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=2.936e^-3)
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_2L_t	0.06733

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.4526	0.0655

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1938 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	16326062	2R_16326062_SNP [dm3] 2R_20438557_SNP [dm6]	G	T	1.110e^-7	0.208	INTRON CG12484
2R	16326083	2R_16326083_SNP [dm3] 2R_20438578_SNP [dm6]	G	A	2.436e^-7	0.228	INTRON CG12484
2L	742378	2L_742378_SNP [dm3] 2L_742378_SNP [dm6]	C	A	5.643e^-6	0.934	UPSTREAM Eaat2 INTRON Eaat2
2L	14924296	2L_14924296_SNP [dm3] 2L_14924296_SNP [dm6]	G	A	6.254e^-6	0.934	UPSTREAM CG3491 INTRON CG42313
2R	8117197	2R_8117197_INS [dm3] 2R_12229692_INS [dm6]	A	AA	7.225e^-6	0.934	UPSTREAM CG8854 INTERGENIC
3R	15521660	3R_15521660_DEL [dm3] 3R_19695938_DEL [dm6]	AG	A	9.031e^-6	0.934	INTRON Naam
X	11199003	X_11199003_DEL [dm3] X_11304970_DEL [dm6]	AA	A	9.212e^-6	0.934	INTERGENIC
2L	14924381	2L_14924381_SNP [dm3] 2L_14924381_SNP [dm6]	G	C	9.348e^-6	0.934	UPSTREAM CG3491 INTRON CG42313
3L	18857160	3L_18857160_SNP [dm3] 3L_18864060_SNP [dm6]	C	G	1.131e^-5	0.934	UPSTREAM CG6865 INTRON CG6865
3L	20481999	3L_20481999_SNP [dm3] 3L_20488899_SNP [dm6]	A	G	1.172e^-5	0.934	INTRON ZnT77C
2L	3387058	2L_3387058_DEL [dm3] 2L_3387058_DEL [dm6]	TT	T	1.187e^-5	0.934	DOWNSTREAM Sfp23F & 1 other EXON CR45301
2L	13768866	2L_13768866_DEL [dm3] 2L_13768866_DEL [dm6]	TGT	T	1.193e^-5	0.934	INTRON TM9SF4
2L	3387042	2L_3387042_DEL [dm3] 2L_3387042_DEL [dm6]	GTCGTGCTGCTGC...	G	1.226e^-5	0.934	DOWNSTREAM Sfp23F & 1 other EXON CR45301
3L	4388149	3L_4388149_SNP [dm3] 3L_4388149_SNP [dm6]	A	C	1.247e^-5	0.934	INTRON slow
2R	8118189	2R_8118189_SNP [dm3] 2R_12230684_SNP [dm6]	A	C	1.250e^-5	0.934	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	20125015	2R_20125015_DEL [dm3] 2R_24237492_DEL [dm6]	TGTATT	T	1.274e^-5	0.934	EXON CR44827
2L	3524452	2L_3524452_SNP [dm3] 2L_3524452_SNP [dm6]	T	A	1.310e^-5	0.934	UPSTREAM Sr-CIV & 1 other INTERGENIC
2L	14924446	2L_14924446_SNP [dm3] 2L_14924446_SNP [dm6]	T	C	1.336e^-5	0.934	UPSTREAM CG3491 INTRON CG42313
2R	8117914	2R_8117914_SNP [dm3] 2R_12230409_SNP [dm6]	G	A	1.407e^-5	0.934	INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	8721954	2L_8721954_SNP [dm3] 2L_8721954_SNP [dm6]	T	A	1.415e^-5	0.934	INTRON raw
3L	5161916	3L_5161916_SNP [dm3] 3L_5168816_SNP [dm6]	C	A	1.469e^-5	0.934	INTRON shep	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr
2L	14924436	2L_14924436_SNP [dm3] 2L_14924436_SNP [dm6]	T	A	1.500e^-5	0.934	UPSTREAM CG3491 INTRON CG42313
2R	6542049	2R_6542049_SNP [dm3] 2R_10654544_SNP [dm6]	A	T	1.563e^-5	0.934	INTERGENIC
3L	5161915	3L_5161915_SNP [dm3] 3L_5168815_SNP [dm6]	A	T	1.641e^-5	0.934	INTRON shep	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr
