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=6.398e^-15)
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	0.03175
In_3R_P	2.014e-06

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	14.2415	0.0008

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

9501 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

Show entries

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	7524523	3R_7524523_SNP [dm3] 3R_11698801_SNP [dm6]	T	G	1.476e^-22	1.536e^-16	DOWNSTREAM CG14717 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1
3R	5058044	3R_5058044_SNP [dm3] 3R_9232322_SNP [dm6]	A	G	3.070e^-22	1.536e^-16	SYNONYMOUS_CODING pum	TF binding site mE1_TFBS_chinmo
3R	7515427	3R_7515427_SNP [dm3] 3R_11689705_SNP [dm6]	T	A	3.302e^-22	1.536e^-16	DOWNSTREAM CG18765 INTRON CG6908
3R	7515611	3R_7515611_SNP [dm3] 3R_11689889_SNP [dm6]	C	T	3.302e^-22	1.536e^-16	SYNONYMOUS_CODING CG6908 DOWNSTREAM CG18765	TF binding site mE1_TFBS_cnc
2R	19402895	2R_19402895_SNP [dm3] 2R_23515372_SNP [dm6]	G	A	2.158e^-21	6.692e^-16	INTERGENIC
2R	19402896	2R_19402896_SNP [dm3] 2R_23515373_SNP [dm6]	G	A	2.158e^-21	6.692e^-16	INTERGENIC
3L	3786620	3L_3786620_SNP [dm3] 3L_3786620_SNP [dm6]	T	A	1.060e^-20	2.817e^-15	INTRON CG32264	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx mE1_TFBS_zfh1
3R	7520555	3R_7520555_SNP [dm3] 3R_11694833_SNP [dm6]	A	T	1.895e^-17	4.406e^-12	UPSTREAM Fer3 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
3L	5847440	3L_5847440_SNP [dm3] 3L_5854340_SNP [dm6]	C	T	2.815e^-17	5.818e^-12	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	3685944	3R_3685944_SNP [dm3] 3R_7860222_SNP [dm6]	A	G	5.056e^-17	9.407e^-12	INTRON CG17816
3R	26070203	3R_26070203_SNP [dm3] 3R_30244481_SNP [dm6]	G	C	5.896e^-17	9.972e^-12	SYNONYMOUS_CODING CG9733	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	18995912	X_18995912_INS [dm3] X_19101879_INS [dm6]	T	TT	6.534e^-16	1.012e^-10	INTERGENIC
2R	8304874	2R_8304874_SNP [dm3] 2R_12417369_SNP [dm6]	C	G	7.069e^-16	1.012e^-10	NON_SYNONYMOUS_CODING CG13157	TF binding site mE1_TFBS_cad
X	18597817	X_18597817_SNP [dm3] X_18703784_SNP [dm6]	A	T	3.131e^-15	3.895e^-10	INTERGENIC
3R	7515446	3R_7515446_SNP [dm3] 3R_11689724_SNP [dm6]	A	C	3.312e^-15	3.895e^-10	SPLICE_SITE_DONOR CG6908 DOWNSTREAM CG18765 INTRON CG6908	TF binding site mE1_TFBS_cnc
X	18996109	X_18996109_INS [dm3] X_19102076_INS [dm6]	C	CTCGAAAAT	3.566e^-15	3.895e^-10	INTERGENIC
2R	17109729	2R_17109729_SNP [dm3] 2R_21222224_SNP [dm6]	A	G	3.768e^-15	3.895e^-10	INTRON ASPP	TF binding site mE1_TFBS_cad
2R	17109742	2R_17109742_SNP [dm3] 2R_21222237_SNP [dm6]	T	G	3.768e^-15	3.895e^-10	INTRON ASPP	TF binding site mE1_TFBS_cad
3L	5847467	3L_5847467_SNP [dm3] 3L_5854367_SNP [dm6]	G	A	5.040e^-15	4.935e^-10	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	18597808	X_18597808_SNP [dm3] X_18703775_SNP [dm6]	A	T	5.842e^-15	5.434e^-10	INTERGENIC
2R	12296156	2R_12296156_SNP [dm3] 2R_16408651_SNP [dm6]	C	T	6.660e^-15	5.901e^-10	INTRON Sema-2b
3R	17894258	3R_17894258_SNP [dm3] 3R_22068536_SNP [dm6]	A	T	7.626e^-15	5.912e^-10	INTRON how
