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=3.612e^-8)
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
wolba	0.0555671
In_3R_K	0.0008425
In_3R_Mo	0.0386778

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	2.8868	0.0893
In_3R_K	6.951	0.0309

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2891 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	5951041	3L_5951041_SNP [dm3] 3L_5957941_SNP [dm6]	G	A	6.240e^-9	0.012	INTERGENIC
2L	12008344	2L_12008344_SNP [dm3] 2L_12008344_SNP [dm6]	G	T	1.469e^-8	0.014	START_GAINED Rh5 UTR_5_PRIME Rh5 UPSTREAM Rh5	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	2746087	3L_2746087_SNP [dm3] 3L_2746087_SNP [dm6]	T	A	1.058e^-7	0.036	INTRON Mrtf	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16041485	2R_16041485_SNP [dm3] 2R_20153980_SNP [dm6]	C	T	1.576e^-7	0.036	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2R	16041682	2R_16041682_SNP [dm3] 2R_20154177_SNP [dm6]	G	T	1.576e^-7	0.036	INTERGENIC
2L	16400842	2L_16400842_SNP [dm3] 2L_16400842_SNP [dm6]	C	T	1.606e^-7	0.036	INTRON CG5888
2L	16400845	2L_16400845_SNP [dm3] 2L_16400845_SNP [dm6]	T	C	1.606e^-7	0.036	INTRON CG5888
3L	20854813	3L_20854813_SNP [dm3] 3L_20861713_SNP [dm6]	A	T	1.746e^-7	0.036	INTRON CG32432
2R	6866515	2R_6866515_SNP [dm3] 2R_10979010_SNP [dm6]	T	G	1.779e^-7	0.036	UTR_3_PRIME luna	TF binding site mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_hkb mE1_TFBS_HSA
3L	11923037	3L_11923037_SNP [dm3] 3L_11929937_SNP [dm6]	G	A	1.941e^-7	0.036	INTRON CG44837 & 1 other	TF binding site mE1_TFBS_cad
2R	17923264	2R_17923264_INS [dm3] 2R_22035759_INS [dm6]	G	GG	2.271e^-7	0.037	DOWNSTREAM CG9308 INTRON CG34370
2L	14681430	2L_14681430_SNP [dm3] 2L_14681430_SNP [dm6]	T	C	2.363e^-7	0.037	INTRON osp
2L	4186178	2L_4186178_SNP [dm3] 2L_4186178_SNP [dm6]	G	T	3.158e^-7	0.045	DOWNSTREAM CG31961 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	9928153	2R_9928153_SNP [dm3] 2R_14040648_SNP [dm6]	G	A	3.379e^-7	0.045	NON_SYNONYMOUS_CODING mam INTRON mam	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_Trl
2R	6747611	2R_6747611_SNP [dm3] 2R_10860106_SNP [dm6]	G	T	3.737e^-7	0.046	INTRON CG30015 EXON CR44302	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	20600688	2L_20600688_SNP [dm3] 2L_20600688_SNP [dm6]	C	G	4.311e^-7	0.047	INTRON CR44909	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	20600689	2L_20600689_SNP [dm3] 2L_20600689_SNP [dm6]	G	C	4.311e^-7	0.047	INTRON CR44909	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	16367475	X_16367475_INS [dm3] X_16473442_INS [dm6]	T	TT	4.659e^-7	0.048	INTRON para
X	13019590	X_13019590_SNP [dm3] X_13125557_SNP [dm6]	T	G	7.393e^-7	0.072	INTRON CG32638
2L	11989628	2L_11989628_SNP [dm3] 2L_11989628_SNP [dm6]	A	G	7.964e^-7	0.072	NON_SYNONYMOUS_CODING zuc UPSTREAM dgt2 DOWNSTREAM CG34163	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
