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=1.810e^-19)
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	0.05337
In_3R_P	<
In_3R_K	<
In_3R_Mo	5.699e-12

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	6.2026	0.045
In_3R_K	16.4862	0.0003

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1860 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	4.737e^-7	0.549	INTERGENIC
2L	15348712	2L_15348712_INS [dm3] 2L_15348712_INS [dm6]	G	AA	7.636e^-7	0.549	INTERGENIC
2L	7723634	2L_7723634_SNP [dm3] 2L_7723634_SNP [dm6]	G	A	1.810e^-6	0.549	SYNONYMOUS_CODING CG13795 UPSTREAM CG13794
3L	12369508	3L_12369508_SNP [dm3] 3L_12376408_SNP [dm6]	T	C	1.855e^-6	0.549	INTRON Ncc69
3L	7628042	3L_7628042_SNP [dm3] 3L_7634942_SNP [dm6]	C	A	2.177e^-6	0.549	INTRON CG33275	TF binding site mE1_TFBS_HSA
X	9023539	X_9023539_SNP [dm3] X_9129506_SNP [dm6]	C	A	2.554e^-6	0.549	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
2R	14171938	2R_14171938_SNP [dm3] 2R_18284433_SNP [dm6]	T	C	2.968e^-6	0.549	SYNONYMOUS_CODING sbb DOWNSTREAM sbb	TF binding site mE1_TFBS_cad
X	10619731	X_10619731_SNP [dm3] X_10725698_SNP [dm6]	G	A	3.095e^-6	0.549	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	4524380	2L_4524380_SNP [dm3] 2L_4524380_SNP [dm6]	G	A	3.117e^-6	0.549	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	3.698e^-6	0.549	EXON CR44485
X	5251757	X_5251757_SNP [dm3] X_5357724_SNP [dm6]	C	T	4.073e^-6	0.549	UPSTREAM SK INTRON SK
2L	4503748	2L_4503748_SNP [dm3] 2L_4503748_SNP [dm6]	T	C	4.187e^-6	0.549	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	5224802	X_5224802_SNP [dm3] X_5330769_SNP [dm6]	A	G	5.314e^-6	0.549	NON_SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	5251741	X_5251741_SNP [dm3] X_5357708_SNP [dm6]	G	T	5.880e^-6	0.549	UPSTREAM SK INTRON SK
3R	20281789	3R_20281789_SNP [dm3] 3R_24456067_SNP [dm6]	C	T	6.298e^-6	0.549	INTRON nAChRalpha1
2L	4562833	2L_4562833_SNP [dm3] 2L_4562833_SNP [dm6]	A	C	7.181e^-6	0.549	INTRON dp
X	10619674	X_10619674_SNP [dm3] X_10725641_SNP [dm6]	G	A	7.199e^-6	0.549	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	15348643	2L_15348643_SNP [dm3] 2L_15348643_SNP [dm6]	G	T	7.597e^-6	0.549	INTERGENIC
3R	20017754	3R_20017754_SNP [dm3] 3R_24192032_SNP [dm6]	G	T	7.949e^-6	0.549	INTRON jnj
X	10619678	X_10619678_SNP [dm3] X_10725645_SNP [dm6]	A	T	7.987e^-6	0.549	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	7531801	2L_7531801_SNP [dm3] 2L_7531801_SNP [dm6]	A	C	8.137e^-6	0.549	INTRON RapGAP1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2R	17896043	2R_17896043_SNP [dm3] 2R_22008538_SNP [dm6]	T	A	8.192e^-6	0.549	INTRON CG34370
X	10619668	X_10619668_SNP [dm3] X_10725635_SNP [dm6]	A	G	8.337e^-6	0.549	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
X	3475525	X_3475525_INS [dm3] X_3581492_INS [dm6]	T	TT	8.804e^-6	0.549	INTRON AstA-R1
3R	20017764	3R_20017764_SNP [dm3] 3R_24192042_SNP [dm6]	C	A	9.006e^-6	0.549	SPLICE_SITE_REGION jnj INTRON jnj
