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=1.880e^-11)
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_K	0.09052

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

5258 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
2R	18142417	2R_18142417_SNP [dm3] 2R_22254912_SNP [dm6]	C	A	1.637e^-13	3.046e^-7	INTRON dve	TF binding site BDTNP1_TFBS_da mE1_TFBS_chinmo
2R	8876273	2R_8876273_SNP [dm3] 2R_12988768_SNP [dm6]	C	T	2.370e^-11	1.112e^-5	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	16402076	2R_16402076_SNP [dm3] 2R_20514571_SNP [dm6]	A	G	2.736e^-11	1.112e^-5	INTERGENIC
X	2657069	X_2657069_SNP [dm3] X_2763036_SNP [dm6]	C	G	3.585e^-11	1.112e^-5	INTRON kirre
X	2657950	X_2657950_SNP [dm3] X_2763917_SNP [dm6]	C	A	3.585e^-11	1.112e^-5	INTRON kirre
X	2657959	X_2657959_SNP [dm3] X_2763926_SNP [dm6]	T	G	3.585e^-11	1.112e^-5	INTRON kirre
X	2656877	X_2656877_SNP [dm3] X_2762844_SNP [dm6]	T	A	5.137e^-11	1.365e^-5	INTRON kirre
2L	925072	2L_925072_SNP [dm3] 2L_925072_SNP [dm6]	T	C	6.105e^-11	1.420e^-5	INTRON CG4341
2L	7562039	2L_7562039_SNP [dm3] 2L_7562039_SNP [dm6]	T	C	4.691e^-10	9.696e^-5	INTRON RapGAP1
2R	18139906	2R_18139906_SNP [dm3] 2R_22252401_SNP [dm6]	C	A	8.992e^-10	1.574e^-4	INTRON dve
2R	8876279	2R_8876279_SNP [dm3] 2R_12988774_SNP [dm6]	A	C	9.307e^-10	1.574e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	10154278	2L_10154278_SNP [dm3] 2L_10154278_SNP [dm6]	C	T	1.785e^-9	1.846e^-4	SYNONYMOUS_CODING CG4839 INTRON CG44153
2L	13317423	2L_13317423_SNP [dm3] 2L_13317423_SNP [dm6]	G	A	2.084e^-9	1.846e^-4	INTRON CG43778
2L	13317426	2L_13317426_SNP [dm3] 2L_13317426_SNP [dm6]	T	C	2.084e^-9	1.846e^-4	INTRON CG43778
2L	13317441	2L_13317441_SNP [dm3] 2L_13317441_SNP [dm6]	A	T	2.084e^-9	1.846e^-4	INTRON CG43778
2L	13317475	2L_13317475_SNP [dm3] 2L_13317475_SNP [dm6]	C	T	2.084e^-9	1.846e^-4	INTRON CG43778
2L	13317477	2L_13317477_SNP [dm3] 2L_13317477_SNP [dm6]	G	T	2.084e^-9	1.846e^-4	INTRON CG43778
2L	13317483	2L_13317483_SNP [dm3] 2L_13317483_SNP [dm6]	G	T	2.084e^-9	1.846e^-4	INTRON CG43778
2L	13317487	2L_13317487_SNP [dm3] 2L_13317487_SNP [dm6]	G	T	2.084e^-9	1.846e^-4	INTRON CG43778
2L	13317508	2L_13317508_SNP [dm3] 2L_13317508_SNP [dm6]	C	G	2.084e^-9	1.846e^-4	INTRON CG43778
2L	13317533	2L_13317533_INS [dm3] 2L_13317533_INS [dm6]	A	ACTACTTAATATCATTAAAT...	2.084e^-9	1.846e^-4	INTRON CG43778
2R	8876288	2R_8876288_SNP [dm3] 2R_12988783_SNP [dm6]	C	T	2.479e^-9	2.096e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	850689	3L_850689_SNP [dm3] 3L_850689_SNP [dm6]	G	A	2.624e^-9	2.122e^-4	SYNONYMOUS_CODING CG13889 UPSTREAM CG13890	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	13317452	2L_13317452_SNP [dm3] 2L_13317452_SNP [dm6]	A	T	2.920e^-9	2.264e^-4	INTRON CG43778
