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=6.369e^-20)
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	0.0315909
In_3R_P	<
In_3R_K	<
In_3R_Mo	1.443e-11

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	6.8811	0.032
In_3R_K	17.2667	0.0002

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1866 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
2L	15348697	2L_15348697_SNP [dm3] 2L_15348697_SNP [dm6]	C	T	4.515e^-7	0.59	INTERGENIC
2L	15348712	2L_15348712_INS [dm3] 2L_15348712_INS [dm6]	G	AA	7.378e^-7	0.59	INTERGENIC
3L	12369508	3L_12369508_SNP [dm3] 3L_12376408_SNP [dm6]	T	C	1.192e^-6	0.59	INTRON Ncc69
2L	7723634	2L_7723634_SNP [dm3] 2L_7723634_SNP [dm6]	G	A	1.259e^-6	0.59	SYNONYMOUS_CODING CG13795 UPSTREAM CG13794
3L	7628042	3L_7628042_SNP [dm3] 3L_7634942_SNP [dm6]	C	A	2.023e^-6	0.624	INTRON CG33275	TF binding site mE1_TFBS_HSA
2R	14171938	2R_14171938_SNP [dm3] 2R_18284433_SNP [dm6]	T	C	2.720e^-6	0.624	SYNONYMOUS_CODING sbb DOWNSTREAM sbb	TF binding site mE1_TFBS_cad
X	9023539	X_9023539_SNP [dm3] X_9129506_SNP [dm6]	C	A	2.758e^-6	0.624	INTRON fend	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_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	4503748	2L_4503748_SNP [dm3] 2L_4503748_SNP [dm6]	T	C	2.773e^-6	0.624	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	5251757	X_5251757_SNP [dm3] X_5357724_SNP [dm6]	C	T	3.164e^-6	0.624	UPSTREAM SK INTRON SK
2L	4524380	2L_4524380_SNP [dm3] 2L_4524380_SNP [dm6]	G	A	3.327e^-6	0.624	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	3288375	2L_3288375_SNP [dm3] 2L_3288375_SNP [dm6]	G	A	4.090e^-6	0.632	EXON CR44485
X	5251741	X_5251741_SNP [dm3] X_5357708_SNP [dm6]	G	T	4.350e^-6	0.632	UPSTREAM SK INTRON SK
2R	17896043	2R_17896043_SNP [dm3] 2R_22008538_SNP [dm6]	T	A	5.097e^-6	0.632	INTRON CG34370
X	5224802	X_5224802_SNP [dm3] X_5330769_SNP [dm6]	A	G	5.131e^-6	0.632	NON_SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	20281789	3R_20281789_SNP [dm3] 3R_24456067_SNP [dm6]	C	T	5.518e^-6	0.632	INTRON nAChRalpha1
X	3475525	X_3475525_INS [dm3] X_3581492_INS [dm6]	T	TT	5.825e^-6	0.632	INTRON AstA-R1
2R	9609124	2R_9609124_SNP [dm3] 2R_13721619_SNP [dm6]	T	G	6.592e^-6	0.632	INTRON fas
2L	4562833	2L_4562833_SNP [dm3] 2L_4562833_SNP [dm6]	A	C	6.602e^-6	0.632	INTRON dp
2L	4503817	2L_4503817_SNP [dm3] 2L_4503817_SNP [dm6]	T	C	6.674e^-6	0.632	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	9609131	2R_9609131_SNP [dm3] 2R_13721626_SNP [dm6]	G	A	6.742e^-6	0.632	INTRON fas
2L	15348643	2L_15348643_SNP [dm3] 2L_15348643_SNP [dm6]	G	T	7.218e^-6	0.642	INTERGENIC
X	10619731	X_10619731_SNP [dm3] X_10725698_SNP [dm6]	G	A	7.584e^-6	0.642	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12369363	3L_12369363_SNP [dm3] 3L_12376263_SNP [dm6]	A	T	7.955e^-6	0.642	INTRON Ncc69
2L	7500266	2L_7500266_SNP [dm3] 2L_7500266_SNP [dm6]	A	G	8.215e^-6	0.642	SYNONYMOUS_CODING RapGAP1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	4524308	2L_4524308_SNP [dm3] 2L_4524308_SNP [dm6]	T	C	8.961e^-6	0.649	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	20017754	3R_20017754_SNP [dm3] 3R_24192032_SNP [dm6]	G	T	9.321e^-6	0.649	INTRON jnj