3L	9091567	3L_9091567_SNP [dm3] 3L_9098467_SNP [dm6]	C	A	1.745e^-5	0.934	UTR_3_PRIME bol DOWNSTREAM CG13315
2R	2784987	2R_2784987_SNP [dm3] 2R_6897482_SNP [dm6]	C	T	1.766e^-5	0.934	INTRON CG30158
2L	20624962	2L_20624962_SNP [dm3] 2L_20624962_SNP [dm6]	T	A	1.824e^-5	0.934	INTRON CR44909
2L	8226988	2L_8226988_SNP [dm3] 2L_8226988_SNP [dm6]	G	A	1.881e^-5	0.934	NON_SYNONYMOUS_CODING Pvr INTRON Pvr	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	18857226	3L_18857226_SNP [dm3] 3L_18864126_SNP [dm6]	G	A	1.929e^-5	0.934	UPSTREAM CG6865 INTRON CG6865
3L	18857211	3L_18857211_SNP [dm3] 3L_18864111_SNP [dm6]	G	T	1.937e^-5	0.934	UPSTREAM CG6865 INTRON CG6865
3L	9295994	3L_9295994_SNP [dm3] 3L_9302894_SNP [dm6]	T	C	2.017e^-5	0.934	INTERGENIC
3R	8439490	3R_8439490_SNP [dm3] 3R_12613768_SNP [dm6]	A	C	2.033e^-5	0.934	INTERGENIC	TF binding site mE1_TFBS_HSA
3R	15521671	3R_15521671_SNP [dm3] 3R_19695949_SNP [dm6]	A	T	2.084e^-5	0.934	INTRON Naam
2L	14924427	2L_14924427_SNP [dm3] 2L_14924427_SNP [dm6]	C	G	2.108e^-5	0.934	UPSTREAM CG3491 INTRON CG42313
2L	4476691	2L_4476691_SNP [dm3] 2L_4476691_SNP [dm6]	G	A	2.148e^-5	0.934	START_GAINED ine UTR_5_PRIME ine DOWNSTREAM dp INTRON ine
3R	2746968	3R_2746968_DEL [dm3] 3R_6921246_DEL [dm6]	TT	T	2.152e^-5	0.934	INTRON Antp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2R	20125014	2R_20125014_SNP [dm3] 2R_24237491_SNP [dm6]	T	A	2.375e^-5	0.934	EXON CR44827
2L	16542801	2L_16542801_SNP [dm3] 2L_16542801_SNP [dm6]	C	A	2.485e^-5	0.934	INTRON CG31816
2L	4284531	2L_4284531_SNP [dm3] 2L_4284531_SNP [dm6]	T	G	2.560e^-5	0.934	INTRON tutl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2L	685941	2L_685941_SNP [dm3] 2L_685941_SNP [dm6]	G	A	2.639e^-5	0.934	INTRON ds
2R	6823074	2R_6823074_SNP [dm3] 2R_10935569_SNP [dm6]	G	A	2.682e^-5	0.934	INTERGENIC
2L	3058871	2L_3058871_SNP [dm3] 2L_3058871_SNP [dm6]	T	C	2.863e^-5	0.934	INTRON CG3523	TF binding site mE1_TFBS_cad mE1_TFBS_Trl
X	11742942	X_11742942_SNP [dm3] X_11848909_SNP [dm6]	A	T	2.922e^-5	0.934	DOWNSTREAM CR45619 INTERGENIC
3R	26621060	3R_26621060_SNP [dm3] 3R_30795338_SNP [dm6]	A	T	2.955e^-5	0.934	INTRON wts	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	2778850	2R_2778850_SNP [dm3] 2R_6891345_SNP [dm6]	T	A	2.957e^-5	0.934	UPSTREAM CG30158 INTERGENIC
2R	6610901	2R_6610901_SNP [dm3] 2R_10723396_SNP [dm6]	T	C	3.037e^-5	0.934	UTR_3_PRIME Rab3	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2R	16104602	2R_16104602_SNP [dm3] 2R_20217097_SNP [dm6]	T	C	3.079e^-5	0.934	INTERGENIC
2R	8120570	2R_8120570_SNP [dm3] 2R_12233065_SNP [dm6]	A	T	3.127e^-5	0.934	DOWNSTREAM CR44313 INTERGENIC
3R	4908150	3R_4908150_SNP [dm3] 3R_9082428_SNP [dm6]	G	C	3.146e^-5	0.934	INTRON pum
3R	23400135	3R_23400135_SNP [dm3] 3R_27574413_SNP [dm6]	C	T	3.159e^-5	0.934	INTRON wdb