2R	8876287	2R_8876287_SNP [dm3] 2R_12988782_SNP [dm6]	T	A	3.671e^-9	2.732e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	14064858	2L_14064858_SNP [dm3] 2L_14064858_SNP [dm6]	T	G	3.825e^-9	2.737e^-4	INTRON nAChRalpha5	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	16841225	2L_16841225_SNP [dm3] 2L_16841225_SNP [dm6]	G	T	4.388e^-9	2.815e^-4	INTRON SclA & 1 other
2L	16841227	2L_16841227_SNP [dm3] 2L_16841227_SNP [dm6]	T	C	4.388e^-9	2.815e^-4	INTRON SclA & 1 other
2L	16856116	2L_16856116_SNP [dm3] 2L_16856116_SNP [dm6]	C	T	4.388e^-9	2.815e^-4	INTRON CG31809	transposable element FlyBase
2L	11288289	2L_11288289_SNP [dm3] 2L_11288289_SNP [dm6]	A	C	5.158e^-9	3.199e^-4	INTERGENIC
2L	4338271	2L_4338271_SNP [dm3] 2L_4338271_SNP [dm6]	A	G	6.297e^-9	3.779e^-4	UPSTREAM Atet INTRON Atet	TF binding site mE1_TFBS_HSA
X	2640925	X_2640925_INS [dm3] X_2746892_INS [dm6]	C	CC	9.918e^-9	5.766e^-4	INTRON kirre
3L	13573518	3L_13573518_SNP [dm3] 3L_13580418_SNP [dm6]	A	T	1.079e^-8	6.081e^-4	INTRON bru-3
2R	15209159	2R_15209159_SNP [dm3] 2R_19321654_SNP [dm6]	C	T	1.232e^-8	6.591e^-4	INTRON Rgk1	TF binding site mE1_TFBS_inv
2R	13021008	2R_13021008_SNP [dm3] 2R_17133503_SNP [dm6]	T	A	1.269e^-8	6.591e^-4	UTR_5_PRIME Acp54A1 UPSTREAM CG11400
2R	17923264	2R_17923264_INS [dm3] 2R_22035759_INS [dm6]	G	GG	1.275e^-8	6.591e^-4	DOWNSTREAM CG9308 INTRON CG34370
2R	15209212	2R_15209212_SNP [dm3] 2R_19321707_SNP [dm6]	C	G	1.403e^-8	7.055e^-4	INTRON Rgk1	TF binding site mE1_TFBS_inv
X	2659263	X_2659263_SNP [dm3] X_2765230_SNP [dm6]	C	T	1.443e^-8	7.067e^-4	INTRON kirre	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	15208776	2R_15208776_SNP [dm3] 2R_19321271_SNP [dm6]	C	G	1.774e^-8	8.462e^-4	INTRON Rgk1
2R	8876322	2R_8876322_INS [dm3] 2R_12988817_INS [dm6]	T	AA	1.866e^-8	8.583e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	15208076	2R_15208076_SNP [dm3] 2R_19320571_SNP [dm6]	A	C	1.918e^-8	8.583e^-4	INTRON Rgk1
2L	10975780	2L_10975780_SNP [dm3] 2L_10975780_SNP [dm6]	G	A	1.938e^-8	8.583e^-4	UTR_3_PRIME l_2_06225 UPSTREAM abo & 1 other	TF binding site BDTNP1_TFBS_dl
2L	2066426	2L_2066426_SNP [dm3] 2L_2066426_SNP [dm6]	G	A	2.110e^-8	9.128e^-4	INTRON dpr3
2L	7214414	2L_7214414_INS [dm3] 2L_7214414_INS [dm6]	A	AAAAAA	2.391e^-8	0.001	INTRON CG13784
X	7148366	X_7148366_SNP [dm3] X_7254333_SNP [dm6]	A	G	2.661e^-8	0.001	INTRON CR44357
X	2660179	X_2660179_INS [dm3] X_2766146_INS [dm6]	G	AA	2.725e^-8	0.001	INTRON kirre	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2L	11288236	2L_11288236_DEL [dm3] 2L_11288236_DEL [dm6]	GG	A	3.010e^-8	0.001	INTERGENIC
2L	11288293	2L_11288293_SNP [dm3] 2L_11288293_SNP [dm6]	A	G	3.010e^-8	0.001	INTERGENIC
2L	11288294	2L_11288294_SNP [dm3] 2L_11288294_SNP [dm6]	T	G	3.010e^-8	0.001	INTERGENIC
X	12662305	X_12662305_SNP [dm3] X_12768272_SNP [dm6]	C	T	3.052e^-8	0.001	INTRON CG3812