3L	7627092	3L_7627092_SNP [dm3] 3L_7633992_SNP [dm6]	C	T	1.054e^-5	0.649	INTRON CG33275
X	10619674	X_10619674_SNP [dm3] X_10725641_SNP [dm6]	G	A	1.068e^-5	0.649	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	20017764	3R_20017764_SNP [dm3] 3R_24192042_SNP [dm6]	C	A	1.072e^-5	0.649	SPLICE_SITE_REGION jnj INTRON jnj
X	10619678	X_10619678_SNP [dm3] X_10725645_SNP [dm6]	A	T	1.183e^-5	0.649	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	8474257	2L_8474257_SNP [dm3] 2L_8474257_SNP [dm6]	T	C	1.219e^-5	0.649	INTRON d
2L	7595046	2L_7595046_SNP [dm3] 2L_7595046_SNP [dm6]	G	A	1.226e^-5	0.649	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
X	10619668	X_10619668_SNP [dm3] X_10725635_SNP [dm6]	A	G	1.227e^-5	0.649	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	7627057	3L_7627057_SNP [dm3] 3L_7633957_SNP [dm6]	A	G	1.235e^-5	0.649	INTRON CG33275
3L	7628058	3L_7628058_SNP [dm3] 3L_7634958_SNP [dm6]	C	T	1.235e^-5	0.649	INTRON CG33275	TF binding site mE1_TFBS_HSA
2L	8474270	2L_8474270_SNP [dm3] 2L_8474270_SNP [dm6]	A	G	1.258e^-5	0.649	INTRON d
2R	6976287	2R_6976287_INS [dm3] 2R_11088782_INS [dm6]	A	ATACACA	1.285e^-5	0.649	DOWNSTREAM CG43188 INTRON luna
2L	6127967	2L_6127967_SNP [dm3] 2L_6127967_SNP [dm6]	C	A	1.320e^-5	0.649	NON_SYNONYMOUS_CODING tectonic UTR_3_PRIME CG42730 UPSTREAM WDR79	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	5954803	2L_5954803_SNP [dm3] 2L_5954803_SNP [dm6]	A	G	1.456e^-5	0.649	SYNONYMOUS_CODING CG9044 DOWNSTREAM CG13999	TF binding site mE1_TFBS_inv
3L	7628047	3L_7628047_SNP [dm3] 3L_7634947_SNP [dm6]	C	T	1.468e^-5	0.649	INTRON CG33275	TF binding site mE1_TFBS_HSA
2L	15348728	2L_15348728_SNP [dm3] 2L_15348728_SNP [dm6]	T	A	1.560e^-5	0.649	INTERGENIC
2L	7531801	2L_7531801_SNP [dm3] 2L_7531801_SNP [dm6]	A	C	1.612e^-5	0.649	INTRON RapGAP1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
X	10619702	X_10619702_SNP [dm3] X_10725669_SNP [dm6]	C	T	1.631e^-5	0.649	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	20281807	3R_20281807_SNP [dm3] 3R_24456085_SNP [dm6]	T	C	1.638e^-5	0.649	INTRON nAChRalpha1
X	5251766	X_5251766_SNP [dm3] X_5357733_SNP [dm6]	C	T	1.659e^-5	0.649	UPSTREAM SK INTRON SK
2L	4524603	2L_4524603_SNP [dm3] 2L_4524603_SNP [dm6]	G	A	1.687e^-5	0.649	NON_SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	5816116	2R_5816116_SNP [dm3] 2R_9928611_SNP [dm6]	G	A	1.688e^-5	0.649	INTRON Mef2
2L	7536026	2L_7536026_SNP [dm3] 2L_7536026_SNP [dm6]	C	G	1.847e^-5	0.649	INTRON RapGAP1	TF binding site mE1_TFBS_cad
3R	21157386	3R_21157386_SNP [dm3] 3R_25331664_SNP [dm6]	T	C	1.986e^-5	0.649	UTR_3_PRIME CG10669 UPSTREAM CHKov2 DOWNSTREAM CG10669
3L	18213474	3L_18213474_SNP [dm3] 3L_18220374_SNP [dm6]	C	G	2.019e^-5	0.649	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
2L	9333751	2L_9333751_SNP [dm3] 2L_9333751_SNP [dm6]	A	T	2.056e^-5	0.649	START_GAINED Eaat1 UTR_5_PRIME Eaat1 INTRON Eaat1
