022_DEL [dm3] 2L_6826022_DEL [dm6]	TGT	T	3.024e^-5	0.9	INTRON sens-2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3L	11999003	3L_11999003_SNP [dm3] 3L_12005903_SNP [dm6]	T	C	3.149e^-5	0.9	INTRON CG6928
X	11940008	X_11940008_SNP [dm3] X_12045975_SNP [dm6]	G	A	3.278e^-5	0.9	INTRON CR43960 & 1 other
3R	26493928	3R_26493928_DEL [dm3] 3R_30668206_DEL [dm6]	TGTAT	T	3.364e^-5	0.9	INTERGENIC	TF binding site mE1_TFBS_cad
2L	21020153	2L_21020153_SNP [dm3] 2L_21020153_SNP [dm6]	T	C	3.374e^-5	0.9	INTRON CG42238
3R	11494454	3R_11494454_SNP [dm3] 3R_15668732_SNP [dm6]	C	G	3.452e^-5	0.9	DOWNSTREAM CR43849 INTRON pxb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	7802249	3L_7802249_SNP [dm3] 3L_7809149_SNP [dm6]	T	A	3.543e^-5	0.9	UTR_5_PRIME CG32369	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2R	4324395	2R_4324395_SNP [dm3] 2R_8436890_SNP [dm6]	A	T	3.716e^-5	0.9	UPSTREAM Lcp4 DOWNSTREAM Lcp3 INTERGENIC
X	21465899	X_21465899_SNP [dm3] X_21594872_SNP [dm6]	C	T	3.749e^-5	0.9	INTERGENIC
2L	13754697	2L_13754697_SNP [dm3] 2L_13754697_SNP [dm6]	C	A	3.756e^-5	0.9	DOWNSTREAM CR44846 INTRON CR44846 & 1 other
2L	8228159	2L_8228159_SNP [dm3] 2L_8228159_SNP [dm6]	G	A	3.802e^-5	0.9	SYNONYMOUS_CODING Pvr INTRON Pvr
X	4825101	X_4825101_SNP [dm3] X_4931068_SNP [dm6]	A	C	3.831e^-5	0.9	START_GAINED CG44774 UTR_5_PRIME CG44774 INTRON CG44774	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	22687503	3R_22687503_SNP [dm3] 3R_26861781_SNP [dm6]	C	T	4.001e^-5	0.9	NON_SYNONYMOUS_CODING Lerp UPSTREAM mir-1012
X	2626792	X_2626792_SNP [dm3] X_2732759_SNP [dm6]	C	T	4.031e^-5	0.9	SYNONYMOUS_CODING CG2712 UPSTREAM ttm50	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2R	15451247	2R_15451247_SNP [dm3] 2R_19563742_SNP [dm6]	G	A	4.042e^-5	0.9	INTRON sm
3L	2483458	3L_2483458_SNP [dm3] 3L_2483458_SNP [dm6]	C	T	4.073e^-5	0.9	INTRON CG45186	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_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	18576538	2L_18576538_SNP [dm3] 2L_18576538_SNP [dm6]	T	G	4.139e^-5	0.9	INTRON Pde11
3R	20396951	3R_20396951_SNP [dm3] 3R_24571229_SNP [dm6]	C	T	4.152e^-5	0.9	INTRON CG13624
2L	15058467	2L_15058467_SNP [dm3] 2L_15058467_SNP [dm6]	T	A	4.162e^-5	0.9	SYNONYMOUS_CODING CG33679 UPSTREAM ck DOWNSTREAM TfIIS	TF binding site BDTNP1_TFBS_dl
3R	22687498	3R_22687498_SNP [dm3] 3R_26861776_SNP [dm6]	C	A	4.178e^-5	0.9	SYNONYMOUS_CODING Lerp UPSTREAM mir-1012
X	7434766	X_7434766_SNP [dm3] X_7540733_SNP [dm6]	G	A	4.213e^-5	0.9	INTRON CG32719
