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=3.586e^-5)
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_P	0.02423
In_3R_Mo	0.06437

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1773 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	10221094	3L_10221094_SNP [dm3] 3L_10227994_SNP [dm6]	A	T	1.127e^-6	0.615	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
3L	19072143	3L_19072143_SNP [dm3] 3L_19079043_SNP [dm6]	C	A	1.206e^-6	0.615	INTRON Mkp3	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	17341520	2R_17341520_SNP [dm3] 2R_21454015_SNP [dm6]	T	G	1.721e^-6	0.615	INTRON Sdc	TF binding site BDTNP1_TFBS_dl
3L	105174	3L_105174_SNP [dm3] 3L_105174_SNP [dm6]	C	T	2.808e^-6	0.615	INTERGENIC
X	19197180	X_19197180_SNP [dm3] X_19303147_SNP [dm6]	A	T	3.351e^-6	0.615	INTRON CG8051
X	19197185	X_19197185_SNP [dm3] X_19303152_SNP [dm6]	G	C	3.351e^-6	0.615	INTRON CG8051
X	19197275	X_19197275_DEL [dm3] X_19303242_DEL [dm6]	GTAA	G	3.351e^-6	0.615	INTRON CG8051
X	4441850	X_4441850_SNP [dm3] X_4547817_SNP [dm6]	A	G	3.535e^-6	0.615	SYNONYMOUS_CODING Usf INTRON CR32773	TF binding site mE1_TFBS_sens
3R	5039341	3R_5039341_SNP [dm3] 3R_9213619_SNP [dm6]	A	G	3.635e^-6	0.615	INTRON pum	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2R	1805958	2R_1805958_DEL [dm3] 2R_5918453_DEL [dm6]	GTCCGTGAGTGGCG...	G	3.980e^-6	0.615	INTRON CG43366
X	19197213	X_19197213_SNP [dm3] X_19303180_SNP [dm6]	T	A	4.159e^-6	0.615	INTRON CG8051
X	15794609	X_15794609_SNP [dm3] X_15900576_SNP [dm6]	A	C	4.765e^-6	0.615	INTRON shi
3L	9835345	3L_9835345_DEL [dm3] 3L_9842245_DEL [dm6]	CCATCT	C	5.016e^-6	0.615	INTRON RasGAP1
3L	16248171	3L_16248171_DEL [dm3] 3L_16255071_DEL [dm6]	GGACGAG	G	5.484e^-6	0.615	DOWNSTREAM CG13054 INTERGENIC
3L	4357626	3L_4357626_SNP [dm3] 3L_4357626_SNP [dm6]	A	G	6.541e^-6	0.615	INTRON Cip4	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	10221101	3L_10221101_SNP [dm3] 3L_10228001_SNP [dm6]	C	G	7.003e^-6	0.615	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
3R	9530934	3R_9530934_SNP [dm3] 3R_13705212_SNP [dm6]	G	T	8.129e^-6	0.615	INTRON Adgf-D
3R	9574975	3R_9574975_SNP [dm3] 3R_13749253_SNP [dm6]	T	A	8.174e^-6	0.615	INTRON CG34383	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	16899518	X_16899518_SNP [dm3] X_17005485_SNP [dm6]	G	T	8.608e^-6	0.615	INTRON CG45002	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
2L	3109170	2L_3109170_SNP [dm3] 2L_3109170_SNP [dm6]	G	A	8.921e^-6	0.615	UPSTREAM PpD6 INTRON toc	TF binding site mE1_TFBS_inv
3R	25451499	3R_25451499_SNP [dm3] 3R_29625777_SNP [dm6]	A	G	8.961e^-6	0.615	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	9583715	3R_9583715_SNP [dm3] 3R_13757993_SNP [dm6]	C	A	9.332e^-6	0.615	INTRON CG34383
2L	11308479	2L_11308479_INS [dm3] 2L_11308479_INS [dm6]	G	GG	9.402e^-6	0.615	DOWNSTREAM CR43721 INTERGENIC
