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=2.299e^-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_2R_NS	0.0100874
In_3R_Mo	0.0009098

Kruskal-Wallis test

Covariate	χ²	p-value
In_2L_t	4.7055	0.0951
In_2R_NS	12.4882	0.0019
In_3R_Mo	7.2414	0.0268

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1586 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
3L	8023934	3L_8023934_SNP [dm3] 3L_8030834_SNP [dm6]	T	G	4.715e^-7	0.884	INTRON nmo
2R	13860330	2R_13860330_SNP [dm3] 2R_17972825_SNP [dm6]	T	C	1.576e^-6	1	INTERGENIC
3R	26676395	3R_26676395_DEL [dm3] 3R_30850673_DEL [dm6]	TT	G	2.982e^-6	1	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	672765	2L_672765_SNP [dm3] 2L_672765_SNP [dm6]	A	T	4.670e^-6	1	INTRON ds	TF binding site mE1_TFBS_HSA
2R	13860324	2R_13860324_SNP [dm3] 2R_17972819_SNP [dm6]	G	C	4.973e^-6	1	INTERGENIC
2L	20398927	2L_20398927_SNP [dm3] 2L_20398927_SNP [dm6]	T	A	5.916e^-6	1	INTRON CG10947
3L	4034312	3L_4034312_SNP [dm3] 3L_4034312_SNP [dm6]	G	T	8.235e^-6	1	NON_SYNONYMOUS_CODING Gr64e UTR_3_PRIME Gr64d DOWNSTREAM Gr64d EXON CR45042
3L	15186426	3L_15186426_SNP [dm3] 3L_15193326_SNP [dm6]	G	T	9.117e^-6	1	INTERGENIC
X	3705371	X_3705371_SNP [dm3] X_3811338_SNP [dm6]	T	C	9.883e^-6	1	UPSTREAM ec DOWNSTREAM fd3F INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
2R	13860417	2R_13860417_SNP [dm3] 2R_17972912_SNP [dm6]	G	A	1.018e^-5	1	INTERGENIC
3R	9698944	3R_9698944_SNP [dm3] 3R_13873222_SNP [dm6]	T	A	1.041e^-5	1	INTRON E5	TF binding site mE1_TFBS_cad
3L	1275927	3L_1275927_SNP [dm3] 3L_1275927_SNP [dm6]	T	G	1.046e^-5	1	UPSTREAM CG32333 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
X	13153157	X_13153157_SNP [dm3] X_13259124_SNP [dm6]	C	T	1.079e^-5	1	UTR_5_PRIME comt UPSTREAM CG15742 & 1 other
3L	10101968	3L_10101968_SNP [dm3] 3L_10108868_SNP [dm6]	T	C	1.125e^-5	1	INTRON dpr6	TF binding site BDTNP1_TFBS_twi
3L	8744765	3L_8744765_SNP [dm3] 3L_8751665_SNP [dm6]	C	T	1.192e^-5	1	EXON CR44527	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	3467760	3L_3467760_SNP [dm3] 3L_3467760_SNP [dm6]	G	T	1.247e^-5	1	NON_SYNONYMOUS_CODING CycJ UTR_3_PRIME CycJ DOWNSTREAM CG14971
3L	3468506	3L_3468506_SNP [dm3] 3L_3468506_SNP [dm6]	C	A	1.247e^-5	1	UTR_3_PRIME CG14971 DOWNSTREAM CycJ
2R	8717051	2R_8717051_SNP [dm3] 2R_12829546_SNP [dm6]	T	G	1.253e^-5	1	INTERGENIC	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
2L	20401614	2L_20401614_SNP [dm3] 2L_20401614_SNP [dm6]	C	T	1.256e^-5	1	INTRON CG10947
3L	10101971	3L_10101971_DEL [dm3] 3L_10108871_DEL [dm6]	TT	T	1.265e^-5	1	INTRON dpr6	TF binding site BDTNP1_TFBS_twi
2R	17366933	2R_17366933_SNP [dm3] 2R_21479428_SNP [dm6]	T	A	1.294e^-5	1	INTRON Sdc	TF binding site BDTNP1_TFBS_dl