2L	4524308	2L_4524308_SNP [dm3] 2L_4524308_SNP [dm6]	T	C	9.681e^-6	0.549	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	8474270	2L_8474270_SNP [dm3] 2L_8474270_SNP [dm6]	A	G	9.689e^-6	0.549	INTRON d
3L	7627092	3L_7627092_SNP [dm3] 3L_7633992_SNP [dm6]	C	T	9.705e^-6	0.549	INTRON CG33275
3L	12369363	3L_12369363_SNP [dm3] 3L_12376263_SNP [dm6]	A	T	1.024e^-5	0.549	INTRON Ncc69
2L	8474257	2L_8474257_SNP [dm3] 2L_8474257_SNP [dm6]	T	C	1.059e^-5	0.549	INTRON d
X	10619702	X_10619702_SNP [dm3] X_10725669_SNP [dm6]	C	T	1.089e^-5	0.549	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	1.095e^-5	0.549	INTRON CG33275
3L	7628058	3L_7628058_SNP [dm3] 3L_7634958_SNP [dm6]	C	T	1.095e^-5	0.549	INTRON CG33275	TF binding site mE1_TFBS_HSA
2L	7536026	2L_7536026_SNP [dm3] 2L_7536026_SNP [dm6]	C	G	1.154e^-5	0.549	INTRON RapGAP1	TF binding site mE1_TFBS_cad
2L	4503817	2L_4503817_SNP [dm3] 2L_4503817_SNP [dm6]	T	C	1.169e^-5	0.549	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	9609124	2R_9609124_SNP [dm3] 2R_13721619_SNP [dm6]	T	G	1.174e^-5	0.549	INTRON fas
2L	7500266	2L_7500266_SNP [dm3] 2L_7500266_SNP [dm6]	A	G	1.174e^-5	0.549	SYNONYMOUS_CODING RapGAP1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	10619939	X_10619939_SNP [dm3] X_10725906_SNP [dm6]	C	T	1.199e^-5	0.549	INTRON CG32676	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA
2R	9609131	2R_9609131_SNP [dm3] 2R_13721626_SNP [dm6]	G	A	1.202e^-5	0.549	INTRON fas
X	10619769	X_10619769_SNP [dm3] X_10725736_SNP [dm6]	T	A	1.206e^-5	0.549	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	15348728	2L_15348728_SNP [dm3] 2L_15348728_SNP [dm6]	T	A	1.220e^-5	0.549	INTERGENIC
2L	6127967	2L_6127967_SNP [dm3] 2L_6127967_SNP [dm6]	C	A	1.235e^-5	0.549	NON_SYNONYMOUS_CODING tectonic UTR_3_PRIME CG42730 UPSTREAM WDR79	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	7628047	3L_7628047_SNP [dm3] 3L_7634947_SNP [dm6]	C	T	1.303e^-5	0.549	INTRON CG33275	TF binding site mE1_TFBS_HSA
2R	6976287	2R_6976287_INS [dm3] 2R_11088782_INS [dm6]	A	ATACACA	1.310e^-5	0.549	DOWNSTREAM CG43188 INTRON luna
2R	5816116	2R_5816116_SNP [dm3] 2R_9928611_SNP [dm6]	G	A	1.317e^-5	0.549	INTRON Mef2
X	10619711	X_10619711_INS [dm3] X_10725678_INS [dm6]	C	ATA	1.367e^-5	0.558	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	26851591	3R_26851591_SNP [dm3] 3R_31025869_SNP [dm6]	C	T	1.413e^-5	0.564	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	18435029	2R_18435029_SNP [dm3] 2R_22547524_SNP [dm6]	A	G	1.446e^-5	0.565	UPSTREAM px INTRON px
3L	7628011	3L_7628011_SNP [dm3] 3L_7634911_SNP [dm6]	A	G	1.755e^-5	0.661	INTRON CG33275	TF binding site mE1_TFBS_HSA
X	10619721	X_10619721_SNP [dm3] X_10725688_SNP [dm6]	T	G	1.763e^-5	0.661	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	8474278	2L_8474278_SNP [dm3] 2L_8474278_SNP [dm6]	G	A	1.845e^-5	0.663	INTRON d
2L	5954803	2L_5954803_SNP [dm3] 2L_5954803_SNP [dm6]	A	G	1.900e^-5	0.663	SYNONYMOUS_CODING CG9044 DOWNSTREAM CG13999	TF binding site mE1_TFBS_inv