3R	17894397	3R_17894397_SNP [dm3] 3R_22068675_SNP [dm6]	C	A	7.626e^-15	5.912e^-10	INTRON how
3R	17896037	3R_17896037_SNP [dm3] 3R_22070315_SNP [dm6]	C	A	7.626e^-15	5.912e^-10	INTRON how	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
X	20318815	X_20318815_SNP [dm3] X_20447788_SNP [dm6]	G	A	1.035e^-14	7.702e^-10	INTERGENIC
3R	26234558	3R_26234558_SNP [dm3] 3R_30408836_SNP [dm6]	A	G	1.216e^-14	8.141e^-10	INTERGENIC
3R	26237203	3R_26237203_SNP [dm3] 3R_30411481_SNP [dm6]	C	T	1.216e^-14	8.141e^-10	INTERGENIC	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
X	18597814	X_18597814_SNP [dm3] X_18703781_SNP [dm6]	G	T	1.225e^-14	8.141e^-10	INTERGENIC
3R	17891723	3R_17891723_SNP [dm3] 3R_22066001_SNP [dm6]	T	A	1.356e^-14	8.698e^-10	INTRON how
3R	19530873	3R_19530873_SNP [dm3] 3R_23705151_SNP [dm6]	T	C	1.479e^-14	9.171e^-10	DOWNSTREAM CG31413 INTRON CG31414	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2R	19646653	2R_19646653_SNP [dm3] 2R_23759130_SNP [dm6]	G	T	2.404e^-14	1.443e^-9	INTRON CG9850	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3R	7520556	3R_7520556_SNP [dm3] 3R_11694834_SNP [dm6]	G	T	3.108e^-14	1.700e^-9	UPSTREAM Fer3 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
3R	7520558	3R_7520558_SNP [dm3] 3R_11694836_SNP [dm6]	A	G	3.108e^-14	1.700e^-9	UPSTREAM Fer3 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
3R	7520595	3R_7520595_SNP [dm3] 3R_11694873_SNP [dm6]	T	A	3.108e^-14	1.700e^-9	UPSTREAM Fer3 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
3R	26236645	3R_26236645_SNP [dm3] 3R_30410923_SNP [dm6]	C	G	3.369e^-14	1.791e^-9	INTERGENIC
3R	17891188	3R_17891188_SNP [dm3] 3R_22065466_SNP [dm6]	G	A	3.725e^-14	1.925e^-9	INTRON how
3R	7520569	3R_7520569_SNP [dm3] 3R_11694847_SNP [dm6]	C	T	5.374e^-14	2.702e^-9	UPSTREAM Fer3 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
X	9901037	X_9901037_SNP [dm3] X_10007004_SNP [dm6]	T	C	1.490e^-13	7.293e^-9	DOWNSTREAM CG32694 INTERGENIC
3R	5055986	3R_5055986_SNP [dm3] 3R_9230264_SNP [dm6]	C	A	1.756e^-13	8.378e^-9	INTRON pum EXON CR45196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
X	9901366	X_9901366_SNP [dm3] X_10007333_SNP [dm6]	C	T	2.400e^-13	1.116e^-8	DOWNSTREAM CG32694 INTERGENIC
X	8803433	X_8803433_SNP [dm3] X_8909400_SNP [dm6]	G	C	2.530e^-13	1.148e^-8	INTRON rdgA
3R	7512657	3R_7512657_SNP [dm3] 3R_11686935_SNP [dm6]	A	G	2.778e^-13	1.202e^-8	SYNONYMOUS_CODING CG6834
3R	7512806	3R_7512806_SNP [dm3] 3R_11687084_SNP [dm6]	A	C	2.778e^-13	1.202e^-8	NON_SYNONYMOUS_CODING CG6834
2R	12805870	2R_12805870_SNP [dm3] 2R_16918365_SNP [dm6]	T	G	2.987e^-13	1.247e^-8	INTERGENIC
3R	23490827	3R_23490827_SNP [dm3] 3R_27665105_SNP [dm6]	C	A	3.015e^-13	1.247e^-8	SYNONYMOUS_CODING unc80	TF binding site mE1_TFBS_cad
3R	12047750	3R_12047750_SNP [dm3] 3R_16222028_SNP [dm6]	A	G	6.291e^-13	2.490e^-8	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	12047765	3R_12047765_SNP [dm3] 3R_16222043_SNP [dm6]	G	A	6.291e^-13	2.490e^-8	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	17872212	X_17872212_SNP [dm3] X_17978179_SNP [dm6]	A	G	7.472e^-13	2.827e^-8	INTRON Sh
