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=9.683e^-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_K	0.0215109

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	5.4605	0.0652
In_3R_Mo	4.8946	0.0865

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2280 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	7442907	2R_7442907_SNP [dm3] 2R_11555402_SNP [dm6]	T	C	1.624e^-7	0.302	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	25451499	3R_25451499_SNP [dm3] 3R_29625777_SNP [dm6]	A	G	6.436e^-7	0.332	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	10287406	3L_10287406_SNP [dm3] 3L_10294306_SNP [dm6]	C	G	6.802e^-7	0.332	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	21980761	X_21980761_SNP [dm3] X_22578925_SNP [dm6]	A	T	1.010e^-6	0.332	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	13569252	3R_13569252_SNP [dm3] 3R_17743530_SNP [dm6]	G	A	1.251e^-6	0.332	INTRON TyrRII	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	21980775	X_21980775_SNP [dm3] X_22578939_SNP [dm6]	T	A	1.333e^-6	0.332	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	21981036	X_21981036_INS [dm3] X_22579200_INS [dm6]	T	TAT	1.333e^-6	0.332	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	12306884	3L_12306884_SNP [dm3] 3L_12313784_SNP [dm6]	C	T	1.611e^-6	0.332	INTERGENIC
3L	6111784	3L_6111784_SNP [dm3] 3L_6118684_SNP [dm6]	A	G	1.659e^-6	0.332	INTRON Ets65A
3L	7497052	3L_7497052_SNP [dm3] 3L_7503952_SNP [dm6]	A	T	1.786e^-6	0.332	INTERGENIC
3L	12173728	3L_12173728_SNP [dm3] 3L_12180628_SNP [dm6]	T	C	2.648e^-6	0.399	INTRON CAH2
X	21952338	X_21952338_SNP [dm3] X_22550502_SNP [dm6]	T	C	2.658e^-6	0.399	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3L	11304890	3L_11304890_SNP [dm3] 3L_11311790_SNP [dm6]	A	G	2.856e^-6	0.399	START_GAINED CG7573 UTR_5_PRIME CG7573
2L	11192334	2L_11192334_SNP [dm3] 2L_11192334_SNP [dm6]	T	A	3.140e^-6	0.399	INTRON Ca-beta
3L	11303552	3L_11303552_SNP [dm3] 3L_11310452_SNP [dm6]	T	C	3.940e^-6	0.399	INTERGENIC
3L	18824273	3L_18824273_SNP [dm3] 3L_18831173_SNP [dm6]	G	A	4.117e^-6	0.399	SYNONYMOUS_CODING Indy	TF binding site mE1_TFBS_cad
2L	11288248	2L_11288248_SNP [dm3] 2L_11288248_SNP [dm6]	T	C	4.758e^-6	0.399	INTERGENIC
2L	11288249	2L_11288249_SNP [dm3] 2L_11288249_SNP [dm6]	T	A	4.758e^-6	0.399	INTERGENIC
3R	25451580	3R_25451580_SNP [dm3] 3R_29625858_SNP [dm6]	C	A	5.120e^-6	0.399	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	25451581	3R_25451581_SNP [dm3] 3R_29625859_SNP [dm6]	C	A	5.120e^-6	0.399	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	11288289	2L_11288289_SNP [dm3] 2L_11288289_SNP [dm6]	A	C	5.251e^-6	0.399	INTERGENIC
2L	11288236	2L_11288236_DEL [dm3] 2L_11288236_DEL [dm6]	GG	A	5.419e^-6	0.399	INTERGENIC
2L	11288293	2L_11288293_SNP [dm3] 2L_11288293_SNP [dm6]	A	G	5.419e^-6	0.399	INTERGENIC