3R	9574949	3R_9574949_SNP [dm3] 3R_13749227_SNP [dm6]	A	G	9.556e^-6	0.615	INTRON CG34383	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	13835421	3R_13835421_SNP [dm3] 3R_18009699_SNP [dm6]	G	T	9.677e^-6	0.615	INTRON cpo
3L	12173911	3L_12173911_SNP [dm3] 3L_12180811_SNP [dm6]	C	T	9.771e^-6	0.615	INTRON CAH2
3R	9530674	3R_9530674_SNP [dm3] 3R_13704952_SNP [dm6]	T	C	9.830e^-6	0.615	INTRON Adgf-D
3L	76712	3L_76712_SNP [dm3] 3L_76712_SNP [dm6]	A	C	9.973e^-6	0.615	INTERGENIC
X	5026239	X_5026239_SNP [dm3] X_5132206_SNP [dm6]	A	C	9.996e^-6	0.615	SYNONYMOUS_CODING Rpn13R INTRON rg & 1 other
3L	1463180	3L_1463180_SNP [dm3] 3L_1463180_SNP [dm6]	C	T	1.052e^-5	0.615	UPSTREAM CR44842 & 1 other INTRON Ptp61F	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_Trl
3L	3869604	3L_3869604_SNP [dm3] 3L_3869604_SNP [dm6]	T	A	1.055e^-5	0.615	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
3R	7684139	3R_7684139_SNP [dm3] 3R_11858417_SNP [dm6]	C	A	1.087e^-5	0.615	INTRON CG6959
3L	63430	3L_63430_SNP [dm3] 3L_63430_SNP [dm6]	G	A	1.099e^-5	0.615	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	16608815	X_16608815_SNP [dm3] X_16714782_SNP [dm6]	T	C	1.124e^-5	0.615	UTR_3_PRIME CG34325 DOWNSTREAM CG13008
3L	9839120	3L_9839120_SNP [dm3] 3L_9846020_SNP [dm6]	G	A	1.289e^-5	0.672	INTRON RasGAP1	TF binding site BDTNP1_TFBS_dl
X	3456866	X_3456866_SNP [dm3] X_3562833_SNP [dm6]	G	T	1.301e^-5	0.672	INTRON CG32791 & 1 other
2L	2965886	2L_2965886_SNP [dm3] 2L_2965886_SNP [dm6]	A	G	1.364e^-5	0.673	UTR_3_PRIME Rbp9
2R	17478087	2R_17478087_SNP [dm3] 2R_21590582_SNP [dm6]	A	G	1.378e^-5	0.673	NON_SYNONYMOUS_CODING CG33225
3L	10221108	3L_10221108_SNP [dm3] 3L_10228008_SNP [dm6]	C	A	1.492e^-5	0.673	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
3L	12306884	3L_12306884_SNP [dm3] 3L_12313784_SNP [dm6]	C	T	1.510e^-5	0.673	INTERGENIC
2R	3618313	2R_3618313_SNP [dm3] 2R_7730808_SNP [dm6]	G	A	1.513e^-5	0.673	INTRON CG18812
3L	7501123	3L_7501123_SNP [dm3] 3L_7508023_SNP [dm6]	C	T	1.543e^-5	0.673	INTERGENIC
3R	17009847	3R_17009847_SNP [dm3] 3R_21184125_SNP [dm6]	A	T	1.555e^-5	0.673	INTRON SNF4Agamma	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	9571777	3R_9571777_SNP [dm3] 3R_13746055_SNP [dm6]	A	C	1.770e^-5	0.699	SYNONYMOUS_CODING CG34383	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	9572824	3R_9572824_SNP [dm3] 3R_13747102_SNP [dm6]	T	C	1.770e^-5	0.699	SYNONYMOUS_CODING CG34383	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2L	14249779	2L_14249779_SNP [dm3] 2L_14249779_SNP [dm6]	A	T	1.866e^-5	0.699	INTERGENIC
2L	14249788	2L_14249788_SNP [dm3] 2L_14249788_SNP [dm6]	G	A	1.866e^-5	0.699	INTERGENIC
3L	9646792	3L_9646792_SNP [dm3] 3L_9653692_SNP [dm6]	T	C	1.938e^-5	0.699	INTRON fry & 1 other
3L	4025597	3L_4025597_SNP [dm3] 3L_4025597_SNP [dm6]	T	C	1.977e^-5	0.699	UTR_5_PRIME CG11594 UPSTREAM CG11594 INTRON CG11594