3L	9296468	3L_9296468_SNP [dm3] 3L_9303368_SNP [dm6]	G	C	3.191e^-5	0.934	INTERGENIC
3R	25353341	3R_25353341_SNP [dm3] 3R_29527619_SNP [dm6]	G	T	3.212e^-5	0.934	INTERGENIC	TF binding site mE1_TFBS_inv
X	8049259	X_8049259_SNP [dm3] X_8155226_SNP [dm6]	A	G	3.269e^-5	0.934	UTR_3_PRIME Traf6 DOWNSTREAM CG18262
3R	25620269	3R_25620269_SNP [dm3] 3R_29794547_SNP [dm6]	G	A	3.503e^-5	0.934	UPSTREAM sro DOWNSTREAM kay INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	14924429	2L_14924429_SNP [dm3] 2L_14924429_SNP [dm6]	C	A	3.527e^-5	0.934	UPSTREAM CG3491 INTRON CG42313
2L	9862700	2L_9862700_SNP [dm3] 2L_9862700_SNP [dm6]	T	C	3.554e^-5	0.934	INTRON nAChRalpha6
2R	20125072	2R_20125072_SNP [dm3] 2R_24237549_SNP [dm6]	T	C	3.615e^-5	0.934	EXON CR44827
2L	14993247	2L_14993247_SNP [dm3] 2L_14993247_SNP [dm6]	G	A	3.627e^-5	0.934	INTRON mol
2L	14993394	2L_14993394_SNP [dm3] 2L_14993394_SNP [dm6]	C	T	3.629e^-5	0.934	INTRON mol
3L	18857152	3L_18857152_SNP [dm3] 3L_18864052_SNP [dm6]	A	T	3.687e^-5	0.934	UPSTREAM CG6865 INTRON CG6865
3L	13086689	3L_13086689_SNP [dm3] 3L_13093589_SNP [dm6]	A	G	3.709e^-5	0.934	INTERGENIC
2L	4319879	2L_4319879_SNP [dm3] 2L_4319879_SNP [dm6]	C	T	3.710e^-5	0.934	SYNONYMOUS_CODING tutl UTR_3_PRIME tutl	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	8057674	2L_8057674_SNP [dm3] 2L_8057674_SNP [dm6]	C	T	3.722e^-5	0.934	SYNONYMOUS_CODING poe
2L	1722348	2L_1722348_SNP [dm3] 2L_1722348_SNP [dm6]	A	G	3.771e^-5	0.934	INTRON Rim2
2L	9859200	2L_9859200_SNP [dm3] 2L_9859200_SNP [dm6]	T	A	3.803e^-5	0.934	INTRON nAChRalpha6
2L	16527310	2L_16527310_INS [dm3] 2L_16527310_INS [dm6]	T	TT	3.824e^-5	0.934	INTRON CG5953	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	10921067	3L_10921067_SNP [dm3] 3L_10927967_SNP [dm6]	G	A	3.857e^-5	0.934	INTERGENIC
2R	6634160	2R_6634160_SNP [dm3] 2R_10746655_SNP [dm6]	T	G	3.859e^-5	0.934	INTRON CG33144
2L	2548057	2L_2548057_SNP [dm3] 2L_2548057_SNP [dm6]	T	G	3.964e^-5	0.934	INTERGENIC
3L	20456601	3L_20456601_SNP [dm3] 3L_20463501_SNP [dm6]	T	A	3.968e^-5	0.934	INTRON CG5195
3R	11325721	3R_11325721_SNP [dm3] 3R_15499999_SNP [dm6]	G	A	4.000e^-5	0.934	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	18918330	2R_18918330_SNP [dm3] 2R_23030807_SNP [dm6]	C	T	4.091e^-5	0.934	INTRON twi & 1 other
2L	19451705	2L_19451705_DEL [dm3] 2L_19451705_DEL [dm6]	AA	A	4.142e^-5	0.934	INTRON Top2	TF binding site mE1_TFBS_sens
2L	15244672	2L_15244672_SNP [dm3] 2L_15244672_SNP [dm6]	G	A	4.171e^-5	0.934	INTRON ZnT35C
X	7001657	X_7001657_SNP [dm3] X_7107624_SNP [dm6]	C	T	4.174e^-5	0.934	SYNONYMOUS_CODING fz4	TF binding site mE1_TFBS_sens
2L	2548055	2L_2548055_SNP [dm3] 2L_2548055_SNP [dm6]	T	A	4.298e^-5	0.934	INTERGENIC
2L	5090990	2L_5090990_SNP [dm3] 2L_5090990_SNP [dm6]	A	G	4.371e^-5	0.934	INTRON pgant5