3L	8430562	3L_8430562_SNP [dm3] 3L_8437462_SNP [dm6]	A	T	8.473e^-7	0.072	INTRON Unr
3L	8430713	3L_8430713_SNP [dm3] 3L_8437613_SNP [dm6]	G	C	8.473e^-7	0.072	SYNONYMOUS_CODING Unr
2R	16041785	2R_16041785_SNP [dm3] 2R_20154280_SNP [dm6]	T	C	8.853e^-7	0.072	INTERGENIC
2R	14667008	2R_14667008_SNP [dm3] 2R_18779503_SNP [dm6]	G	T	9.324e^-7	0.072	INTERGENIC
X	13019591	X_13019591_SNP [dm3] X_13125558_SNP [dm6]	T	C	9.733e^-7	0.072	INTRON CG32638
2R	15210073	2R_15210073_SNP [dm3] 2R_19322568_SNP [dm6]	C	T	1.070e^-6	0.077	INTRON Rgk1
2R	14667007	2R_14667007_SNP [dm3] 2R_18779502_SNP [dm6]	A	G	1.185e^-6	0.081	INTERGENIC
2L	10131049	2L_10131049_SNP [dm3] 2L_10131049_SNP [dm6]	A	T	1.282e^-6	0.081	INTRON CG44153
2L	10131058	2L_10131058_SNP [dm3] 2L_10131058_SNP [dm6]	C	A	1.282e^-6	0.081	INTRON CG44153
2R	16042250	2R_16042250_SNP [dm3] 2R_20154745_SNP [dm6]	G	T	1.361e^-6	0.081	INTERGENIC
X	11690225	X_11690225_SNP [dm3] X_11796192_SNP [dm6]	A	T	1.382e^-6	0.081	UTR_3_PRIME CkIIbeta DOWNSTREAM CkIIbeta INTRON CkIIbeta	TF binding site BDTNP1_TFBS_dl
2R	16041970	2R_16041970_SNP [dm3] 2R_20154465_SNP [dm6]	T	A	1.419e^-6	0.081	INTERGENIC
2R	15210077	2R_15210077_SNP [dm3] 2R_19322572_SNP [dm6]	C	A	1.476e^-6	0.081	INTRON Rgk1
2R	15210082	2R_15210082_SNP [dm3] 2R_19322577_SNP [dm6]	G	A	1.476e^-6	0.081	INTRON Rgk1
2R	16041895	2R_16041895_SNP [dm3] 2R_20154390_SNP [dm6]	T	C	1.574e^-6	0.081	INTERGENIC
2R	16042245	2R_16042245_SNP [dm3] 2R_20154740_SNP [dm6]	C	T	1.574e^-6	0.081	INTERGENIC
X	5413005	X_5413005_SNP [dm3] X_5518972_SNP [dm6]	A	G	1.829e^-6	0.088	DOWNSTREAM CG12730 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	4438218	X_4438218_SNP [dm3] X_4544185_SNP [dm6]	G	T	1.833e^-6	0.088	DOWNSTREAM Usf INTRON CR32773 & 1 other
2L	4186205	2L_4186205_SNP [dm3] 2L_4186205_SNP [dm6]	T	A	1.842e^-6	0.088	DOWNSTREAM CG31961 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	14667120	2R_14667120_SNP [dm3] 2R_18779615_SNP [dm6]	T	G	2.073e^-6	0.091	INTERGENIC
2R	9602919	2R_9602919_SNP [dm3] 2R_13715414_SNP [dm6]	C	G	2.084e^-6	0.091	INTRON fas
2L	8098983	2L_8098983_SNP [dm3] 2L_8098983_SNP [dm6]	T	A	2.093e^-6	0.091	INTRON Bsg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2R	13724689	2R_13724689_INS [dm3] 2R_17837184_INS [dm6]	T	TGT	2.103e^-6	0.091	INTRON grh
3L	9741188	3L_9741188_SNP [dm3] 3L_9748088_SNP [dm6]	A	G	2.436e^-6	0.101	INTRON CG42268	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	9703831	3R_9703831_SNP [dm3] 3R_13878109_SNP [dm6]	A	G	2.478e^-6	0.101	UPSTREAM E5 INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	7936500	2L_7936500_SNP [dm3] 2L_7936500_SNP [dm6]	C	A	2.501e^-6	0.101	INTRON Snoo
3L	850689	3L_850689_SNP [dm3] 3L_850689_SNP [dm6]	G	A	2.703e^-6	0.101	SYNONYMOUS_CODING CG13889 UPSTREAM CG13890	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