3R	9558471	3R_9558471_SNP [dm3] 3R_13732749_SNP [dm6]	C	T	2.034e^-5	0.699	INTRON CG34383	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	830400	3L_830400_SNP [dm3] 3L_830400_SNP [dm6]	C	A	2.035e^-5	0.699	UPSTREAM CR45184 & 1 other DOWNSTREAM snoRNA:Me28S-A771 INTRON CG13900	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	9530521	3R_9530521_SNP [dm3] 3R_13704799_SNP [dm6]	C	T	2.109e^-5	0.699	SYNONYMOUS_CODING Adgf-D
X	19133448	X_19133448_INS [dm3] X_19239415_INS [dm6]	A	AAGCCAATA	2.187e^-5	0.699	INTRON CG14196
2L	14249774	2L_14249774_SNP [dm3] 2L_14249774_SNP [dm6]	T	C	2.214e^-5	0.699	INTERGENIC
X	11354722	X_11354722_SNP [dm3] X_11460689_SNP [dm6]	C	G	2.245e^-5	0.699	INTRON CG43155
3L	4722156	3L_4722156_SNP [dm3] 3L_4722156_SNP [dm6]	T	A	2.263e^-5	0.699	INTRON RhoGEF64C
3L	7152104	3L_7152104_SNP [dm3] 3L_7159004_SNP [dm6]	A	G	2.282e^-5	0.699	DOWNSTREAM Dscam2 & 1 other INTERGENIC
3R	9558621	3R_9558621_SNP [dm3] 3R_13732899_SNP [dm6]	A	T	2.320e^-5	0.699	INTRON CG34383	TF binding site BDTNP1_TFBS_dl
3L	5213562	3L_5213562_SNP [dm3] 3L_5220462_SNP [dm6]	C	T	2.328e^-5	0.699	INTRON shep
3R	9573889	3R_9573889_SNP [dm3] 3R_13748167_SNP [dm6]	T	A	2.444e^-5	0.699	INTRON CG34383	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	16174539	3L_16174539_SNP [dm3] 3L_16181439_SNP [dm6]	A	T	2.477e^-5	0.699	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	62954	3L_62954_SNP [dm3] 3L_62954_SNP [dm6]	G	C	2.482e^-5	0.699	INTERGENIC
3L	18820962	3L_18820962_SNP [dm3] 3L_18827862_SNP [dm6]	C	T	2.487e^-5	0.699	SYNONYMOUS_CODING Cat DOWNSTREAM Indy	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2L	19793931	2L_19793931_SNP [dm3] 2L_19793931_SNP [dm6]	C	A	2.501e^-5	0.699	UTR_3_PRIME fs_2_ltoPP43 INTRON fs_2_ltoPP43
3R	9557265	3R_9557265_SNP [dm3] 3R_13731543_SNP [dm6]	A	C	2.526e^-5	0.699	INTRON CG34383	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	18233527	3R_18233527_SNP [dm3] 3R_22407805_SNP [dm6]	T	G	2.556e^-5	0.699	DOWNSTREAM CG13850 INTRON CG13855
3L	69908	3L_69908_SNP [dm3] 3L_69908_SNP [dm6]	A	C	2.570e^-5	0.699	UPSTREAM CG43150 DOWNSTREAM Lsp1gamma & 2 others INTERGENIC
X	15794685	X_15794685_SNP [dm3] X_15900652_SNP [dm6]	A	G	2.590e^-5	0.699	INTRON shi
3L	7050133	3L_7050133_SNP [dm3] 3L_7057033_SNP [dm6]	G	C	2.717e^-5	0.699	INTERGENIC
X	4651672	X_4651672_SNP [dm3] X_4757639_SNP [dm6]	T	C	2.796e^-5	0.699	INTERGENIC
X	5026296	X_5026296_SNP [dm3] X_5132263_SNP [dm6]	T	C	2.856e^-5	0.699	SYNONYMOUS_CODING Rpn13R INTRON rg & 1 other
3R	9571154	3R_9571154_SNP [dm3] 3R_13745432_SNP [dm6]	T	C	2.912e^-5	0.699	INTRON CG34383
3L	12509202	3L_12509202_SNP [dm3] 3L_12516102_SNP [dm6]	T	C	2.922e^-5	0.699	INTRON tral	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Trl
3L	60465	3L_60465_SNP [dm3] 3L_60465_SNP [dm6]	A	G	3.003e^-5	0.699	INTERGENIC	silencer mE1_HDAC_PRE TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	22096918	X_22096918_SNP [dm3] X_22695082_SNP [dm6]	G	A	3.084e^-5	0.699	INTRON CR44997
X	17423175	X_17423175_SNP [dm3] X_17529142_SNP [dm6]	A	G	3.090e^-5	0.699	INTRON CG43658
