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=7.423e^-7)
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	0.005024

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	3.103	0.0781

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2317 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
3R	21721824	3R_21721824_SNP [dm3] 3R_25896102_SNP [dm6]	C	T	4.435e^-8	0.03	SYNONYMOUS_CODING CG5948
3R	25157860	3R_25157860_SNP [dm3] 3R_29332138_SNP [dm6]	T	A	8.199e^-8	0.03	INTERGENIC
2L	16702560	2L_16702560_SNP [dm3] 2L_16702560_SNP [dm6]	A	T	1.213e^-7	0.03	EXON CR43670	TF binding site mE1_TFBS_sens
2L	16702612	2L_16702612_SNP [dm3] 2L_16702612_SNP [dm6]	C	T	1.213e^-7	0.03	EXON CR43670	TF binding site BDTNP1_TFBS_Med mE1_TFBS_sens
2L	16702618	2L_16702618_SNP [dm3] 2L_16702618_SNP [dm6]	G	A	1.213e^-7	0.03	EXON CR43670	TF binding site BDTNP1_TFBS_Med mE1_TFBS_sens
2L	16702622	2L_16702622_SNP [dm3] 2L_16702622_SNP [dm6]	T	C	1.213e^-7	0.03	EXON CR43670	TF binding site BDTNP1_TFBS_Med mE1_TFBS_sens
2L	16702664	2L_16702664_SNP [dm3] 2L_16702664_SNP [dm6]	T	C	1.213e^-7	0.03	EXON CR43670	TF binding site BDTNP1_TFBS_Med mE1_TFBS_sens
2L	2816946	2L_2816946_SNP [dm3] 2L_2816946_SNP [dm6]	T	C	1.273e^-7	0.03	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	2816943	2L_2816943_SNP [dm3] 2L_2816943_SNP [dm6]	G	A	2.189e^-7	0.045	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	16702691	2L_16702691_SNP [dm3] 2L_16702691_SNP [dm6]	C	A	4.051e^-7	0.069	EXON CR43670	TF binding site BDTNP1_TFBS_Med mE1_TFBS_sens
2L	2817393	2L_2817393_SNP [dm3] 2L_2817393_SNP [dm6]	A	G	4.126e^-7	0.069	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	16702596	2L_16702596_DEL [dm3] 2L_16702596_DEL [dm6]	TGATTTT	T	4.995e^-7	0.069	EXON CR43670	TF binding site BDTNP1_TFBS_Med mE1_TFBS_sens
2R	18357988	2R_18357988_SNP [dm3] 2R_22470483_SNP [dm6]	C	A	5.463e^-7	0.069	INTRON CG10384	TF binding site mE1_TFBS_chinmo
2L	2817129	2L_2817129_SNP [dm3] 2L_2817129_SNP [dm6]	G	A	5.562e^-7	0.069	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	12540675	3L_12540675_DEL [dm3] 3L_12547575_DEL [dm6]	TA	T	5.727e^-7	0.069	INTRON sowah
2L	2818275	2L_2818275_SNP [dm3] 2L_2818275_SNP [dm6]	A	G	5.918e^-7	0.069	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3L	12540678	3L_12540678_SNP [dm3] 3L_12547578_SNP [dm6]	T	G	6.728e^-7	0.074	INTRON sowah
2L	795992	2L_795992_SNP [dm3] 2L_795992_SNP [dm6]	A	G	7.358e^-7	0.076	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	2818389	2L_2818389_SNP [dm3] 2L_2818389_SNP [dm6]	C	T	7.888e^-7	0.077	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	2818208	2L_2818208_SNP [dm3] 2L_2818208_SNP [dm6]	G	A	8.308e^-7	0.077	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	16702527	2L_16702527_SNP [dm3] 2L_16702527_SNP [dm6]	T	C	9.530e^-7	0.084	EXON CR43670	TF binding site mE1_TFBS_sens
2R	9263204	2R_9263204_SNP [dm3] 2R_13375699_SNP [dm6]	A	C	1.287e^-6	0.109	DOWNSTREAM CG10814 INTERGENIC
X	12029569	X_12029569_DEL [dm3] X_12135536_DEL [dm6]	AATTC	T	1.641e^-6	0.123	INTRON Ten-a
