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=1.281e^-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_Mo	0.05383

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2372 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
3R	10665993	3R_10665993_SNP [dm3] 3R_14840271_SNP [dm6]	T	C	2.053e^-7	0.289	INTRON btsz
2L	795992	2L_795992_SNP [dm3] 2L_795992_SNP [dm6]	A	G	4.130e^-7	0.289	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	13817690	X_13817690_SNP [dm3] X_13923657_SNP [dm6]	A	G	4.668e^-7	0.289	INTRON mamo
3R	10669748	3R_10669748_SNP [dm3] 3R_14844026_SNP [dm6]	T	C	6.403e^-7	0.298	INTRON btsz
3L	7184956	3L_7184956_SNP [dm3] 3L_7191856_SNP [dm6]	T	G	9.986e^-7	0.342	INTERGENIC
3R	3445344	3R_3445344_SNP [dm3] 3R_7619622_SNP [dm6]	C	T	1.104e^-6	0.342	INTRON CG34127
3L	8441217	3L_8441217_SNP [dm3] 3L_8448117_SNP [dm6]	A	T	1.662e^-6	0.414	INTRON CG6983	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3L	16439894	3L_16439894_DEL [dm3] 3L_16446794_DEL [dm6]	CA	C	1.781e^-6	0.414	INTRON CG33158 & 1 other
X	11226214	X_11226214_SNP [dm3] X_11332181_SNP [dm6]	T	C	2.433e^-6	0.503	NON_SYNONYMOUS_CODING CG1657	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	10679072	3R_10679072_SNP [dm3] 3R_14853350_SNP [dm6]	C	G	3.265e^-6	0.512	INTRON btsz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_Trl
2R	6929905	2R_6929905_SNP [dm3] 2R_11042400_SNP [dm6]	G	A	3.299e^-6	0.512	INTRON luna	TF binding site mE1_TFBS_cad
3L	7958413	3L_7958413_SNP [dm3] 3L_7965313_SNP [dm6]	A	G	3.348e^-6	0.512	INTERGENIC
X	11225811	X_11225811_SNP [dm3] X_11331778_SNP [dm6]	G	A	3.674e^-6	0.512	SYNONYMOUS_CODING CG1657	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	10749024	3R_10749024_SNP [dm3] 3R_14923302_SNP [dm6]	A	G	4.897e^-6	0.512	DOWNSTREAM Sdr EXON CR45598
3R	3372756	3R_3372756_SNP [dm3] 3R_7547034_SNP [dm6]	A	G	4.959e^-6	0.512	SYNONYMOUS_CODING alpha-Est1	TF binding site mE1_TFBS_cad
3L	5702891	3L_5702891_DEL [dm3] 3L_5709791_DEL [dm6]	TT	T	4.970e^-6	0.512	INTRON sif
X	6936777	X_6936777_SNP [dm3] X_7042744_SNP [dm6]	C	A	5.148e^-6	0.512	DOWNSTREAM CG14427 INTRON CG12541	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb
3R	24236159	3R_24236159_SNP [dm3] 3R_28410437_SNP [dm6]	T	G	5.416e^-6	0.512	INTERGENIC
3R	10665990	3R_10665990_SNP [dm3] 3R_14840268_SNP [dm6]	T	A	6.268e^-6	0.512	INTRON btsz
3R	10665996	3R_10665996_SNP [dm3] 3R_14840274_SNP [dm6]	T	C	6.268e^-6	0.512	INTRON btsz
2L	19755308	2L_19755308_SNP [dm3] 2L_19755308_SNP [dm6]	T	C	6.510e^-6	0.512	INTRON CG10631	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
3R	10667071	3R_10667071_SNP [dm3] 3R_14841349_SNP [dm6]	T	A	7.231e^-6	0.512	INTRON btsz
3R	2725645	3R_2725645_SNP [dm3] 3R_6899923_SNP [dm6]	C	T	7.926e^-6	0.512	INTRON Antp
3L	22043940	3L_22043940_SNP [dm3] 3L_22050840_SNP [dm6]	G	A	8.633e^-6	0.512	INTRON Oct-TyrR
2L	20518653	2L_20518653_SNP [dm3] 2L_20518653_SNP [dm6]	C	A	8.758e^-6	0.512	INTERGENIC