2L	5335461	2L_5335461_SNP [dm3] 2L_5335461_SNP [dm6]	C	T	2.085e^-5	0.649	SPLICE_SITE_REGION fusl UTR_5_PRIME fusl INTRON fusl
2L	12238491	2L_12238491_SNP [dm3] 2L_12238491_SNP [dm6]	C	T	2.097e^-5	0.649	INTRON aret
3L	7628011	3L_7628011_SNP [dm3] 3L_7634911_SNP [dm6]	A	G	2.117e^-5	0.649	INTRON CG33275	TF binding site mE1_TFBS_HSA
X	10619711	X_10619711_INS [dm3] X_10725678_INS [dm6]	C	ATA	2.134e^-5	0.649	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4313712	3L_4313712_SNP [dm3] 3L_4313712_SNP [dm6]	C	T	2.155e^-5	0.649	SYNONYMOUS_CODING Claspin	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	14060614	2R_14060614_SNP [dm3] 2R_18173109_SNP [dm6]	C	T	2.170e^-5	0.649	UPSTREAM Dgp-1 & 1 other EXON CR45315	TF binding site BDTNP1_TFBS_dl
2L	1819310	2L_1819310_SNP [dm3] 2L_1819310_SNP [dm6]	G	A	2.170e^-5	0.649	INTERGENIC
X	5224806	X_5224806_SNP [dm3] X_5330773_SNP [dm6]	G	C	2.191e^-5	0.649	NON_SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	26851591	3R_26851591_SNP [dm3] 3R_31025869_SNP [dm6]	C	T	2.192e^-5	0.649	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	8360247	2L_8360247_SNP [dm3] 2L_8360247_SNP [dm6]	A	G	2.203e^-5	0.649	SYNONYMOUS_CODING CG7627	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	8474278	2L_8474278_SNP [dm3] 2L_8474278_SNP [dm6]	G	A	2.255e^-5	0.649	INTRON d
X	10619769	X_10619769_SNP [dm3] X_10725736_SNP [dm6]	T	A	2.331e^-5	0.649	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	25240219	3R_25240219_SNP [dm3] 3R_29414497_SNP [dm6]	C	A	2.336e^-5	0.649	INTRON Ptp99A
2R	14072871	2R_14072871_SNP [dm3] 2R_18185366_SNP [dm6]	A	T	2.375e^-5	0.649	SYNONYMOUS_CODING CG33958	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	20017745	3R_20017745_DEL [dm3] 3R_24192023_DEL [dm6]	TT	T	2.378e^-5	0.649	INTRON jnj
2L	4503838	2L_4503838_SNP [dm3] 2L_4503838_SNP [dm6]	A	G	2.404e^-5	0.649	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	7476161	X_7476161_SNP [dm3] X_7582128_SNP [dm6]	C	T	2.438e^-5	0.649	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	16914317	X_16914317_SNP [dm3] X_17020284_SNP [dm6]	C	A	2.455e^-5	0.649	INTRON CG45002
2L	5335596	2L_5335596_SNP [dm3] 2L_5335596_SNP [dm6]	C	T	2.533e^-5	0.649	UTR_5_PRIME fusl INTRON fusl
3R	25002934	3R_25002934_SNP [dm3] 3R_29177212_SNP [dm6]	C	A	2.556e^-5	0.649	INTRON CG14509
2L	8474287	2L_8474287_SNP [dm3] 2L_8474287_SNP [dm6]	G	A	2.656e^-5	0.649	INTRON d
X	5224774	X_5224774_SNP [dm3] X_5330741_SNP [dm6]	G	A	2.671e^-5	0.649	SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	4561954	2L_4561954_SNP [dm3] 2L_4561954_SNP [dm6]	G	A	2.706e^-5	0.649	SYNONYMOUS_CODING dp INTRON dp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2R	18435029	2R_18435029_SNP [dm3] 2R_22547524_SNP [dm6]	A	G	2.725e^-5	0.649	UPSTREAM px INTRON px
