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=2.263e^-9)
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_3R_Mo	0.09663

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	5.4177	0.0666
In_3R_Mo	5.7557	0.0563

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2167 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	16997846	2R_16997846_SNP [dm3] 2R_21110341_SNP [dm6]	C	T	1.863e^-7	0.35	INTRON ktub
3R	23267160	3R_23267160_SNP [dm3] 3R_27441438_SNP [dm6]	C	T	9.165e^-7	0.537	UPSTREAM CG44290 DOWNSTREAM CG43447 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	23286867	3R_23286867_SNP [dm3] 3R_27461145_SNP [dm6]	C	T	1.740e^-6	0.537	INTERGENIC
2R	6388804	2R_6388804_SNP [dm3] 2R_10501299_SNP [dm6]	C	G	1.774e^-6	0.537	SYNONYMOUS_CODING lola DOWNSTREAM lola INTRON lola	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2L	6726865	2L_6726865_SNP [dm3] 2L_6726865_SNP [dm6]	T	A	2.383e^-6	0.537	INTRON Liprin-alpha
2L	6726842	2L_6726842_SNP [dm3] 2L_6726842_SNP [dm6]	A	G	2.659e^-6	0.537	INTRON Liprin-alpha
2L	6541787	2L_6541787_SNP [dm3] 2L_6541787_SNP [dm6]	A	T	2.908e^-6	0.537	INTRON eya	TF binding site mE1_TFBS_inv mE1_TFBS_Kr
3L	5379735	3L_5379735_SNP [dm3] 3L_5386635_SNP [dm6]	T	C	2.954e^-6	0.537	INTERGENIC
3R	25981669	3R_25981669_SNP [dm3] 3R_30155947_SNP [dm6]	G	A	3.065e^-6	0.537	SYNONYMOUS_CODING CG11498	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	15062239	3R_15062239_SNP [dm3] 3R_19236517_SNP [dm6]	C	T	3.557e^-6	0.537	INTRON unc79
3R	25981617	3R_25981617_SNP [dm3] 3R_30155895_SNP [dm6]	C	A	3.576e^-6	0.537	INTRON CG11498	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	12993472	2R_12993472_SNP [dm3] 2R_17105967_SNP [dm6]	C	T	3.628e^-6	0.537	SYNONYMOUS_CODING CG30456
2L	12495504	2L_12495504_DEL [dm3] 2L_12495504_DEL [dm6]	GATACGG	G	3.932e^-6	0.537	INTRON bun
3L	936635	3L_936635_INS [dm3] 3L_936635_INS [dm6]	G	GCATCCG	4.362e^-6	0.537	INTRON Glut1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	23321121	3R_23321121_SNP [dm3] 3R_27495399_SNP [dm6]	G	A	4.509e^-6	0.537	INTERGENIC
3L	15760116	3L_15760116_SNP [dm3] 3L_15767016_SNP [dm6]	C	T	4.795e^-6	0.537	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	17424740	2R_17424740_SNP [dm3] 2R_21537235_SNP [dm6]	G	A	4.870e^-6	0.537	SYNONYMOUS_CODING CG30287 UPSTREAM CG30286 INTRON Egfr	TF binding site mE1_TFBS_sens
3L	18760149	3L_18760149_SNP [dm3] 3L_18767049_SNP [dm6]	A	T	5.611e^-6	0.585	INTRON ftz-f1
3L	5379727	3L_5379727_SNP [dm3] 3L_5386627_SNP [dm6]	C	T	6.517e^-6	0.626	INTERGENIC
3R	13349142	3R_13349142_SNP [dm3] 3R_17523420_SNP [dm6]	G	A	6.676e^-6	0.626	INTERGENIC
3R	17823564	3R_17823564_SNP [dm3] 3R_21997842_SNP [dm6]	T	A	9.651e^-6	0.762	INTRON Eip93F
2L	12346148	2L_12346148_SNP [dm3] 2L_12346148_SNP [dm6]	A	T	1.008e^-5	0.762	INTRON bru-2
3L	2807667	3L_2807667_SNP [dm3] 3L_2807667_SNP [dm6]	G	T	1.009e^-5	0.762	INTRON CG43444	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
3R	11495013	3R_11495013_SNP [dm3] 3R_15669291_SNP [dm6]	A	T	1.016e^-5	0.762	DOWNSTREAM CR43849 INTRON pxb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	19198824	2L_19198824_SNP [dm3] 2L_19198824_SNP [dm6]	T	C	1.090e^-5	0.762	INTRON drl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd
3R	19140810	3R_19140810_DEL [dm3] 3R_23315088_DEL [dm6]	TTT	T	1.102e^-5	0.762	UPSTREAM pnt INTRON pnt	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_tll BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
X	21136189	X_21136189_SNP [dm3] X_21265162_SNP [dm6]	G	A	1.203e^-5	0.762	INTRON CG32521
2L	12490796	2L_12490796_SNP [dm3] 2L_12490796_SNP [dm6]	G	A	1.280e^-5	0.762	INTRON bun
2R	6681216	2R_6681216_SNP [dm3] 2R_10793711_SNP [dm6]	A	G	1.300e^-5	0.762	DOWNSTREAM mthl13 INTRON CG33144
X	7018239	X_7018239_SNP [dm3] X_7124206_SNP [dm6]	C	G	1.404e^-5	0.762	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	6353025	2L_6353025_SNP [dm3] 2L_6353025_SNP [dm6]	G	A	1.433e^-5	0.762	INTRON ppk7	TF binding site mE1_TFBS_cad
2R	11768749	2R_11768749_SNP [dm3] 2R_15881244_SNP [dm6]	C	A	1.455e^-5	0.762	INTRON sli	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	15062248	3R_15062248_SNP [dm3] 3R_19236526_SNP [dm6]	T	A	1.500e^-5	0.762	INTRON unc79
3R	15062247	3R_15062247_SNP [dm3] 3R_19236525_SNP [dm6]	G	A	1.578e^-5	0.762	INTRON unc79
2L	6035179	2L_6035179_SNP [dm3] 2L_6035179_SNP [dm6]	C	A	1.582e^-5	0.762	SYNONYMOUS_CODING mtm UPSTREAM CG9109	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3L	16818936	3L_16818936_SNP [dm3] 3L_16825836_SNP [dm6]	T	A	1.608e^-5	0.762	INTRON CG13024
3L	15760239	3L_15760239_SNP [dm3] 3L_15767139_SNP [dm6]	T	C	1.612e^-5	0.762	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	12269717	2R_12269717_SNP [dm3] 2R_16382212_SNP [dm6]	G	T	1.642e^-5	0.762	UTR_3_PRIME CG43187 DOWNSTREAM CG43187
3L	5383897	3L_5383897_SNP [dm3] 3L_5390797_SNP [dm6]	A	T	1.675e^-5	0.762	INTERGENIC
3R	15062216	3R_15062216_SNP [dm3] 3R_19236494_SNP [dm6]	T	C	1.844e^-5	0.762	INTRON unc79
2L	5196557	2L_5196557_INS [dm3] 2L_5196557_INS [dm6]	G	GCTGACACATT...	2.019e^-5	0.762	DOWNSTREAM snmRNA:128 INTRON Msp300	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2L	5196559	2L_5196559_SNP [dm3] 2L_5196559_SNP [dm6]	A	C	2.019e^-5	0.762	DOWNSTREAM snmRNA:128 INTRON Msp300	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2L	5196560	2L_5196560_SNP [dm3] 2L_5196560_SNP [dm6]	A	C	2.019e^-5	0.762	DOWNSTREAM snmRNA:128 INTRON Msp300	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2R	17424716	2R_17424716_SNP [dm3] 2R_21537211_SNP [dm6]	G	A	2.089e^-5	0.762	SYNONYMOUS_CODING CG30287 UPSTREAM CG30286 INTRON Egfr	TF binding site mE1_TFBS_sens
2L	12621211	2L_12621211_SNP [dm3] 2L_12621211_SNP [dm6]	A	T	2.156e^-5	0.762	INTRON Ref2 & 1 other
2R	6681119	2R_6681119_SNP [dm3] 2R_10793614_SNP [dm6]	A	G	2.165e^-5	0.762	DOWNSTREAM mthl13 INTRON CG33144
2R	12269740	2R_12269740_SNP [dm3] 2R_16382235_SNP [dm6]	C	T	2.172e^-5	0.762	UTR_3_PRIME CG43187 DOWNSTREAM CG43187
X	11558741	X_11558741_SNP [dm3] X_11664708_SNP [dm6]	G	C	2.175e^-5	0.762	INTRON Ptp10D
X	14808101	X_14808101_SNP [dm3] X_14914068_SNP [dm6]	C	T	2.192e^-5	0.762	UPSTREAM CG12398 INTRON Flo2