2L	11288294	2L_11288294_SNP [dm3] 2L_11288294_SNP [dm6]	T	G	5.419e^-6	0.399	INTERGENIC
3R	10314647	3R_10314647_SNP [dm3] 3R_14488925_SNP [dm6]	T	G	5.512e^-6	0.399	INTERGENIC	TF binding site mE1_TFBS_HSA
2L	2051124	2L_2051124_SNP [dm3] 2L_2051124_SNP [dm6]	T	G	5.654e^-6	0.399	INTERGENIC
2L	11288243	2L_11288243_SNP [dm3] 2L_11288243_SNP [dm6]	G	T	6.428e^-6	0.399	INTERGENIC
2L	11288275	2L_11288275_SNP [dm3] 2L_11288275_SNP [dm6]	T	C	6.706e^-6	0.399	INTERGENIC
X	15794685	X_15794685_SNP [dm3] X_15900652_SNP [dm6]	A	G	6.922e^-6	0.399	INTRON shi
2L	8098939	2L_8098939_SNP [dm3] 2L_8098939_SNP [dm6]	T	C	7.162e^-6	0.399	INTRON Bsg	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3L	11505068	3L_11505068_SNP [dm3] 3L_11511968_SNP [dm6]	G	C	7.393e^-6	0.399	UPSTREAM Sgs3 INTERGENIC	regulatory region REDfly_CRMs transposable element FlyBase
2L	11192164	2L_11192164_SNP [dm3] 2L_11192164_SNP [dm6]	A	G	7.501e^-6	0.399	INTRON Ca-beta
2L	8752094	2L_8752094_SNP [dm3] 2L_8752094_SNP [dm6]	T	C	7.833e^-6	0.399	UTR_5_PRIME CG45307 UPSTREAM CG12438
2L	11288345	2L_11288345_SNP [dm3] 2L_11288345_SNP [dm6]	T	A	7.934e^-6	0.399	INTERGENIC
2L	8371319	2L_8371319_INS [dm3] 2L_8371319_INS [dm6]	A	ATCTA	8.260e^-6	0.399	UPSTREAM CR45341 INTRON CG17292
2R	10796875	2R_10796875_SNP [dm3] 2R_14909370_SNP [dm6]	C	A	8.659e^-6	0.399	INTRON CG10249
X	21964738	X_21964738_SNP [dm3] X_22562902_SNP [dm6]	A	G	9.131e^-6	0.399	INTERGENIC
2L	15759696	2L_15759696_SNP [dm3] 2L_15759696_SNP [dm6]	G	A	9.184e^-6	0.399	SYNONYMOUS_CODING Gli	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	1712706	2L_1712706_SNP [dm3] 2L_1712706_SNP [dm6]	C	A	9.743e^-6	0.399	SYNONYMOUS_CODING frtz	TF binding site mE1_TFBS_chinmo
2L	4568520	2L_4568520_SNP [dm3] 2L_4568520_SNP [dm6]	T	C	9.765e^-6	0.399	INTRON dp	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	18820962	3L_18820962_SNP [dm3] 3L_18827862_SNP [dm6]	C	T	9.906e^-6	0.399	SYNONYMOUS_CODING Cat DOWNSTREAM Indy	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
X	21979618	X_21979618_SNP [dm3] X_22577782_SNP [dm6]	T	A	1.079e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	21979628	X_21979628_SNP [dm3] X_22577792_SNP [dm6]	C	T	1.079e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	19447315	3R_19447315_SNP [dm3] 3R_23621593_SNP [dm6]	T	A	1.086e^-5	0.399	INTRON CG31145
X	21965798	X_21965798_SNP [dm3] X_22563962_SNP [dm6]	T	C	1.139e^-5	0.399	INTERGENIC
X	21975409	X_21975409_SNP [dm3] X_22573573_SNP [dm6]	C	T	1.139e^-5	0.399	INTERGENIC	transposable element FlyBase
X	21985152	X_21985152_SNP [dm3] X_22583316_SNP [dm6]	G	A	1.181e^-5	0.399	DOWNSTREAM Cda4 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	15794712	X_15794712_SNP [dm3] X_15900679_SNP [dm6]	A	G	1.227e^-5	0.399	INTRON shi
3L	5417071	3L_5417071_SNP [dm3] 3L_5423971_SNP [dm6]	A	G	1.462e^-5	0.399	UPSTREAM CG34391 INTERGENIC