2L	21788039	2L_21788039_SNP [dm3] 2L_21788039_SNP [dm6]	T	C	1.330e^-5	1	INTRON CG31612	TF binding site mE1_TFBS_HSA transposable element FlyBase
2R	20514458	2R_20514458_SNP [dm3] 2R_24626935_SNP [dm6]	C	T	1.418e^-5	1	INTRON CG13594	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
3R	19766626	3R_19766626_SNP [dm3] 3R_23940904_SNP [dm6]	C	T	1.436e^-5	1	INTRON Gdh
3L	1491832	3L_1491832_SNP [dm3] 3L_1491832_SNP [dm6]	G	A	1.510e^-5	1	SYNONYMOUS_CODING CG12084	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	672790	2L_672790_SNP [dm3] 2L_672790_SNP [dm6]	T	C	1.653e^-5	1	INTRON ds	TF binding site mE1_TFBS_HSA
3L	10101824	3L_10101824_INS [dm3] 3L_10108724_INS [dm6]	T	TTTATAAATT	1.697e^-5	1	INTRON dpr6
2R	13860309	2R_13860309_SNP [dm3] 2R_17972804_SNP [dm6]	T	C	1.717e^-5	1	INTERGENIC
2R	5643635	2R_5643635_SNP [dm3] 2R_9756130_SNP [dm6]	G	A	1.756e^-5	1	SYNONYMOUS_CODING trpl DOWNSTREAM CG1690
2L	1635286	2L_1635286_SNP [dm3] 2L_1635286_SNP [dm6]	T	C	1.768e^-5	1	INTERGENIC
3R	10245642	3R_10245642_SNP [dm3] 3R_14419920_SNP [dm6]	T	C	1.792e^-5	1	INTRON cv-c & 1 other
2L	13310562	2L_13310562_SNP [dm3] 2L_13310562_SNP [dm6]	T	C	1.861e^-5	1	INTRON CG43778
3R	19293255	3R_19293255_SNP [dm3] 3R_23467533_SNP [dm6]	T	G	1.920e^-5	1	INTRON CG4374
3R	17793294	3R_17793294_SNP [dm3] 3R_21967572_SNP [dm6]	G	C	2.146e^-5	1	INTRON Eip93F
2L	672766	2L_672766_SNP [dm3] 2L_672766_SNP [dm6]	A	G	2.247e^-5	1	INTRON ds	TF binding site mE1_TFBS_HSA
3L	10283129	3L_10283129_SNP [dm3] 3L_10290029_SNP [dm6]	C	A	2.497e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	10464425	3R_10464425_SNP [dm3] 3R_14638703_SNP [dm6]	G	T	2.520e^-5	1	SYNONYMOUS_CODING Cad88C INTRON CG7886	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	16257345	3R_16257345_SNP [dm3] 3R_20431623_SNP [dm6]	A	G	2.569e^-5	1	INTRON Gfrl
3R	23358350	3R_23358350_SNP [dm3] 3R_27532628_SNP [dm6]	G	A	2.688e^-5	1	SYNONYMOUS_CODING CG12885	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3L	8023719	3L_8023719_SNP [dm3] 3L_8030619_SNP [dm6]	T	C	2.706e^-5	1	INTRON nmo
3L	10283082	3L_10283082_SNP [dm3] 3L_10289982_SNP [dm6]	G	T	2.848e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3L	8023762	3L_8023762_SNP [dm3] 3L_8030662_SNP [dm6]	A	G	2.856e^-5	1	INTRON nmo
X	5575305	X_5575305_SNP [dm3] X_5681272_SNP [dm6]	G	A	3.184e^-5	1	SYNONYMOUS_CODING Gr5a EXON CR44958	TF binding site mE1_TFBS_cad
3R	21073552	3R_21073552_SNP [dm3] 3R_25247830_SNP [dm6]	A	G	3.220e^-5	1	UPSTREAM Nup37 & 1 other INTRON Nup37	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens mE1_TFBS_Ubx
3L	10283073	3L_10283073_SNP [dm3] 3L_10289973_SNP [dm6]	G	T	3.334e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
2L	11693202	2L_11693202_SNP [dm3] 2L_11693202_SNP [dm6]	T	C	3.336e^-5	1	INTERGENIC	TF binding site mE1_TFBS_inv
2R	13860423	2R_13860423_SNP [dm3] 2R_17972918_SNP [dm6]	T	C	3.438e^-5	1	INTERGENIC