2R	7959641	2R_7959641_SNP [dm3] 2R_12072136_SNP [dm6]	T	A	3.076e^-8	0.001	INTRON CG8888
2R	15209207	2R_15209207_SNP [dm3] 2R_19321702_SNP [dm6]	C	T	3.170e^-8	0.001	INTRON Rgk1	TF binding site mE1_TFBS_inv
3L	2746087	3L_2746087_SNP [dm3] 3L_2746087_SNP [dm6]	T	A	3.221e^-8	0.001	INTRON Mrtf	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	7147751	X_7147751_SNP [dm3] X_7253718_SNP [dm6]	C	T	3.356e^-8	0.001	INTRON CR44357
2R	4866582	2R_4866582_SNP [dm3] 2R_8979077_SNP [dm6]	A	G	3.400e^-8	0.001	INTRON CG8213	TF binding site BDTNP1_TFBS_dl
2L	7214905	2L_7214905_SNP [dm3] 2L_7214905_SNP [dm6]	A	T	3.505e^-8	0.001	INTRON CG13784
3L	2570029	3L_2570029_SNP [dm3] 3L_2570029_SNP [dm6]	A	C	3.630e^-8	0.001	INTRON msn	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	11288275	2L_11288275_SNP [dm3] 2L_11288275_SNP [dm6]	T	C	4.029e^-8	0.001	INTERGENIC
2R	8876156	2R_8876156_SNP [dm3] 2R_12988651_SNP [dm6]	G	A	4.329e^-8	0.001	INTERGENIC
2R	8876161	2R_8876161_SNP [dm3] 2R_12988656_SNP [dm6]	A	C	4.329e^-8	0.001	INTERGENIC
2R	15208078	2R_15208078_SNP [dm3] 2R_19320573_SNP [dm6]	G	T	4.665e^-8	0.001	INTRON Rgk1
2L	5105137	2L_5105137_SNP [dm3] 2L_5105137_SNP [dm6]	T	A	4.673e^-8	0.001	INTRON Msp300
2L	11288345	2L_11288345_SNP [dm3] 2L_11288345_SNP [dm6]	T	A	5.190e^-8	0.002	INTERGENIC
2R	15207208	2R_15207208_SNP [dm3] 2R_19319703_SNP [dm6]	G	A	5.676e^-8	0.002	INTRON Rgk1
2R	4225121	2R_4225121_SNP [dm3] 2R_8337616_SNP [dm6]	C	T	5.974e^-8	0.002	INTRON pdm3
2R	4225144	2R_4225144_SNP [dm3] 2R_8337639_SNP [dm6]	G	T	5.974e^-8	0.002	INTRON pdm3
2R	4225146	2R_4225146_SNP [dm3] 2R_8337641_SNP [dm6]	C	T	5.974e^-8	0.002	INTRON pdm3
3L	5416444	3L_5416444_DEL [dm3] 3L_5423344_DEL [dm6]	CAAG	T	6.406e^-8	0.002	UPSTREAM CG34391 INTERGENIC
2R	15209334	2R_15209334_SNP [dm3] 2R_19321829_SNP [dm6]	C	T	6.779e^-8	0.002	INTRON Rgk1	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	14874470	X_14874470_SNP [dm3] X_14980437_SNP [dm6]	T	A	7.197e^-8	0.002	INTRON eag
X	14874471	X_14874471_SNP [dm3] X_14980438_SNP [dm6]	C	G	7.197e^-8	0.002	INTRON eag
X	14874519	X_14874519_SNP [dm3] X_14980486_SNP [dm6]	T	C	7.197e^-8	0.002	INTRON eag
2R	13617146	2R_13617146_SNP [dm3] 2R_17729641_SNP [dm6]	C	T	8.965e^-8	0.002	INTRON CG4984 & 1 other
X	14870611	X_14870611_SNP [dm3] X_14976578_SNP [dm6]	C	T	9.218e^-8	0.002	INTRON eag
X	14870633	X_14870633_SNP [dm3] X_14976600_SNP [dm6]	A	T	9.421e^-8	0.002	INTRON eag
X	14874351	X_14874351_SNP [dm3] X_14980318_SNP [dm6]	G	A	9.421e^-8	0.002	INTRON eag
2R	10547226	2R_10547226_SNP [dm3] 2R_14659721_SNP [dm6]	A	T	9.729e^-8	0.002	UPSTREAM Adgf-E INTERGENIC	TF binding site mE1_TFBS_cad
X	21952338	X_21952338_SNP [dm3] X_22550502_SNP [dm6]	T	C	9.774e^-8	0.002	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	5352793	2L_5352793_INS [dm3] 2L_5352793_INS [dm6]	T	TGGCT	1.082e^-7	0.002	INTRON nompC