3L	9499529	3L_9499529_SNP [dm3] 3L_9506429_SNP [dm6]	A	T	1.511e^-5	0.399	DOWNSTREAM CG3408 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3R	10810457	3R_10810457_SNP [dm3] 3R_14984735_SNP [dm6]	G	C	1.524e^-5	0.399	INTERGENIC
2R	16764707	2R_16764707_SNP [dm3] 2R_20877202_SNP [dm6]	A	T	1.595e^-5	0.399	INTRON Ipk1
2L	2498298	2L_2498298_SNP [dm3] 2L_2498298_SNP [dm6]	C	T	1.725e^-5	0.399	UTR_3_PRIME oaf DOWNSTREAM oaf
X	2324822	X_2324822_SNP [dm3] X_2430789_SNP [dm6]	G	T	1.726e^-5	0.399	INTERGENIC	regulatory region REDfly_CRMs 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_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3L	7221082	3L_7221082_SNP [dm3] 3L_7227982_SNP [dm6]	T	A	1.779e^-5	0.399	INTERGENIC
X	19398092	X_19398092_SNP [dm3] X_19504059_SNP [dm6]	G	T	1.792e^-5	0.399	UPSTREAM Pfrx INTRON Pfrx & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	9499501	3L_9499501_SNP [dm3] 3L_9506401_SNP [dm6]	G	A	1.809e^-5	0.399	DOWNSTREAM CG3408 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
X	21981584	X_21981584_SNP [dm3] X_22579748_SNP [dm6]	G	C	1.826e^-5	0.399	INTERGENIC
X	21972159	X_21972159_SNP [dm3] X_22570323_SNP [dm6]	C	A	1.854e^-5	0.399	INTERGENIC
X	21961909	X_21961909_SNP [dm3] X_22560073_SNP [dm6]	G	A	1.902e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	11184069	2L_11184069_SNP [dm3] 2L_11184069_SNP [dm6]	A	T	1.920e^-5	0.399	INTRON Ca-beta
3L	7395815	3L_7395815_SNP [dm3] 3L_7402715_SNP [dm6]	C	A	1.959e^-5	0.399	INTRON CG8560	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	21979128	X_21979128_INS [dm3] X_22577292_INS [dm6]	A	AACGAAAA	1.961e^-5	0.399	INTERGENIC
3R	11613964	3R_11613964_SNP [dm3] 3R_15788242_SNP [dm6]	A	G	1.994e^-5	0.399	UTR_3_PRIME CG9590 UPSTREAM CG9589	TF binding site mE1_TFBS_cad
X	21961830	X_21961830_DEL [dm3] X_22559994_DEL [dm6]	TCAACATTATGACAG...	T	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	21972015	X_21972015_SNP [dm3] X_22570179_SNP [dm6]	T	A	1.994e^-5	0.399	INTERGENIC
X	21972016	X_21972016_SNP [dm3] X_22570180_SNP [dm6]	C	A	1.994e^-5	0.399	INTERGENIC
X	21972056	X_21972056_SNP [dm3] X_22570220_SNP [dm6]	T	A	1.994e^-5	0.399	INTERGENIC
X	21972083	X_21972083_SNP [dm3] X_22570247_SNP [dm6]	G	A	1.994e^-5	0.399	INTERGENIC
X	21972923	X_21972923_SNP [dm3] X_22571087_SNP [dm6]	C	A	1.994e^-5	0.399	INTERGENIC
X	21972928	X_21972928_SNP [dm3] X_22571092_SNP [dm6]	G	T	1.994e^-5	0.399	INTERGENIC
X	21973164	X_21973164_SNP [dm3] X_22571328_SNP [dm6]	G	A	1.994e^-5	0.399	INTERGENIC
X	21973311	X_21973311_SNP [dm3] X_22571475_SNP [dm6]	A	T	1.994e^-5	0.399	INTERGENIC
X	21973312	X_21973312_SNP [dm3] X_22571476_SNP [dm6]	T	C	1.994e^-5	0.399	INTERGENIC
X	21973382	X_21973382_SNP [dm3] X_22571546_SNP [dm6]	T	C	1.994e^-5	0.399	INTERGENIC