X	10746102	X_10746102_DEL [dm3] X_10852069_DEL [dm6]	CTTGCATCAGTGC...	C	3.584e^-5	1	UTR_3_PRIME CG2202 DOWNSTREAM feo	TF binding site mE1_TFBS_cad
2L	13310536	2L_13310536_SNP [dm3] 2L_13310536_SNP [dm6]	G	A	3.696e^-5	1	INTRON CG43778
3R	10248180	3R_10248180_SNP [dm3] 3R_14422458_SNP [dm6]	C	G	3.727e^-5	1	DOWNSTREAM natalisin INTRON cv-c EXON CR44176
3R	26542582	3R_26542582_SNP [dm3] 3R_30716860_SNP [dm6]	G	A	3.790e^-5	1	INTERGENIC
3L	1491923	3L_1491923_SNP [dm3] 3L_1491923_SNP [dm6]	G	A	3.836e^-5	1	INTRON CG12084	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	14540205	3R_14540205_SNP [dm3] 3R_18714483_SNP [dm6]	A	G	3.900e^-5	1	SYNONYMOUS_CODING VAChT INTRON Cha
3L	12404074	3L_12404074_SNP [dm3] 3L_12410974_SNP [dm6]	A	T	4.197e^-5	1	INTRON CG32103
3R	24574649	3R_24574649_SNP [dm3] 3R_28748927_SNP [dm6]	G	A	4.251e^-5	1	UTR_3_PRIME CG10000	TF binding site mE1_TFBS_chinmo
3R	27200894	3R_27200894_SNP [dm3] 3R_31375172_SNP [dm6]	G	T	4.432e^-5	1	DOWNSTREAM gskt INTERGENIC
3R	15099260	3R_15099260_SNP [dm3] 3R_19273538_SNP [dm6]	C	A	4.573e^-5	1	INTERGENIC
3R	4918479	3R_4918479_SNP [dm3] 3R_9092757_SNP [dm6]	T	C	4.593e^-5	1	INTRON pum
2R	20524562	2R_20524562_INS [dm3] 2R_24637039_INS [dm6]	G	GTTCTAAGTTTTCATTG...	4.625e^-5	1	INTRON CG13594	TF binding site mE1_TFBS_chinmo
2R	20524611	2R_20524611_SNP [dm3] 2R_24637088_SNP [dm6]	T	A	4.702e^-5	1	INTRON CG13594	TF binding site mE1_TFBS_chinmo
3L	1269381	3L_1269381_SNP [dm3] 3L_1269381_SNP [dm6]	G	A	4.751e^-5	1	INTRON CG9134
3L	1273531	3L_1273531_SNP [dm3] 3L_1273531_SNP [dm6]	C	G	4.780e^-5	1	INTRON CG9134
3R	16138212	3R_16138212_SNP [dm3] 3R_20312490_SNP [dm6]	C	T	4.810e^-5	1	INTRON CG42668
3L	1273264	3L_1273264_SNP [dm3] 3L_1273264_SNP [dm6]	A	T	4.835e^-5	1	INTRON CG9134
3L	1273267	3L_1273267_SNP [dm3] 3L_1273267_SNP [dm6]	C	G	4.835e^-5	1	INTRON CG9134
3R	23630469	3R_23630469_DEL [dm3] 3R_27804747_DEL [dm6]	GG	G	5.018e^-5	1	INTRON CG34353
2L	13310557	2L_13310557_SNP [dm3] 2L_13310557_SNP [dm6]	A	T	5.030e^-5	1	INTRON CG43778
3L	21968130	3L_21968130_SNP [dm3] 3L_21975030_SNP [dm6]	G	A	5.316e^-5	1	INTRON CG7470
3L	1261305	3L_1261305_SNP [dm3] 3L_1261305_SNP [dm6]	A	G	5.319e^-5	1	INTRON CG9134
3R	26481688	3R_26481688_SNP [dm3] 3R_30655966_SNP [dm6]	T	G	5.323e^-5	1	INTERGENIC
3L	1491889	3L_1491889_SNP [dm3] 3L_1491889_SNP [dm6]	C	T	5.403e^-5	1	SYNONYMOUS_CODING CG12084	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3L	1273263	3L_1273263_SNP [dm3] 3L_1273263_SNP [dm6]	G	C	5.473e^-5	1	INTRON CG9134
3L	10166386	3L_10166386_SNP [dm3] 3L_10173286_SNP [dm6]	C	T	5.504e^-5	1	INTRON dpr10
X	11822640	X_11822640_SNP [dm3] X_11928607_SNP [dm6]	A	G	5.710e^-5	1	SYNONYMOUS_CODING CG10362
2R	13860306	2R_13860306_SNP [dm3] 2R_17972801_SNP [dm6]	A	T	5.745e^-5	1	INTERGENIC