2L	9035540	2L_9035540_SNP [dm3] 2L_9035540_SNP [dm6]	G	C	4.236e^-5	0.9	INTERGENIC
2R	6115652	2R_6115652_SNP [dm3] 2R_10228147_SNP [dm6]	G	T	4.338e^-5	0.9	UPSTREAM Hr46 INTRON Hr46 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2R	15059588	2R_15059588_SNP [dm3] 2R_19172083_SNP [dm6]	G	A	4.421e^-5	0.9	INTRON CG10737
2R	16272399	2R_16272399_SNP [dm3] 2R_20384894_SNP [dm6]	A	C	4.450e^-5	0.9	INTERGENIC
2L	6826029	2L_6826029_DEL [dm3] 2L_6826029_DEL [dm6]	GGT	G	4.529e^-5	0.9	INTRON sens-2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2R	3192999	2R_3192999_DEL [dm3] 2R_7305494_DEL [dm6]	ATG	A	4.564e^-5	0.9	INTERGENIC
3L	6560978	3L_6560978_SNP [dm3] 3L_6567878_SNP [dm6]	T	C	4.590e^-5	0.9	SYNONYMOUS_CODING jv INTRON CG18769	TF binding site mE1_TFBS_HSA
2R	3840978	2R_3840978_INS [dm3] 2R_7953473_INS [dm6]	G	GG	4.648e^-5	0.9	INTRON CG14764	TF binding site mE1_TFBS_inv
3R	22334010	3R_22334010_SNP [dm3] 3R_26508288_SNP [dm6]	T	C	4.649e^-5	0.9	INTRON plum
X	3303571	X_3303571_SNP [dm3] X_3409538_SNP [dm6]	T	C	4.759e^-5	0.9	INTRON CR44999 & 1 other
3R	19845152	3R_19845152_SNP [dm3] 3R_24019430_SNP [dm6]	T	G	4.784e^-5	0.9	INTRON KrT95D
X	13001278	X_13001278_SNP [dm3] X_13107245_SNP [dm6]	T	G	4.815e^-5	0.9	DOWNSTREAM Fer3HCH INTRON CG43313
3R	12924367	3R_12924367_SNP [dm3] 3R_17098645_SNP [dm6]	C	T	4.824e^-5	0.9	UTR_5_PRIME cher INTRON cher
3R	12924388	3R_12924388_SNP [dm3] 3R_17098666_SNP [dm6]	G	A	4.830e^-5	0.9	START_GAINED cher UTR_5_PRIME cher INTRON cher
3L	7799455	3L_7799455_SNP [dm3] 3L_7806355_SNP [dm6]	A	T	4.936e^-5	0.9	INTRON CG32369	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	20037817	3L_20037817_SNP [dm3] 3L_20044717_SNP [dm6]	G	A	4.948e^-5	0.9	INTERGENIC
2L	14325524	2L_14325524_SNP [dm3] 2L_14325524_SNP [dm6]	T	C	4.986e^-5	0.9	SYNONYMOUS_CODING wb	TF binding site mE1_TFBS_cad
2R	16696898	2R_16696898_SNP [dm3] 2R_20809393_SNP [dm6]	T	C	5.080e^-5	0.9	INTERGENIC
3L	6560534	3L_6560534_SNP [dm3] 3L_6567434_SNP [dm6]	G	A	5.097e^-5	0.9	SYNONYMOUS_CODING jv INTRON CG18769
2L	3229825	2L_3229825_SNP [dm3] 2L_3229825_SNP [dm6]	T	C	5.197e^-5	0.9	INTERGENIC
2R	7056931	2R_7056931_SNP [dm3] 2R_11169426_SNP [dm6]	A	G	5.220e^-5	0.9	INTRON shn & 1 other
2L	17245420	2L_17245420_SNP [dm3] 2L_17245420_SNP [dm6]	A	G	5.282e^-5	0.9	DOWNSTREAM CR44396 INTRON beat-IIIc
X	17212325	X_17212325_SNP [dm3] X_17318292_SNP [dm6]	T	C	5.337e^-5	0.9	INTRON B-H2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

PC4_Nutri_Score_Low phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results