X	10619661	X_10619661_SNP [dm3] X_10725628_SNP [dm6]	G	A	1.903e^-5	0.663	INTRON CG32676	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	8360247	2L_8360247_SNP [dm3] 2L_8360247_SNP [dm6]	A	G	1.909e^-5	0.663	SYNONYMOUS_CODING CG7627	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	20017745	3R_20017745_DEL [dm3] 3R_24192023_DEL [dm6]	TT	T	1.967e^-5	0.665	INTRON jnj
3L	16334602	3L_16334602_SNP [dm3] 3L_16341502_SNP [dm6]	T	C	1.989e^-5	0.665	SYNONYMOUS_CODING CG4998	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	7407114	X_7407114_SNP [dm3] X_7513081_SNP [dm6]	T	G	2.022e^-5	0.665	INTRON CG32719
2L	4524603	2L_4524603_SNP [dm3] 2L_4524603_SNP [dm6]	G	A	2.103e^-5	0.674	NON_SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	5251766	X_5251766_SNP [dm3] X_5357733_SNP [dm6]	C	T	2.163e^-5	0.674	UPSTREAM SK INTRON SK
X	5224806	X_5224806_SNP [dm3] X_5330773_SNP [dm6]	G	C	2.210e^-5	0.674	NON_SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	8474287	2L_8474287_SNP [dm3] 2L_8474287_SNP [dm6]	G	A	2.231e^-5	0.674	INTRON d
3R	20281807	3R_20281807_SNP [dm3] 3R_24456085_SNP [dm6]	T	C	2.262e^-5	0.674	INTRON nAChRalpha1
X	10619759	X_10619759_SNP [dm3] X_10725726_SNP [dm6]	C	G	2.315e^-5	0.674	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9333751	2L_9333751_SNP [dm3] 2L_9333751_SNP [dm6]	A	T	2.356e^-5	0.674	START_GAINED Eaat1 UTR_5_PRIME Eaat1 INTRON Eaat1
3R	11594068	3R_11594068_SNP [dm3] 3R_15768346_SNP [dm6]	A	G	2.390e^-5	0.674	UPSTREAM CG5623 INTERGENIC
2L	4561954	2L_4561954_SNP [dm3] 2L_4561954_SNP [dm6]	G	A	2.407e^-5	0.674	SYNONYMOUS_CODING dp INTRON dp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	8390565	2L_8390565_SNP [dm3] 2L_8390565_SNP [dm6]	C	A	2.443e^-5	0.674	NON_SYNONYMOUS_CODING CG42820 DOWNSTREAM snRNA:U6atac:29B	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	3521484	2L_3521484_SNP [dm3] 2L_3521484_SNP [dm6]	G	A	2.533e^-5	0.674	SYNONYMOUS_CODING CG8851	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	4313712	3L_4313712_SNP [dm3] 3L_4313712_SNP [dm6]	C	T	2.542e^-5	0.674	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	2.558e^-5	0.674	UPSTREAM Dgp-1 & 1 other EXON CR45315	TF binding site BDTNP1_TFBS_dl
2L	4561546	2L_4561546_SNP [dm3] 2L_4561546_SNP [dm6]	T	G	2.565e^-5	0.674	SYNONYMOUS_CODING dp INTRON dp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	7595046	2L_7595046_SNP [dm3] 2L_7595046_SNP [dm6]	G	A	2.669e^-5	0.674	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
X	16914317	X_16914317_SNP [dm3] X_17020284_SNP [dm6]	C	A	2.675e^-5	0.674	INTRON CG45002
2L	1819310	2L_1819310_SNP [dm3] 2L_1819310_SNP [dm6]	G	A	2.739e^-5	0.674	INTERGENIC
3L	12597490	3L_12597490_SNP [dm3] 3L_12604390_SNP [dm6]	A	T	2.789e^-5	0.674	INTERGENIC
X	10619718	X_10619718_SNP [dm3] X_10725685_SNP [dm6]	A	T	2.801e^-5	0.674	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	2.851e^-5	0.674	INTRON Ptp99A
X	10619720	X_10619720_SNP [dm3] X_10725687_SNP [dm6]	G	C	2.860e^-5	0.674	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