X	10185930	X_10185930_INS [dm3] X_10291897_INS [dm6]	G	GTTGGACAATTATTACTTAA...	3.016e^-6	0.101	INTRON alpha-Man-I
3L	1403877	3L_1403877_SNP [dm3] 3L_1403877_SNP [dm6]	G	C	3.099e^-6	0.101	INTRON Ptp61F	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad
2R	6747597	2R_6747597_SNP [dm3] 2R_10860092_SNP [dm6]	C	A	3.271e^-6	0.101	INTRON CG30015 EXON CR44302	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	14667017	2R_14667017_SNP [dm3] 2R_18779512_SNP [dm6]	T	A	3.307e^-6	0.101	INTERGENIC
2R	14667019	2R_14667019_SNP [dm3] 2R_18779514_SNP [dm6]	T	A	3.307e^-6	0.101	INTERGENIC
2R	14667058	2R_14667058_SNP [dm3] 2R_18779553_SNP [dm6]	G	T	3.307e^-6	0.101	INTERGENIC
2R	14667071	2R_14667071_SNP [dm3] 2R_18779566_SNP [dm6]	A	T	3.307e^-6	0.101	INTERGENIC
2R	14667073	2R_14667073_SNP [dm3] 2R_18779568_SNP [dm6]	G	T	3.307e^-6	0.101	INTERGENIC
2R	14667115	2R_14667115_SNP [dm3] 2R_18779610_SNP [dm6]	T	C	3.307e^-6	0.101	INTERGENIC
2R	14667116	2R_14667116_SNP [dm3] 2R_18779611_SNP [dm6]	T	A	3.307e^-6	0.101	INTERGENIC
2R	14667123	2R_14667123_SNP [dm3] 2R_18779618_SNP [dm6]	A	C	3.307e^-6	0.101	INTERGENIC
2R	14667132	2R_14667132_MNP [dm3] 2R_18779627_MNP [dm6]	AAAG	TGTT	3.307e^-6	0.101	INTERGENIC
3L	4096819	3L_4096819_SNP [dm3] 3L_4096819_SNP [dm6]	C	T	3.367e^-6	0.101	INTRON CG14995	TF binding site mE1_TFBS_cad
X	19159525	X_19159525_SNP [dm3] X_19265492_SNP [dm6]	G	A	3.367e^-6	0.101	INTRON Vav	TF binding site mE1_TFBS_HSA
2R	8535595	2R_8535595_SNP [dm3] 2R_12648090_SNP [dm6]	T	A	3.471e^-6	0.101	UTR_5_PRIME CG8785
2R	6752115	2R_6752115_SNP [dm3] 2R_10864610_SNP [dm6]	A	T	3.509e^-6	0.101	INTRON CG30015
X	13411201	X_13411201_SNP [dm3] X_13517168_SNP [dm6]	A	T	3.647e^-6	0.101	INTRON Neto
2R	14666986	2R_14666986_SNP [dm3] 2R_18779481_SNP [dm6]	C	T	3.671e^-6	0.101	INTERGENIC
2R	14667009	2R_14667009_DEL [dm3] 2R_18779504_DEL [dm6]	ATTTT	A	3.671e^-6	0.101	INTERGENIC
2R	14667023	2R_14667023_DEL [dm3] 2R_18779518_DEL [dm6]	TATATAT	T	3.671e^-6	0.101	INTERGENIC
X	16748411	X_16748411_SNP [dm3] X_16854378_SNP [dm6]	G	T	3.691e^-6	0.101	INTRON CG13003
X	9118120	X_9118120_SNP [dm3] X_9224087_SNP [dm6]	G	A	3.873e^-6	0.103	UPSTREAM t INTERGENIC
3L	18209302	3L_18209302_INS [dm3] 3L_18216202_INS [dm6]	G	GG	3.956e^-6	0.103	INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	20017205	2L_20017205_DEL [dm3] 2L_20017205_DEL [dm6]	TT	T	3.962e^-6	0.103	UTR_5_PRIME CG43861
2L	16941562	2L_16941562_SNP [dm3] 2L_16941562_SNP [dm6]	G	A	4.081e^-6	0.103	INTERGENIC
2L	4187058	2L_4187058_SNP [dm3] 2L_4187058_SNP [dm6]	C	T	4.094e^-6	0.103	SYNONYMOUS_CODING CG31961 DOWNSTREAM CR44057	TF binding site mE1_TFBS_sens
2L	16856081	2L_16856081_DEL [dm3] 2L_16856081_DEL [dm6]	GTATCAATTTGGATTA...	C	4.140e^-6	0.103	INTRON CG31809	transposable element FlyBase
X	21952338	X_21952338_SNP [dm3] X_22550502_SNP [dm6]	T	C	4.225e^-6	0.103	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	8114962	2R_8114962_SNP [dm3] 2R_12227457_SNP [dm6]	C	T	4.227e^-6	0.103	UPSTREAM CG8854 INTRON CG8854