3R	17904057	3R_17904057_SNP [dm3] 3R_22078335_SNP [dm6]	A	G	7.641e^-13	2.827e^-8	UTR_3_PRIME how
X	17870981	X_17870981_SNP [dm3] X_17976948_SNP [dm6]	A	T	7.900e^-13	2.827e^-8	INTRON Sh
X	17871057	X_17871057_SNP [dm3] X_17977024_SNP [dm6]	C	T	7.900e^-13	2.827e^-8	INTRON Sh
X	17871070	X_17871070_SNP [dm3] X_17977037_SNP [dm6]	A	G	7.900e^-13	2.827e^-8	INTRON Sh
3R	22521293	3R_22521293_SNP [dm3] 3R_26695571_SNP [dm6]	G	T	9.327e^-13	3.274e^-8	INTERGENIC
3R	12047739	3R_12047739_SNP [dm3] 3R_16222017_SNP [dm6]	A	T	9.893e^-13	3.408e^-8	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	26236589	3R_26236589_SNP [dm3] 3R_30410867_SNP [dm6]	A	C	1.788e^-12	5.941e^-8	INTERGENIC
3R	26236749	3R_26236749_SNP [dm3] 3R_30411027_SNP [dm6]	C	A	1.788e^-12	5.941e^-8	INTERGENIC	TF binding site BDTNP1_TFBS_slp1
X	5225260	X_5225260_SNP [dm3] X_5331227_SNP [dm6]	G	A	1.851e^-12	6.041e^-8	SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	8368307	2R_8368307_SNP [dm3] 2R_12480802_SNP [dm6]	A	G	2.264e^-12	7.019e^-8	UTR_5_PRIME Dh44-R2
3R	3736357	3R_3736357_SNP [dm3] 3R_7910635_SNP [dm6]	G	A	2.264e^-12	7.019e^-8	SYNONYMOUS_CODING Prat DOWNSTREAM Taf7	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	6573557	X_6573557_SNP [dm3] X_6679524_SNP [dm6]	T	C	2.264e^-12	7.019e^-8	UPSTREAM l_1_G0255 & 1 other INTRON l_1_G0255
2R	17810265	2R_17810265_INS [dm3] 2R_21922760_INS [dm6]	T	TAAAT	3.244e^-12	9.680e^-8	INTRON Fili
2R	17810301	2R_17810301_SNP [dm3] 2R_21922796_SNP [dm6]	C	T	3.244e^-12	9.680e^-8	INTRON Fili
3R	26496802	3R_26496802_SNP [dm3] 3R_30671080_SNP [dm6]	C	T	3.382e^-12	9.680e^-8	INTERGENIC
3R	26496809	3R_26496809_INS [dm3] 3R_30671087_INS [dm6]	T	TCA	3.382e^-12	9.680e^-8	INTERGENIC
3R	26496811	3R_26496811_INS [dm3] 3R_30671089_INS [dm6]	G	GTATACGAAT	3.382e^-12	9.680e^-8	INTERGENIC
X	9901008	X_9901008_SNP [dm3] X_10006975_SNP [dm6]	G	A	6.791e^-12	1.914e^-7	DOWNSTREAM CG32694 INTERGENIC
2L	6811469	2L_6811469_SNP [dm3] 2L_6811469_SNP [dm6]	C	T	7.990e^-12	2.219e^-7	INTERGENIC
X	18597730	X_18597730_SNP [dm3] X_18703697_SNP [dm6]	A	T	9.142e^-12	2.465e^-7	INTERGENIC
X	18597731	X_18597731_SNP [dm3] X_18703698_SNP [dm6]	T	A	9.142e^-12	2.465e^-7	INTERGENIC
3R	5056680	3R_5056680_SNP [dm3] 3R_9230958_SNP [dm6]	G	A	9.772e^-12	2.525e^-7	DOWNSTREAM CR45196 INTRON pum	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_Trl
3R	5057505	3R_5057505_SNP [dm3] 3R_9231783_SNP [dm6]	G	A	9.772e^-12	2.525e^-7	INTRON pum	TF binding site mE1_TFBS_D mE1_TFBS_sens mE1_TFBS_Trl
3R	5059052	3R_5059052_SNP [dm3] 3R_9233330_SNP [dm6]	A	C	9.772e^-12	2.525e^-7	INTRON pum	TF binding site BDTNP1_TFBS_dl
3L	12860995	3L_12860995_SNP [dm3] 3L_12867895_SNP [dm6]	A	G	1.213e^-11	3.093e^-7	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	12550816	3R_12550816_SNP [dm3] 3R_16725094_SNP [dm6]	A	T	1.371e^-11	3.415e^-7	INTRON Ubx
3R	6056230	3R_6056230_SNP [dm3] 3R_10230508_SNP [dm6]	T	A	1.377e^-11	3.415e^-7	INTRON CG42795