X	12029576	X_12029576_SNP [dm3] X_12135543_SNP [dm6]	T	A	1.641e^-6	0.123	INTRON Ten-a
2R	9263203	2R_9263203_SNP [dm3] 2R_13375698_SNP [dm6]	A	C	1.646e^-6	0.123	DOWNSTREAM CG10814 INTERGENIC
2L	5028463	2L_5028463_SNP [dm3] 2L_5028463_SNP [dm6]	A	G	1.729e^-6	0.124	UPSTREAM vkg INTERGENIC	regulatory region REDfly_CRMs
2L	4726336	2L_4726336_SNP [dm3] 2L_4726336_SNP [dm6]	G	A	1.820e^-6	0.125	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
2L	2819082	2L_2819082_SNP [dm3] 2L_2819082_SNP [dm6]	A	G	1.960e^-6	0.13	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	2819145	2L_2819145_SNP [dm3] 2L_2819145_SNP [dm6]	A	G	2.299e^-6	0.147	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	2817312	2L_2817312_SNP [dm3] 2L_2817312_SNP [dm6]	C	T	2.371e^-6	0.147	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	9433676	2R_9433676_INS [dm3] 2R_13546171_INS [dm6]	T	TTT	2.455e^-6	0.147	UPSTREAM CG6145 INTRON CG6145	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Ubx
2L	2816934	2L_2816934_SNP [dm3] 2L_2816934_SNP [dm6]	A	G	2.617e^-6	0.152	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	11528228	3L_11528228_SNP [dm3] 3L_11535128_SNP [dm6]	G	T	2.877e^-6	0.162	UPSTREAM Mob2 INTRON Mob2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	7023691	2R_7023691_SNP [dm3] 2R_11136186_SNP [dm6]	C	G	2.973e^-6	0.163	SYNONYMOUS_CODING BBS4
2L	14098648	2L_14098648_SNP [dm3] 2L_14098648_SNP [dm6]	C	G	3.448e^-6	0.183	INTERGENIC
3L	14523305	3L_14523305_INS [dm3] 3L_14530205_INS [dm6]	T	TTTAGGAAAATGTT...	3.666e^-6	0.189	INTRON bbg
2L	5028460	2L_5028460_SNP [dm3] 2L_5028460_SNP [dm6]	G	C	3.756e^-6	0.189	UPSTREAM vkg INTERGENIC	regulatory region REDfly_CRMs
2L	5966473	2L_5966473_SNP [dm3] 2L_5966473_SNP [dm6]	C	T	3.992e^-6	0.192	SYNONYMOUS_CODING CG13992	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	12543270	3L_12543270_SNP [dm3] 3L_12550170_SNP [dm6]	C	T	4.035e^-6	0.192	INTRON sowah	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	16702548	2L_16702548_SNP [dm3] 2L_16702548_SNP [dm6]	A	G	4.704e^-6	0.197	EXON CR43670	TF binding site mE1_TFBS_sens
2L	16702573	2L_16702573_SNP [dm3] 2L_16702573_SNP [dm6]	C	A	4.704e^-6	0.197	EXON CR43670	TF binding site BDTNP1_TFBS_Med mE1_TFBS_sens
2L	16702682	2L_16702682_SNP [dm3] 2L_16702682_SNP [dm6]	A	G	4.704e^-6	0.197	EXON CR43670	TF binding site BDTNP1_TFBS_Med mE1_TFBS_sens
2L	16702706	2L_16702706_SNP [dm3] 2L_16702706_SNP [dm6]	G	T	4.704e^-6	0.197	EXON CR43670	TF binding site BDTNP1_TFBS_Med mE1_TFBS_sens
2L	16703229	2L_16703229_SNP [dm3] 2L_16703229_SNP [dm6]	C	T	4.704e^-6	0.197	UPSTREAM CR43670 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	16703121	2L_16703121_SNP [dm3] 2L_16703121_SNP [dm6]	C	T	4.768e^-6	0.197	INTRON CR43670	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	622941	2L_622941_SNP [dm3] 2L_622941_SNP [dm6]	C	G	4.859e^-6	0.197	UPSTREAM CR44797 DOWNSTREAM CR44798 INTERGENIC
3L	10807098	3L_10807098_SNP [dm3] 3L_10813998_SNP [dm6]	C	A	5.445e^-6	0.216	UPSTREAM CG42831 INTERGENIC