3R	27495978	3R_27495978_SNP [dm3] 3R_31670256_SNP [dm6]	T	C	9.250e^-6	0.512	INTRON CG1815	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd
X	11225826	X_11225826_SNP [dm3] X_11331793_SNP [dm6]	G	T	9.723e^-6	0.512	SYNONYMOUS_CODING CG1657	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	10679083	3R_10679083_SNP [dm3] 3R_14853361_SNP [dm6]	C	T	1.010e^-5	0.512	INTRON btsz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
3L	15177832	3L_15177832_SNP [dm3] 3L_15184732_SNP [dm6]	C	A	1.030e^-5	0.512	INTERGENIC
3R	10669778	3R_10669778_INS [dm3] 3R_14844056_INS [dm6]	T	TTT	1.037e^-5	0.512	UPSTREAM CG3610 INTRON btsz
3R	25200307	3R_25200307_SNP [dm3] 3R_29374585_SNP [dm6]	A	T	1.087e^-5	0.512	INTERGENIC
3R	25200308	3R_25200308_INS [dm3] 3R_29374586_INS [dm6]	G	GC	1.087e^-5	0.512	INTERGENIC
2L	19755335	2L_19755335_SNP [dm3] 2L_19755335_SNP [dm6]	T	C	1.102e^-5	0.512	INTRON CG10631	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv
2R	1230515	2R_1230515_SNP [dm3] 2R_5343010_SNP [dm6]	A	G	1.117e^-5	0.512	INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	27495863	3R_27495863_SNP [dm3] 3R_31670141_SNP [dm6]	T	C	1.201e^-5	0.512	INTRON CG1815	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	6929830	2R_6929830_SNP [dm3] 2R_11042325_SNP [dm6]	G	A	1.219e^-5	0.512	INTRON luna	TF binding site mE1_TFBS_cad
3L	15177785	3L_15177785_SNP [dm3] 3L_15184685_SNP [dm6]	T	C	1.244e^-5	0.512	INTERGENIC
3L	15177783	3L_15177783_INS [dm3] 3L_15184683_INS [dm6]	T	TC	1.272e^-5	0.512	INTERGENIC
3L	8437793	3L_8437793_SNP [dm3] 3L_8444693_SNP [dm6]	C	A	1.281e^-5	0.512	INTRON CG6983	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	10180808	2L_10180808_SNP [dm3] 2L_10180808_SNP [dm6]	G	A	1.282e^-5	0.512	UPSTREAM CG44153 INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	14313074	3L_14313074_SNP [dm3] 3L_14319974_SNP [dm6]	C	G	1.328e^-5	0.512	INTRON fz
2L	6251579	2L_6251579_SNP [dm3] 2L_6251579_SNP [dm6]	A	G	1.372e^-5	0.512	INTERGENIC	TF binding site mE1_TFBS_cnc
3R	3358829	3R_3358829_SNP [dm3] 3R_7533107_SNP [dm6]	A	G	1.391e^-5	0.512	DOWNSTREAM alpha-Est5 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	14313146	3L_14313146_SNP [dm3] 3L_14320046_SNP [dm6]	T	G	1.391e^-5	0.512	INTRON fz
3L	17337446	3L_17337446_SNP [dm3] 3L_17344346_SNP [dm6]	C	T	1.432e^-5	0.512	SYNONYMOUS_CODING brv2 DOWNSTREAM Mip
3L	14313214	3L_14313214_SNP [dm3] 3L_14320114_SNP [dm6]	C	G	1.460e^-5	0.512	INTRON fz
2L	3766024	2L_3766024_SNP [dm3] 2L_3766024_SNP [dm6]	C	T	1.468e^-5	0.512	SYNONYMOUS_CODING CG43707 UPSTREAM CG43707 DOWNSTREAM CG43703 INTRON CG43707	TF binding site mE1_TFBS_Trl
3R	10679084	3R_10679084_SNP [dm3] 3R_14853362_SNP [dm6]	C	G	1.470e^-5	0.512	INTRON btsz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
2R	6929901	2R_6929901_SNP [dm3] 2R_11042396_SNP [dm6]	T	C	1.484e^-5	0.512	INTRON luna	TF binding site mE1_TFBS_cad
2L	1308915	2L_1308915_SNP [dm3] 2L_1308915_SNP [dm6]	C	G	1.487e^-5	0.512	INTERGENIC