3L	2062396	3L_2062396_SNP [dm3] 3L_2062396_SNP [dm6]	T	G	1.718e^-11	4.204e^-7	INTRON sls
3L	12860978	3L_12860978_INS [dm3] 3L_12867878_INS [dm6]	T	TC	1.814e^-11	4.384e^-7	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11976568	3L_11976568_SNP [dm3] 3L_11983468_SNP [dm6]	T	A	1.982e^-11	4.659e^-7	NON_SYNONYMOUS_CODING CG43896	TF binding site mE1_TFBS_chinmo
2R	9192574	2R_9192574_SNP [dm3] 2R_13305069_SNP [dm6]	A	G	1.991e^-11	4.659e^-7	INTERGENIC
3L	6101965	3L_6101965_SNP [dm3] 3L_6108865_SNP [dm6]	G	T	2.003e^-11	4.659e^-7	INTRON Ets65A
2R	10007376	2R_10007376_SNP [dm3] 2R_14119871_SNP [dm6]	T	C	2.056e^-11	4.664e^-7	INTRON Prosap	TF binding site mE1_TFBS_HSA
2R	10007386	2R_10007386_SNP [dm3] 2R_14119881_SNP [dm6]	T	C	2.056e^-11	4.664e^-7	INTRON Prosap	TF binding site mE1_TFBS_HSA
3L	10530386	3L_10530386_SNP [dm3] 3L_10537286_SNP [dm6]	T	A	2.167e^-11	4.858e^-7	INTRON A2bp1
3R	12550953	3R_12550953_SNP [dm3] 3R_16725231_SNP [dm6]	G	A	2.299e^-11	5.032e^-7	INTRON Ubx
3R	6818774	3R_6818774_SNP [dm3] 3R_10993052_SNP [dm6]	C	A	2.299e^-11	5.032e^-7	UTR_5_PRIME CG34114
X	18597721	X_18597721_SNP [dm3] X_18703688_SNP [dm6]	T	A	2.411e^-11	5.130e^-7	INTERGENIC
3L	5846589	3L_5846589_SNP [dm3] 3L_5853489_SNP [dm6]	T	A	2.482e^-11	5.130e^-7	INTERGENIC
3L	5846745	3L_5846745_SNP [dm3] 3L_5853645_SNP [dm6]	G	T	2.482e^-11	5.130e^-7	INTERGENIC
3L	5847291	3L_5847291_SNP [dm3] 3L_5854191_SNP [dm6]	G	T	2.482e^-11	5.130e^-7	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	17874126	X_17874126_SNP [dm3] X_17980093_SNP [dm6]	T	C	2.482e^-11	5.130e^-7	INTRON Sh
2R	10537633	2R_10537633_SNP [dm3] 2R_14650128_SNP [dm6]	T	A	2.851e^-11	5.829e^-7	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	9819355	X_9819355_SNP [dm3] X_9925322_SNP [dm6]	C	A	3.452e^-11	6.966e^-7	INTERGENIC
3R	14223496	3R_14223496_SNP [dm3] 3R_18397774_SNP [dm6]	A	G	3.514e^-11	6.966e^-7	UPSTREAM Vha100-2 INTRON Vha100-2 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Trl
3R	26071981	3R_26071981_SNP [dm3] 3R_30246259_SNP [dm6]	A	C	3.520e^-11	6.966e^-7	INTRON CG9733
2R	9658051	2R_9658051_DEL [dm3] 2R_13770546_DEL [dm6]	TTC	T	4.558e^-11	8.927e^-7	INTRON Cpr50Ca	TF binding site mE1_TFBS_HSA
3R	26070190	3R_26070190_SNP [dm3] 3R_30244468_SNP [dm6]	G	A	4.733e^-11	9.172e^-7	SYNONYMOUS_CODING CG9733	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	12047735	3R_12047735_SNP [dm3] 3R_16222013_SNP [dm6]	A	T	4.829e^-11	9.261e^-7	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	8804240	X_8804240_SNP [dm3] X_8910207_SNP [dm6]	T	A	5.196e^-11	9.864e^-7	INTRON rdgA
2R	9107654	2R_9107654_SNP [dm3] 2R_13220149_SNP [dm6]	G	C	5.383e^-11	1.012e^-6	NON_SYNONYMOUS_CODING CG4646 UPSTREAM CG4630 & 1 other DOWNSTREAM Fsn	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Ubx
X	5225293	X_5225293_SNP [dm3] X_5331260_SNP [dm6]	G	A	6.452e^-11	1.200e^-6	SYNONYMOUS_CODING XRCC1	TF binding site mE1_TFBS_sens

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By genomic position
Variant impact
Gene name

Microbiota_OTU021 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results