2R	20703654	2R_20703654_SNP [dm3] 2R_24816131_SNP [dm6]	A	G	4.376e^-5	0.934	INTRON Dll
X	11742936	X_11742936_SNP [dm3] X_11848903_SNP [dm6]	A	G	4.428e^-5	0.934	DOWNSTREAM CR45619 INTERGENIC
2R	2768828	2R_2768828_SNP [dm3] 2R_6881323_SNP [dm6]	A	T	4.464e^-5	0.934	UPSTREAM Spn42Dc & 1 other INTRON Spn42Dc
3R	23875684	3R_23875684_SNP [dm3] 3R_28049962_SNP [dm6]	C	A	4.571e^-5	0.934	NON_SYNONYMOUS_CODING CG34362 INTRON CG34362	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
X	7001513	X_7001513_SNP [dm3] X_7107480_SNP [dm6]	C	G	4.575e^-5	0.934	SYNONYMOUS_CODING fz4
2L	2170559	2L_2170559_SNP [dm3] 2L_2170559_SNP [dm6]	G	A	4.648e^-5	0.934	INTRON aop	regulatory region REDfly_CRMs
X	19416192	X_19416192_SNP [dm3] X_19522159_SNP [dm6]	T	C	4.741e^-5	0.934	UTR_5_PRIME CoRest UPSTREAM l_1_G0156 INTRON CoRest	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens mE1_TFBS_Ubx mE1_TFBS_zfh1
3R	21979327	3R_21979327_DEL [dm3] 3R_26153605_DEL [dm6]	GG	G	4.755e^-5	0.934	INTERGENIC
2L	4811922	2L_4811922_SNP [dm3] 2L_4811922_SNP [dm6]	A	G	4.799e^-5	0.934	EXON CR45297	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_zfh1
3L	14387814	3L_14387814_SNP [dm3] 3L_14394714_SNP [dm6]	G	A	4.830e^-5	0.934	INTERGENIC
2L	1414167	2L_1414167_SNP [dm3] 2L_1414167_SNP [dm6]	C	A	4.853e^-5	0.934	INTRON lea	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	1414177	2L_1414177_SNP [dm3] 2L_1414177_SNP [dm6]	C	T	4.853e^-5	0.934	INTRON lea	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	2548073	2L_2548073_SNP [dm3] 2L_2548073_SNP [dm6]	G	A	4.872e^-5	0.934	INTERGENIC
2R	8121141	2R_8121141_SNP [dm3] 2R_12233636_SNP [dm6]	G	A	4.949e^-5	0.934	DOWNSTREAM CR44313 INTERGENIC
X	6854738	X_6854738_SNP [dm3] X_6960705_SNP [dm6]	C	G	4.999e^-5	0.934	INTRON CG14431 & 1 other
3R	22587358	3R_22587358_SNP [dm3] 3R_26761636_SNP [dm6]	C	T	5.013e^-5	0.934	INTERGENIC
2R	2497620	2R_2497620_SNP [dm3] 2R_6610115_SNP [dm6]	G	T	5.068e^-5	0.934	UPSTREAM jing INTRON jing	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	8536111	3L_8536111_SNP [dm3] 3L_8543011_SNP [dm6]	G	A	5.129e^-5	0.934	INTERGENIC	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA
2R	2747286	2R_2747286_SNP [dm3] 2R_6859781_SNP [dm6]	C	A	5.209e^-5	0.934	INTERGENIC
3R	20245171	3R_20245171_SNP [dm3] 3R_24419449_SNP [dm6]	G	A	5.241e^-5	0.934	INTRON nAChRalpha1
X	11742946	X_11742946_SNP [dm3] X_11848913_SNP [dm6]	C	T	5.267e^-5	0.934	DOWNSTREAM CR45619 INTERGENIC
2L	8057506	2L_8057506_SNP [dm3] 2L_8057506_SNP [dm6]	C	T	5.315e^-5	0.934	SYNONYMOUS_CODING poe
2L	17111901	2L_17111901_SNP [dm3] 2L_17111901_SNP [dm6]	T	C	5.338e^-5	0.934	INTERGENIC

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By genomic position
Variant impact
Gene name

Food_Intake_SUC phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results