3L	16334602	3L_16334602_SNP [dm3] 3L_16341502_SNP [dm6]	T	C	2.747e^-5	0.649	SYNONYMOUS_CODING CG4998	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	10619721	X_10619721_SNP [dm3] X_10725688_SNP [dm6]	T	G	2.753e^-5	0.649	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	4561546	2L_4561546_SNP [dm3] 2L_4561546_SNP [dm6]	T	G	2.755e^-5	0.649	SYNONYMOUS_CODING dp INTRON dp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	4559329	2L_4559329_SNP [dm3] 2L_4559329_SNP [dm6]	A	G	2.758e^-5	0.649	SYNONYMOUS_CODING dp INTRON dp	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
2L	7536931	2L_7536931_SNP [dm3] 2L_7536931_SNP [dm6]	C	A	2.770e^-5	0.649	INTRON RapGAP1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	10619939	X_10619939_SNP [dm3] X_10725906_SNP [dm6]	C	T	2.807e^-5	0.65	INTRON CG32676	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA
X	18160861	X_18160861_SNP [dm3] X_18266828_SNP [dm6]	G	A	2.842e^-5	0.65	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	10619661	X_10619661_SNP [dm3] X_10725628_SNP [dm6]	G	A	3.035e^-5	0.675	INTRON CG32676	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	5224782	X_5224782_SNP [dm3] X_5330749_SNP [dm6]	C	T	3.072e^-5	0.675	NON_SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	6373170	3L_6373170_SNP [dm3] 3L_6380070_SNP [dm6]	G	A	3.073e^-5	0.675	INTERGENIC
3R	20281790	3R_20281790_SNP [dm3] 3R_24456068_SNP [dm6]	A	G	3.096e^-5	0.675	INTRON nAChRalpha1
3R	21963098	3R_21963098_SNP [dm3] 3R_26137376_SNP [dm6]	T	G	3.137e^-5	0.676	DOWNSTREAM CG6142 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_zfh1
2L	3345001	2L_3345001_SNP [dm3] 2L_3345001_SNP [dm6]	G	A	3.231e^-5	0.676	INTRON E23
2L	19886711	2L_19886711_SNP [dm3] 2L_19886711_SNP [dm6]	G	A	3.246e^-5	0.676	INTRON sick	TF binding site mE1_TFBS_cad mE1_TFBS_inv
3L	11416149	3L_11416149_SNP [dm3] 3L_11423049_SNP [dm6]	C	G	3.346e^-5	0.676	INTERGENIC	TF binding site mE1_TFBS_D
3L	14156468	3L_14156468_SNP [dm3] 3L_14163368_SNP [dm6]	T	C	3.390e^-5	0.676	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA
X	9497046	X_9497046_SNP [dm3] X_9603013_SNP [dm6]	T	A	3.390e^-5	0.676	SYNONYMOUS_CODING Gga	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	11594068	3R_11594068_SNP [dm3] 3R_15768346_SNP [dm6]	A	G	3.398e^-5	0.676	UPSTREAM CG5623 INTERGENIC
2L	10426736	2L_10426736_INS [dm3] 2L_10426736_INS [dm6]	T	TGTT	3.414e^-5	0.676	UPSTREAM KdelR & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Ubx
2L	2893295	2L_2893295_SNP [dm3] 2L_2893295_SNP [dm6]	C	T	3.499e^-5	0.676	INTRON lilli	TF binding site BDTNP1_TFBS_twi
2L	4560127	2L_4560127_SNP [dm3] 2L_4560127_SNP [dm6]	A	G	3.578e^-5	0.676	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	20017662	3R_20017662_SNP [dm3] 3R_24191940_SNP [dm6]	A	C	3.621e^-5	0.676	SYNONYMOUS_CODING jnj
X	16914213	X_16914213_SNP [dm3] X_17020180_SNP [dm6]	G	C	3.624e^-5	0.676	INTRON CG45002
3R	11602936	3R_11602936_SNP [dm3] 3R_15777214_SNP [dm6]	C	T	3.634e^-5	0.676	SYNONYMOUS_CODING CG4525
2L	9469433	2L_9469433_SNP [dm3] 2L_9469433_SNP [dm6]	C	T	3.665e^-5	0.676	UPSTREAM CR43769 INTERGENIC

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Missing results

By genomic position
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Gene name

SegregVariants_3R phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results