X	19777797	X_19777797_INS [dm3] X_19883764_INS [dm6]	C	CATAC	5.800e^-5	1	INTRON Hers	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
X	21908202	X_21908202_SNP [dm3] X_22506366_SNP [dm6]	A	G	5.862e^-5	1	INTRON l_1_G0196
2R	20524511	2R_20524511_DEL [dm3] 2R_24636988_DEL [dm6]	CT	C	5.964e^-5	1	INTRON CG13594	TF binding site mE1_TFBS_chinmo
3R	23869287	3R_23869287_SNP [dm3] 3R_28043565_SNP [dm6]	A	T	6.023e^-5	1	INTRON CG34362
X	16010164	X_16010164_SNP [dm3] X_16116131_SNP [dm6]	T	A	6.213e^-5	1	INTERGENIC
3L	8796526	3L_8796526_SNP [dm3] 3L_8803426_SNP [dm6]	C	T	6.253e^-5	1	SYNONYMOUS_CODING CG34426 DOWNSTREAM CG32023
3L	1495747	3L_1495747_SNP [dm3] 3L_1495747_SNP [dm6]	C	T	6.298e^-5	1	INTRON CG12084	TF binding site BDTNP1_TFBS_dl
3L	17475875	3L_17475875_SNP [dm3] 3L_17482775_SNP [dm6]	C	T	6.334e^-5	1	INTRON CG6333
3L	9305767	3L_9305767_SNP [dm3] 3L_9312667_SNP [dm6]	C	T	6.349e^-5	1	INTERGENIC
2R	20213635	2R_20213635_SNP [dm3] 2R_24326112_SNP [dm6]	G	A	6.363e^-5	1	INTRON CR44810
3R	26481685	3R_26481685_SNP [dm3] 3R_30655963_SNP [dm6]	A	G	6.401e^-5	1	INTERGENIC
2L	11668299	2L_11668299_SNP [dm3] 2L_11668299_SNP [dm6]	G	A	6.451e^-5	1	INTERGENIC
2R	17840108	2R_17840108_SNP [dm3] 2R_21952603_SNP [dm6]	G	T	6.564e^-5	1	DOWNSTREAM CG13488 INTERGENIC	TF binding site mE1_TFBS_inv
2L	4609387	2L_4609387_DEL [dm3] 2L_4609387_DEL [dm6]	AT	G	6.645e^-5	1	INTRON dp	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	26633501	3R_26633501_SNP [dm3] 3R_30807779_SNP [dm6]	C	T	6.851e^-5	1	SYNONYMOUS_CODING dj-1beta UPSTREAM cindr	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2L	7263113	2L_7263113_SNP [dm3] 2L_7263113_SNP [dm6]	G	C	6.895e^-5	1	INTRON Wnt4	TF binding site mE1_TFBS_cad
3L	13260162	3L_13260162_SNP [dm3] 3L_13267062_SNP [dm6]	T	C	6.914e^-5	1	INTRON caps	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	10901196	3L_10901196_SNP [dm3] 3L_10908096_SNP [dm6]	T	C	6.947e^-5	1	INTERGENIC
3L	5096637	3L_5096637_SNP [dm3] 3L_5096637_SNP [dm6]	C	A	6.998e^-5	1	INTERGENIC
X	16010160	X_16010160_SNP [dm3] X_16116127_SNP [dm6]	G	T	7.183e^-5	1	INTERGENIC
X	16010161	X_16010161_SNP [dm3] X_16116128_SNP [dm6]	T	A	7.183e^-5	1	INTERGENIC
2R	16381813	2R_16381813_INS [dm3] 2R_20494308_INS [dm6]	C	CATCC	7.194e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	8259604	3L_8259604_INS [dm3] 3L_8266504_INS [dm6]	A	ATATA	7.264e^-5	1	INTRON Dscam4
3L	4599980	3L_4599980_SNP [dm3] 3L_4599980_SNP [dm6]	G	A	7.319e^-5	1	INTRON Src64B	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
X	5336233	X_5336233_SNP [dm3] X_5442200_SNP [dm6]	T	G	7.399e^-5	1	INTERGENIC

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By genomic position
Variant impact
Gene name

pc_Surv_MeHg_0 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results