2R	15208978	2R_15208978_SNP [dm3] 2R_19321473_SNP [dm6]	C	A	1.082e^-7	0.002	INTRON Rgk1	TF binding site mE1_TFBS_inv
2L	4600797	2L_4600797_SNP [dm3] 2L_4600797_SNP [dm6]	T	G	1.120e^-7	0.002	INTRON dp
3L	4688096	3L_4688096_SNP [dm3] 3L_4688096_SNP [dm6]	C	T	1.120e^-7	0.002	SYNONYMOUS_CODING CG7514 UPSTREAM axo DOWNSTREAM CG18418	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	4688416	3L_4688416_SNP [dm3] 3L_4688416_SNP [dm6]	C	T	1.120e^-7	0.002	NON_SYNONYMOUS_CODING CG7514 DOWNSTREAM CG18418	TF binding site mE1_TFBS_cad
3L	4696720	3L_4696720_SNP [dm3] 3L_4696720_SNP [dm6]	T	A	1.120e^-7	0.002	UPSTREAM CG13713 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_Kr
3L	4697267	3L_4697267_SNP [dm3] 3L_4697267_SNP [dm6]	A	G	1.120e^-7	0.002	UPSTREAM CG13713 INTRON RhoGEF64C	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
2R	14451431	2R_14451431_DEL [dm3] 2R_18563926_DEL [dm6]	GGCCCCACTCGAC...	G	1.124e^-7	0.002	INTRON GEFmeso	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
2L	7423130	2L_7423130_SNP [dm3] 2L_7423130_SNP [dm6]	A	T	1.213e^-7	0.003	UPSTREAM CR43857 DOWNSTREAM chm INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	11579835	2R_11579835_DEL [dm3] 2R_15692330_DEL [dm6]	ATTTCTTGGA	A	1.268e^-7	0.003	UPSTREAM CG30087 DOWNSTREAM CG30088 EXON CR44372
3R	3621377	3R_3621377_SNP [dm3] 3R_7795655_SNP [dm6]	T	A	1.388e^-7	0.003	SYNONYMOUS_CODING CG2641
2R	13385144	2R_13385144_SNP [dm3] 2R_17497639_SNP [dm6]	T	C	1.422e^-7	0.003	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	20586267	2R_20586267_SNP [dm3] 2R_24698744_SNP [dm6]	A	T	1.428e^-7	0.003	UTR_3_PRIME Mid1 DOWNSTREAM Mid1
2R	11484336	2R_11484336_SNP [dm3] 2R_15596831_SNP [dm6]	A	T	1.455e^-7	0.003	INTERGENIC
X	5552898	X_5552898_SNP [dm3] X_5658865_SNP [dm6]	C	T	1.495e^-7	0.003	INTRON CG42265	TF binding site mE1_TFBS_chinmo
X	14873087	X_14873087_SNP [dm3] X_14979054_SNP [dm6]	A	G	1.557e^-7	0.003	INTRON eag
X	14870590	X_14870590_SNP [dm3] X_14976557_SNP [dm6]	C	T	1.650e^-7	0.003	INTRON eag
2R	17387122	2R_17387122_SNP [dm3] 2R_21499617_SNP [dm6]	G	A	1.656e^-7	0.003	SYNONYMOUS_CODING TAF1C-like	TF binding site mE1_TFBS_sens
2L	5352778	2L_5352778_INS [dm3] 2L_5352778_INS [dm6]	T	ACTTTAAAAAAA...	1.753e^-7	0.003	INTRON nompC
2R	20586215	2R_20586215_SNP [dm3] 2R_24698692_SNP [dm6]	C	T	1.820e^-7	0.003	UTR_3_PRIME Mid1 DOWNSTREAM Mid1
2L	1276250	2L_1276250_SNP [dm3] 2L_1276250_SNP [dm6]	A	G	1.829e^-7	0.003	INTRON robo3
X	18191570	X_18191570_SNP [dm3] X_18297537_SNP [dm6]	T	C	1.893e^-7	0.003	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens

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By genomic position
Variant impact
Gene name

Microbiota_OTU004 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results