3L	79409	3L_79409_SNP [dm3] 3L_79409_SNP [dm6]	G	A	3.122e^-5	0.699	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	62478	3L_62478_SNP [dm3] 3L_62478_SNP [dm6]	C	T	3.141e^-5	0.699	INTERGENIC
3L	99390	3L_99390_DEL [dm3] 3L_99390_DEL [dm6]	GT	G	3.203e^-5	0.699	INTERGENIC	TF binding site mE1_TFBS_zfh1
3L	12508429	3L_12508429_SNP [dm3] 3L_12515329_SNP [dm6]	T	C	3.224e^-5	0.699	UTR_5_PRIME tral UPSTREAM sti & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl
2R	11207648	2R_11207648_SNP [dm3] 2R_15320143_SNP [dm6]	G	A	3.226e^-5	0.699	SYNONYMOUS_CODING CG8155
2R	17735549	2R_17735549_SNP [dm3] 2R_21848044_SNP [dm6]	T	G	3.280e^-5	0.699	DOWNSTREAM tRNA:CR30406 INTERGENIC
2R	17735653	2R_17735653_SNP [dm3] 2R_21848148_SNP [dm6]	A	C	3.280e^-5	0.699	DOWNSTREAM tRNA:CR30406 INTERGENIC
2R	17433961	2R_17433961_SNP [dm3] 2R_21546456_SNP [dm6]	C	T	3.311e^-5	0.699	UPSTREAM Egfr INTRON Egfr	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_tll BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	25286050	3R_25286050_SNP [dm3] 3R_29460328_SNP [dm6]	C	T	3.331e^-5	0.699	INTRON Ptp99A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	7392890	3L_7392890_SNP [dm3] 3L_7399790_SNP [dm6]	C	T	3.349e^-5	0.699	UTR_3_PRIME CG8562 UPSTREAM CG18417
2R	19775119	2R_19775119_SNP [dm3] 2R_23887596_SNP [dm6]	A	T	3.457e^-5	0.699	INTRON CG5597
2R	3577993	2R_3577993_SNP [dm3] 2R_7690488_SNP [dm6]	T	C	3.462e^-5	0.699	INTRON CG1399
2L	13134402	2L_13134402_SNP [dm3] 2L_13134402_SNP [dm6]	A	C	3.508e^-5	0.699	SYNONYMOUS_CODING CG5122
3L	76713	3L_76713_SNP [dm3] 3L_76713_SNP [dm6]	T	C	3.529e^-5	0.699	INTERGENIC
X	6553034	X_6553034_SNP [dm3] X_6659001_SNP [dm6]	C	T	3.561e^-5	0.699	NON_SYNONYMOUS_CODING l_1_G0148	TF binding site BDTNP1_TFBS_twi
X	8659750	X_8659750_SNP [dm3] X_8765717_SNP [dm6]	T	C	3.572e^-5	0.699	INTRON Lim1	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_sens
3L	86007	3L_86007_DEL [dm3] 3L_86007_DEL [dm6]	GACTTTGCTAG...	G	3.623e^-5	0.699	INTERGENIC
3L	73117	3L_73117_SNP [dm3] 3L_73117_SNP [dm6]	A	T	3.638e^-5	0.699	UPSTREAM CR43988 DOWNSTREAM CG13405 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	521031	2R_521031_INS [dm3] 2R_4633526_INS [dm6]	C	CTATT	3.648e^-5	0.699	INTERGENIC	transposable element FlyBase
2L	3238057	2L_3238057_SNP [dm3] 2L_3238057_SNP [dm6]	C	T	3.682e^-5	0.699	INTERGENIC
2R	6726485	2R_6726485_SNP [dm3] 2R_10838980_SNP [dm6]	A	C	3.713e^-5	0.699	UPSTREAM CG7686 DOWNSTREAM CG30015 INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	8482403	3R_8482403_SNP [dm3] 3R_12656681_SNP [dm6]	A	G	3.768e^-5	0.699	UTR_5_PRIME CG6225
2R	16040583	2R_16040583_SNP [dm3] 2R_20153078_SNP [dm6]	C	A	3.812e^-5	0.699	INTERGENIC
2R	16040762	2R_16040762_SNP [dm3] 2R_20153257_SNP [dm6]	T	C	3.812e^-5	0.699	INTERGENIC

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By genomic position
Variant impact
Gene name

Microbiota_OTU042 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results