2L	16702686	2L_16702686_SNP [dm3] 2L_16702686_SNP [dm6]	G	T	5.677e^-6	0.22	EXON CR43670	TF binding site BDTNP1_TFBS_Med mE1_TFBS_sens
2L	2817858	2L_2817858_SNP [dm3] 2L_2817858_SNP [dm6]	C	T	5.965e^-6	0.226	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	12029567	X_12029567_SNP [dm3] X_12135534_SNP [dm6]	C	T	6.590e^-6	0.238	INTRON Ten-a
3L	11418494	3L_11418494_SNP [dm3] 3L_11425394_SNP [dm6]	T	C	6.661e^-6	0.238	SYNONYMOUS_CODING CG7560	TF binding site mE1_TFBS_cad
2L	11399630	2L_11399630_SNP [dm3] 2L_11399630_SNP [dm6]	G	T	6.791e^-6	0.238	INTERGENIC	regulatory region REDfly_CRMs
3L	5050449	3L_5050449_SNP [dm3] 3L_5050449_SNP [dm6]	C	T	6.791e^-6	0.238	DOWNSTREAM CR43884 INTRON Con
3L	7104263	3L_7104263_SNP [dm3] 3L_7111163_SNP [dm6]	C	T	6.961e^-6	0.239	UTR_5_PRIME form3
3L	7075673	3L_7075673_SNP [dm3] 3L_7082573_SNP [dm6]	T	A	7.065e^-6	0.239	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	17175427	3L_17175427_SNP [dm3] 3L_17182327_SNP [dm6]	T	A	7.285e^-6	0.242	INTRON Rbp6
3R	22824299	3R_22824299_SNP [dm3] 3R_26998577_SNP [dm6]	T	G	8.136e^-6	0.255	INTRON RYa-R
2L	11399731	2L_11399731_SNP [dm3] 2L_11399731_SNP [dm6]	A	C	8.265e^-6	0.255	INTERGENIC	regulatory region REDfly_CRMs
2R	9816395	2R_9816395_SNP [dm3] 2R_13928890_SNP [dm6]	A	T	8.339e^-6	0.255	INTRON shot
3L	9999387	3L_9999387_SNP [dm3] 3L_10006287_SNP [dm6]	A	G	8.592e^-6	0.255	INTRON dpr6
2L	9149731	2L_9149731_SNP [dm3] 2L_9149731_SNP [dm6]	C	T	8.670e^-6	0.255	INTRON CG32982	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13714014	3L_13714014_SNP [dm3] 3L_13720914_SNP [dm6]	T	C	8.673e^-6	0.255	INTRON bru-3
2R	17756199	2R_17756199_SNP [dm3] 2R_21868694_SNP [dm6]	T	A	8.844e^-6	0.255	INTERGENIC
2L	14635489	2L_14635489_SNP [dm3] 2L_14635489_SNP [dm6]	A	T	8.880e^-6	0.255	INTRON osp
3L	13720994	3L_13720994_SNP [dm3] 3L_13727894_SNP [dm6]	G	T	8.923e^-6	0.255	INTRON bru-3
2R	17758846	2R_17758846_SNP [dm3] 2R_21871341_SNP [dm6]	A	T	1.054e^-5	0.294	UPSTREAM Fili INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_inv mE1_TFBS_Trl
3R	22823773	3R_22823773_SNP [dm3] 3R_26998051_SNP [dm6]	C	T	1.069e^-5	0.294	INTRON RYa-R
2R	13132575	2R_13132575_SNP [dm3] 2R_17245070_SNP [dm6]	T	G	1.076e^-5	0.294	DOWNSTREAM CG18469 INTRON mbl
3L	7529598	3L_7529598_SNP [dm3] 3L_7536498_SNP [dm6]	G	A	1.192e^-5	0.321	INTRON lqf
X	5179984	X_5179984_SNP [dm3] X_5285951_SNP [dm6]	G	A	1.298e^-5	0.337	INTERGENIC
3L	1700501	3L_1700501_SNP [dm3] 3L_1700501_SNP [dm6]	G	A	1.327e^-5	0.337	DOWNSTREAM CG13931 INTRON CG7991	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_sna mE1_TFBS_HSA
2L	4427491	2L_4427491_SNP [dm3] 2L_4427491_SNP [dm6]	T	C	1.348e^-5	0.337	INTRON CG15431
3R	27167963	3R_27167963_SNP [dm3] 3R_31342241_SNP [dm6]	G	C	1.357e^-5	0.337	INTRON CG34347
2R	6775239	2R_6775239_SNP [dm3] 2R_10887734_SNP [dm6]	T	G	1.375e^-5	0.337	SYNONYMOUS_CODING CG30020	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	2818035	2L_2818035_SNP [dm3] 2L_2818035_SNP [dm6]	C	T	1.376e^-5	0.337	SYNONYMOUS_CODING Duox	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	7060218	3L_7060218_SNP [dm3] 3L_7067118_SNP [dm6]	T	G	1.404e^-5	0.337	INTRON CG8641 & 1 other