2L	11907079	2L_11907079_SNP [dm3] 2L_11907079_SNP [dm6]	T	C	4.263e^-6	0.103	INTRON Pde1c
2L	6013636	2L_6013636_SNP [dm3] 2L_6013636_SNP [dm6]	G	A	4.727e^-6	0.113	SYNONYMOUS_CODING H2.0	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	11688593	X_11688593_SNP [dm3] X_11794560_SNP [dm6]	C	G	4.954e^-6	0.114	INTRON CkIIbeta	TF binding site BDTNP1_TFBS_dl
2R	6865936	2R_6865936_INS [dm3] 2R_10978431_INS [dm6]	T	TTTTGCT	4.991e^-6	0.114	UTR_3_PRIME luna
2R	15208776	2R_15208776_SNP [dm3] 2R_19321271_SNP [dm6]	C	G	4.994e^-6	0.114	INTRON Rgk1
2L	16844630	2L_16844630_INS [dm3] 2L_16844630_INS [dm6]	A	AC	5.039e^-6	0.114	INTRON CG13284
2L	15404207	2L_15404207_SNP [dm3] 2L_15404207_SNP [dm6]	C	G	5.362e^-6	0.118	INTERGENIC	TF binding site mE1_TFBS_cad
3L	7624224	3L_7624224_SNP [dm3] 3L_7631124_SNP [dm6]	T	C	5.364e^-6	0.118	INTRON CG33275
2R	15208076	2R_15208076_SNP [dm3] 2R_19320571_SNP [dm6]	A	C	5.401e^-6	0.118	INTRON Rgk1
2R	8536595	2R_8536595_SNP [dm3] 2R_12649090_SNP [dm6]	C	A	5.483e^-6	0.118	UPSTREAM CG8785 INTERGENIC
2L	8789650	2L_8789650_SNP [dm3] 2L_8789650_SNP [dm6]	T	C	5.556e^-6	0.118	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	10130931	2L_10130931_SNP [dm3] 2L_10130931_SNP [dm6]	G	T	5.561e^-6	0.118	INTRON CG44153
2L	17993845	2L_17993845_SNP [dm3] 2L_17993845_SNP [dm6]	A	G	5.842e^-6	0.121	EXON CR44767
2L	1510210	2L_1510210_SNP [dm3] 2L_1510210_SNP [dm6]	T	C	5.850e^-6	0.121	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA
2R	19615467	2R_19615467_SNP [dm3] 2R_23727944_SNP [dm6]	G	C	6.339e^-6	0.128	INTRON Sesn	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	8672048	2L_8672048_SNP [dm3] 2L_8672048_SNP [dm6]	C	G	6.456e^-6	0.128	UPSTREAM Glt DOWNSTREAM Sema-1a INTERGENIC
2L	8672057	2L_8672057_INS [dm3] 2L_8672057_INS [dm6]	C	CT	6.456e^-6	0.128	UPSTREAM Glt DOWNSTREAM Sema-1a INTERGENIC
X	13634944	X_13634944_SNP [dm3] X_13740911_SNP [dm6]	T	C	6.460e^-6	0.128	UTR_3_PRIME CG11151 INTRON Grip91	TF binding site BDTNP1_TFBS_dl
2L	8789461	2L_8789461_SNP [dm3] 2L_8789461_SNP [dm6]	T	A	6.682e^-6	0.131	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	10746819	3R_10746819_SNP [dm3] 3R_14921097_SNP [dm6]	G	T	6.904e^-6	0.133	SYNONYMOUS_CODING Sdr
2L	8098984	2L_8098984_SNP [dm3] 2L_8098984_SNP [dm6]	C	T	6.943e^-6	0.133	INTRON Bsg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	7805811	3L_7805811_SNP [dm3] 3L_7812711_SNP [dm6]	G	A	7.284e^-6	0.138	UTR_3_PRIME Pdp1
3L	911193	3L_911193_SNP [dm3] 3L_911193_SNP [dm6]	C	T	7.379e^-6	0.138	UTR_3_PRIME nerfin-1	regulatory region REDfly_CRMs
3L	419039	3L_419039_SNP [dm3] 3L_419039_SNP [dm6]	T	A	7.416e^-6	0.138	INTERGENIC

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By genomic position
Variant impact
Gene name

Microbiota_OTU025 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results