2L	5196555	2L_5196555_SNP [dm3] 2L_5196555_SNP [dm6]	A	T	2.202e^-5	0.762	DOWNSTREAM snmRNA:128 INTRON Msp300	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2R	14693535	2R_14693535_SNP [dm3] 2R_18806030_SNP [dm6]	T	C	2.236e^-5	0.762	INTRON CR44468 EXON CR44468	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	11558730	X_11558730_SNP [dm3] X_11664697_SNP [dm6]	T	C	2.271e^-5	0.762	INTRON Ptp10D
2L	11962505	2L_11962505_SNP [dm3] 2L_11962505_SNP [dm6]	A	T	2.336e^-5	0.762	INTRON CR43314
2L	10620568	2L_10620568_SNP [dm3] 2L_10620568_SNP [dm6]	T	G	2.450e^-5	0.762	SYNONYMOUS_CODING Trim9
3L	15760152	3L_15760152_SNP [dm3] 3L_15767052_SNP [dm6]	A	G	2.473e^-5	0.762	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	12476355	2L_12476355_SNP [dm3] 2L_12476355_SNP [dm6]	T	G	2.610e^-5	0.762	INTRON bun
2R	9333427	2R_9333427_SNP [dm3] 2R_13445922_SNP [dm6]	A	G	2.642e^-5	0.762	SYNONYMOUS_CODING CG30062 UPSTREAM cnn INTRON cnn	TF binding site mE1_TFBS_HSA
2L	5714048	2L_5714048_SNP [dm3] 2L_5714048_SNP [dm6]	T	C	2.657e^-5	0.762	DOWNSTREAM CG7236 INTERGENIC
2L	5196549	2L_5196549_SNP [dm3] 2L_5196549_SNP [dm6]	A	C	2.670e^-5	0.762	DOWNSTREAM snmRNA:128 INTRON Msp300	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
2R	6681118	2R_6681118_SNP [dm3] 2R_10793613_SNP [dm6]	A	T	2.694e^-5	0.762	DOWNSTREAM mthl13 INTRON CG33144
2L	19198821	2L_19198821_SNP [dm3] 2L_19198821_SNP [dm6]	A	C	2.706e^-5	0.762	INTRON drl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd
3R	16647286	3R_16647286_SNP [dm3] 3R_20821564_SNP [dm6]	C	A	2.720e^-5	0.762	UPSTREAM RpS20 INTRON CG17271	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cnc mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx mE1_TFBS_zfh1
2R	11774944	2R_11774944_DEL [dm3] 2R_15887439_DEL [dm6]	CGTTTTCCCCTGGCTT...	TAA	2.728e^-5	0.762	INTRON sli	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	5379584	3L_5379584_SNP [dm3] 3L_5386484_SNP [dm6]	A	G	2.847e^-5	0.762	INTERGENIC
3R	13334653	3R_13334653_SNP [dm3] 3R_17508931_SNP [dm6]	C	T	2.868e^-5	0.762	INTERGENIC
3R	17928836	3R_17928836_SNP [dm3] 3R_22103114_SNP [dm6]	C	T	2.870e^-5	0.762	UPSTREAM CG13407 INTRON CG5778
3R	23623173	3R_23623173_SNP [dm3] 3R_27797451_SNP [dm6]	G	A	2.903e^-5	0.762	SYNONYMOUS_CODING CG34353
2R	9594334	2R_9594334_SNP [dm3] 2R_13706829_SNP [dm6]	C	T	2.968e^-5	0.762	SYNONYMOUS_CODING fas	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
2R	17424737	2R_17424737_SNP [dm3] 2R_21537232_SNP [dm6]	G	A	2.988e^-5	0.762	SYNONYMOUS_CODING CG30287 UPSTREAM CG30286 INTRON Egfr	TF binding site mE1_TFBS_sens
3R	13348981	3R_13348981_SNP [dm3] 3R_17523259_SNP [dm6]	A	G	2.996e^-5	0.762	INTERGENIC
2L	16002284	2L_16002284_SNP [dm3] 2L_16002284_SNP [dm6]	G	T	3.043e^-5	0.762	DOWNSTREAM CG34167 INTRON beat-Ic EXON CR43825	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	6610150	3L_6610150_SNP [dm3] 3L_6617050_SNP [dm6]	C	T	3.050e^-5	0.762	SYNONYMOUS_CODING CG8398
2R	8905442	2R_8905442_SNP [dm3] 2R_13017937_SNP [dm6]	A	T	3.062e^-5	0.762	INTERGENIC	TF binding site BDTNP1_TFBS_da
X	7230857	X_7230857_SNP [dm3] X_7336824_SNP [dm6]	C	A	3.068e^-5	0.762	UPSTREAM CBP INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_z mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_zfh1