2L	19181868	2L_19181868_SNP [dm3] 2L_19181868_SNP [dm6]	C	G	1.413e^-5	0.337	UPSTREAM CG17568 DOWNSTREAM CG42688 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	11528243	3L_11528243_SNP [dm3] 3L_11535143_SNP [dm6]	A	T	1.416e^-5	0.337	UPSTREAM Mob2 INTRON Mob2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	3575953	3L_3575953_SNP [dm3] 3L_3575953_SNP [dm6]	C	A	1.478e^-5	0.337	INTRON Eip63E
3L	7131490	3L_7131490_SNP [dm3] 3L_7138390_SNP [dm6]	C	A	1.489e^-5	0.337	UTR_5_PRIME melt INTRON melt	TF binding site BDTNP1_TFBS_bcd 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
3L	3690682	3L_3690682_SNP [dm3] 3L_3690682_SNP [dm6]	C	T	1.496e^-5	0.337	INTERGENIC
X	8812574	X_8812574_INS [dm3] X_8918541_INS [dm6]	A	AC	1.515e^-5	0.337	INTRON rdgA	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	1811555	3L_1811555_SNP [dm3] 3L_1811555_SNP [dm6]	G	A	1.519e^-5	0.337	INTRON GV1
3L	14772802	3L_14772802_SNP [dm3] 3L_14779702_SNP [dm6]	G	A	1.520e^-5	0.337	INTRON bmm
3L	7529584	3L_7529584_SNP [dm3] 3L_7536484_SNP [dm6]	C	T	1.552e^-5	0.34	INTRON lqf	TF binding site mE1_TFBS_HSA
3L	5644187	3L_5644187_SNP [dm3] 3L_5651087_SNP [dm6]	G	C	1.616e^-5	0.35	UTR_3_PRIME Blimp-1
3L	8387931	3L_8387931_SNP [dm3] 3L_8394831_SNP [dm6]	T	C	1.673e^-5	0.356	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad
3L	11213350	3L_11213350_SNP [dm3] 3L_11220250_SNP [dm6]	A	G	1.701e^-5	0.356	INTRON CG42671	TF binding site mE1_TFBS_cad
2R	17464165	2R_17464165_SNP [dm3] 2R_21576660_SNP [dm6]	T	C	1.702e^-5	0.356	UPSTREAM CG10440 INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	19497825	2R_19497825_SNP [dm3] 2R_23610302_SNP [dm6]	A	T	1.765e^-5	0.363	UPSTREAM CG4019 INTRON CG17664 & 1 other
2L	3968747	2L_3968747_SNP [dm3] 2L_3968747_SNP [dm6]	A	T	1.773e^-5	0.363	INTRON fred	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
X	13817690	X_13817690_SNP [dm3] X_13923657_SNP [dm6]	A	G	1.794e^-5	0.363	INTRON mamo
3L	3690209	3L_3690209_SNP [dm3] 3L_3690209_SNP [dm6]	C	T	1.899e^-5	0.38	DOWNSTREAM CR43484 INTERGENIC
2R	13132576	2R_13132576_SNP [dm3] 2R_17245071_SNP [dm6]	T	A	1.943e^-5	0.384	DOWNSTREAM CG18469 INTRON mbl
3L	13717956	3L_13717956_DEL [dm3] 3L_13724856_DEL [dm6]	GG	G	1.960e^-5	0.384	INTRON bru-3
3L	1388203	3L_1388203_DEL [dm3] 3L_1388203_DEL [dm6]	CTTAAGAGACATC...	C	2.037e^-5	0.392	DOWNSTREAM ru INTRON Ptp61F
3R	25402225	3R_25402225_SNP [dm3] 3R_29576503_SNP [dm6]	C	T	2.046e^-5	0.392	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_eve mE1_TFBS_HSA
2L	19198106	2L_19198106_SNP [dm3] 2L_19198106_SNP [dm6]	C	T	2.113e^-5	0.401	INTRON drl	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	14772868	3L_14772868_SNP [dm3] 3L_14779768_SNP [dm6]	T	G	2.205e^-5	0.414	INTRON bmm
3R	22823769	3R_22823769_SNP [dm3] 3R_26998047_SNP [dm6]	T	C	2.234e^-5	0.414	INTRON RYa-R

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By genomic position
Variant impact
Gene name

Microbiota_OTU124 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results