X	7476161	X_7476161_SNP [dm3] X_7582128_SNP [dm6]	C	T	2.973e^-5	0.674	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	5224774	X_5224774_SNP [dm3] X_5330741_SNP [dm6]	G	A	3.039e^-5	0.674	SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	4559329	2L_4559329_SNP [dm3] 2L_4559329_SNP [dm6]	A	G	3.227e^-5	0.674	SYNONYMOUS_CODING dp INTRON dp	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
2L	4560127	2L_4560127_SNP [dm3] 2L_4560127_SNP [dm6]	A	G	3.251e^-5	0.674	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	7531767	2L_7531767_SNP [dm3] 2L_7531767_SNP [dm6]	A	G	3.299e^-5	0.674	INTRON RapGAP1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	20017662	3R_20017662_SNP [dm3] 3R_24191940_SNP [dm6]	A	C	3.310e^-5	0.674	SYNONYMOUS_CODING jnj
2L	5335461	2L_5335461_SNP [dm3] 2L_5335461_SNP [dm6]	C	T	3.368e^-5	0.674	SPLICE_SITE_REGION fusl UTR_5_PRIME fusl INTRON fusl
X	16914213	X_16914213_SNP [dm3] X_17020180_SNP [dm6]	G	C	3.420e^-5	0.674	INTRON CG45002
X	9497046	X_9497046_SNP [dm3] X_9603013_SNP [dm6]	T	A	3.420e^-5	0.674	SYNONYMOUS_CODING Gga	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	7531766	2L_7531766_SNP [dm3] 2L_7531766_SNP [dm6]	T	A	3.498e^-5	0.674	INTRON RapGAP1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	26925695	3R_26925695_SNP [dm3] 3R_31099973_SNP [dm6]	T	G	3.502e^-5	0.674	SYNONYMOUS_CODING CG15553
3R	25240218	3R_25240218_SNP [dm3] 3R_29414496_SNP [dm6]	T	C	3.572e^-5	0.674	INTRON Ptp99A
X	5224782	X_5224782_SNP [dm3] X_5330749_SNP [dm6]	C	T	3.583e^-5	0.674	NON_SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	18213474	3L_18213474_SNP [dm3] 3L_18220374_SNP [dm6]	C	G	3.597e^-5	0.674	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Kr mE1_TFBS_zfh1
2L	4560346	2L_4560346_SNP [dm3] 2L_4560346_SNP [dm6]	C	G	3.625e^-5	0.674	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3L	14156468	3L_14156468_SNP [dm3] 3L_14163368_SNP [dm6]	T	C	3.678e^-5	0.674	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA
3L	16334434	3L_16334434_SNP [dm3] 3L_16341334_SNP [dm6]	A	C	3.714e^-5	0.674	SYNONYMOUS_CODING CG4998	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	11644789	2L_11644789_SNP [dm3] 2L_11644789_SNP [dm6]	A	G	3.757e^-5	0.674	UTR_3_PRIME CG6614 DOWNSTREAM CG6614
3L	11252075	3L_11252075_SNP [dm3] 3L_11258975_SNP [dm6]	G	A	3.763e^-5	0.674	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	6128174	2L_6128174_SNP [dm3] 2L_6128174_SNP [dm6]	G	C	3.778e^-5	0.674	NON_SYNONYMOUS_CODING tectonic UTR_3_PRIME CG42730 UPSTREAM WDR79	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	5814960	2R_5814960_SNP [dm3] 2R_9927455_SNP [dm6]	C	T	3.802e^-5	0.674	INTRON Mef2
2L	4549707	2L_4549707_DEL [dm3] 2L_4549707_DEL [dm6]	AA	A	3.866e^-5	0.674	INTRON dp

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Missing results

By genomic position
Variant impact
Gene name

pc_SegregVariants_3R phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results