X	21973398	X_21973398_SNP [dm3] X_22571562_SNP [dm6]	C	A	1.994e^-5	0.399	INTERGENIC
X	21973411	X_21973411_SNP [dm3] X_22571575_SNP [dm6]	G	A	1.994e^-5	0.399	INTERGENIC
X	21973474	X_21973474_SNP [dm3] X_22571638_SNP [dm6]	G	C	1.994e^-5	0.399	INTERGENIC
X	21974329	X_21974329_SNP [dm3] X_22572493_SNP [dm6]	C	T	1.994e^-5	0.399	INTERGENIC
X	21975301	X_21975301_SNP [dm3] X_22573465_SNP [dm6]	C	T	1.994e^-5	0.399	INTERGENIC
X	21975373	X_21975373_SNP [dm3] X_22573537_SNP [dm6]	C	T	1.994e^-5	0.399	INTERGENIC	transposable element FlyBase
X	21977231	X_21977231_SNP [dm3] X_22575395_SNP [dm6]	T	C	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA
X	21979525	X_21979525_SNP [dm3] X_22577689_SNP [dm6]	G	A	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	21979538	X_21979538_SNP [dm3] X_22577702_SNP [dm6]	G	A	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	21979545	X_21979545_SNP [dm3] X_22577709_SNP [dm6]	C	T	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	21979559	X_21979559_SNP [dm3] X_22577723_SNP [dm6]	C	T	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	21981074	X_21981074_SNP [dm3] X_22579238_SNP [dm6]	T	G	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	21981377	X_21981377_SNP [dm3] X_22579541_SNP [dm6]	A	G	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	21981409	X_21981409_SNP [dm3] X_22579573_SNP [dm6]	G	C	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	21982300	X_21982300_SNP [dm3] X_22580464_SNP [dm6]	G	A	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	21982557	X_21982557_SNP [dm3] X_22580721_SNP [dm6]	C	G	1.994e^-5	0.399	INTERGENIC
X	21984047	X_21984047_SNP [dm3] X_22582211_SNP [dm6]	A	C	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	21984258	X_21984258_SNP [dm3] X_22582422_SNP [dm6]	T	C	1.994e^-5	0.399	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	12858903	3L_12858903_SNP [dm3] 3L_12865803_SNP [dm6]	A	C	2.067e^-5	0.409	INTERGENIC
3L	1536652	3L_1536652_SNP [dm3] 3L_1536652_SNP [dm6]	A	G	2.114e^-5	0.41	UTR_5_PRIME CG12091 UPSTREAM CG7852	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_sens
3L	1536657	3L_1536657_SNP [dm3] 3L_1536657_SNP [dm6]	G	T	2.114e^-5	0.41	UTR_5_PRIME CG12091 UPSTREAM CG7852	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_sens
2L	5261010	2L_5261010_SNP [dm3] 2L_5261010_SNP [dm6]	G	A	2.137e^-5	0.41	INTRON tkv
2L	11288419	2L_11288419_SNP [dm3] 2L_11288419_SNP [dm6]	A	G	2.171e^-5	0.412	INTERGENIC
3L	9499514	3L_9499514_SNP [dm3] 3L_9506414_SNP [dm6]	A	G	2.194e^-5	0.412	DOWNSTREAM CG3408 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
X	21972251	X_21972251_SNP [dm3] X_22570415_SNP [dm6]	C	T	2.236e^-5	0.414	INTERGENIC

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By genomic position
Variant impact
Gene name

Microbiota_OTU010 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results