2R	7412905	2R_7412905_SNP [dm3] 2R_11525400_SNP [dm6]	C	A	3.089e^-5	0.762	INTRON en	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	15602071	3L_15602071_DEL [dm3] 3L_15608971_DEL [dm6]	TTCT	T	3.089e^-5	0.762	UTR_3_PRIME RhoGAP71E & 1 other
2R	2408449	2R_2408449_SNP [dm3] 2R_6520944_SNP [dm6]	C	T	3.307e^-5	0.797	INTRON jing
3L	12813192	3L_12813192_SNP [dm3] 3L_12820092_SNP [dm6]	G	A	3.341e^-5	0.797	NON_SYNONYMOUS_CODING CG42588
3R	19140723	3R_19140723_SNP [dm3] 3R_23315001_SNP [dm6]	G	A	3.367e^-5	0.797	UPSTREAM pnt INTRON pnt	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_tll BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
3L	14630881	3L_14630881_SNP [dm3] 3L_14637781_SNP [dm6]	C	T	3.401e^-5	0.797	INTRON dlp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
3L	5966799	3L_5966799_INS [dm3] 3L_5973699_INS [dm6]	T	TGGCAGAGTAAGCCCCT...	3.459e^-5	0.801	INTRON CG10479	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi
3R	15062307	3R_15062307_SNP [dm3] 3R_19236585_SNP [dm6]	T	C	3.650e^-5	0.812	INTRON unc79
X	11558448	X_11558448_SNP [dm3] X_11664415_SNP [dm6]	C	T	3.725e^-5	0.812	INTRON Ptp10D
3R	23980433	3R_23980433_SNP [dm3] 3R_28154711_SNP [dm6]	G	A	3.738e^-5	0.812	INTRON CG34354	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	4775134	2L_4775134_SNP [dm3] 2L_4775134_SNP [dm6]	G	A	3.783e^-5	0.812	INTRON CG15630
2L	12447331	2L_12447331_SNP [dm3] 2L_12447331_SNP [dm6]	C	T	3.804e^-5	0.812	SYNONYMOUS_CODING CG5421
2L	5428938	2L_5428938_SNP [dm3] 2L_5428938_SNP [dm6]	T	C	3.804e^-5	0.812	INTERGENIC
2L	19762308	2L_19762308_SNP [dm3] 2L_19762308_SNP [dm6]	G	A	3.834e^-5	0.812	INTRON fbp	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	5714083	2L_5714083_SNP [dm3] 2L_5714083_SNP [dm6]	A	C	3.863e^-5	0.812	DOWNSTREAM CG7236 INTERGENIC
3L	16661555	3L_16661555_SNP [dm3] 3L_16668455_SNP [dm6]	C	T	3.909e^-5	0.812	UPSTREAM Galphaf INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
3R	18568886	3R_18568886_SNP [dm3] 3R_22743164_SNP [dm6]	G	A	3.985e^-5	0.812	SYNONYMOUS_CODING vret DOWNSTREAM CG6985
X	11558451	X_11558451_SNP [dm3] X_11664418_SNP [dm6]	C	T	3.987e^-5	0.812	INTRON Ptp10D
2L	3127602	2L_3127602_SNP [dm3] 2L_3127602_SNP [dm6]	G	A	4.024e^-5	0.812	SYNONYMOUS_CODING toc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	1602538	2R_1602538_SNP [dm3] 2R_5715033_SNP [dm6]	C	A	4.150e^-5	0.814	INTRON ap	TF binding site mE1_TFBS_cad
X	3528281	X_3528281_SNP [dm3] X_3634248_SNP [dm6]	A	G	4.160e^-5	0.814	INTRON AstA-R1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12269971	2R_12269971_SNP [dm3] 2R_16382466_SNP [dm6]	C	T	4.255e^-5	0.814	UTR_3_PRIME CG43187 DOWNSTREAM CG43187
2R	20445422	2R_20445422_INS [dm3] 2R_24557899_INS [dm6]	T	TT	4.279e^-5	0.814	DOWNSTREAM ITP INTRON ITP
3R	12688518	3R_12688518_SNP [dm3] 3R_16862796_SNP [dm6]	T	C	4.329e^-5	0.814	INTRON iab-8	TF binding site mE1_TFBS_cad
X	18184280	X_18184280_SNP [dm3] X_18290247_SNP [dm6]	T	C	4.356e^-5	0.814	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	10349571	2L_10349571_SNP [dm3] 2L_10349571_SNP [dm6]	A	T	4.371e^-5	0.814	INTRON CG34367

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GWAS results