3R	23732387	3R_23732387_SNP [dm3] 3R_27906665_SNP [dm6]	C	G	1.501e^-5	0.512	UPSTREAM CG34353 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	4375889	2R_4375889_SNP [dm3] 2R_8488384_SNP [dm6]	T	C	1.581e^-5	0.512	INTRON mtt
3R	14944077	3R_14944077_SNP [dm3] 3R_19118355_SNP [dm6]	G	T	1.617e^-5	0.512	INTRON CG6040
X	11225976	X_11225976_SNP [dm3] X_11331943_SNP [dm6]	C	T	1.632e^-5	0.512	SYNONYMOUS_CODING CG1657	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	11511131	2R_11511131_SNP [dm3] 2R_15623626_SNP [dm6]	C	A	1.702e^-5	0.512	INTRON CG42524	TF binding site mE1_TFBS_chinmo
2L	1143858	2L_1143858_SNP [dm3] 2L_1143858_SNP [dm6]	G	A	1.709e^-5	0.512	DOWNSTREAM CR45717 INTRON MFS3
3R	9762612	3R_9762612_SNP [dm3] 3R_13936890_SNP [dm6]	G	T	1.812e^-5	0.512	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	4484634	2L_4484634_SNP [dm3] 2L_4484634_SNP [dm6]	G	A	1.833e^-5	0.512	SPLICE_SITE_REGION dp INTRON dp	TF binding site mE1_TFBS_cad
2R	6741193	2R_6741193_SNP [dm3] 2R_10853688_SNP [dm6]	T	G	1.878e^-5	0.512	UTR_5_PRIME CG30015 INTRON CG30015 & 1 other	TF binding site BDTNP1_TFBS_twi
X	11225931	X_11225931_SNP [dm3] X_11331898_SNP [dm6]	T	C	2.011e^-5	0.512	SYNONYMOUS_CODING CG1657	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	9249027	2R_9249027_SNP [dm3] 2R_13361522_SNP [dm6]	G	C	2.022e^-5	0.512	DOWNSTREAM CR45312 INTERGENIC
2L	22340867	2L_22340867_SNP [dm3] 2L_22340867_SNP [dm6]	A	C	2.043e^-5	0.512	INTRON CG17018 EXON CR43359
2L	22340868	2L_22340868_SNP [dm3] 2L_22340868_SNP [dm6]	T	C	2.086e^-5	0.512	INTRON CG17018 EXON CR43359
2L	545511	2L_545511_SNP [dm3] 2L_545511_SNP [dm6]	A	G	2.119e^-5	0.512	NON_SYNONYMOUS_CODING nAChRbeta3 UTR_3_PRIME Ets21C UPSTREAM Spp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	1859693	3L_1859693_SNP [dm3] 3L_1859693_SNP [dm6]	T	C	2.131e^-5	0.512	UTR_3_PRIME R DOWNSTREAM CG12024
2L	16870062	2L_16870062_SNP [dm3] 2L_16870062_SNP [dm6]	C	A	2.133e^-5	0.512	UPSTREAM CR31781 EXON CR31781	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	13685847	3L_13685847_SNP [dm3] 3L_13692747_SNP [dm6]	G	A	2.176e^-5	0.512	INTRON bru-3
3L	17365713	3L_17365713_SNP [dm3] 3L_17372613_SNP [dm6]	T	A	2.191e^-5	0.512	NON_SYNONYMOUS_CODING Cad74A	TF binding site mE1_TFBS_cad
2L	1251182	2L_1251182_SNP [dm3] 2L_1251182_SNP [dm6]	A	C	2.200e^-5	0.512	INTERGENIC
3L	17166870	3L_17166870_SNP [dm3] 3L_17173770_SNP [dm6]	T	A	2.255e^-5	0.512	INTRON Rbp6
3L	17166952	3L_17166952_INS [dm3] 3L_17173852_INS [dm6]	C	ACA	2.255e^-5	0.512	INTRON Rbp6
2R	3418130	2R_3418130_SNP [dm3] 2R_7530625_SNP [dm6]	G	A	2.268e^-5	0.512	UTR_5_PRIME Drat INTRON Drat	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
3L	17167810	3L_17167810_SNP [dm3] 3L_17174710_SNP [dm6]	A	G	2.270e^-5	0.512	INTRON Rbp6
3L	17168134	3L_17168134_SNP [dm3] 3L_17175034_SNP [dm6]	G	T	2.270e^-5	0.512	INTRON Rbp6
3L	17171119	3L_17171119_SNP [dm3] 3L_17178019_SNP [dm6]	C	T	2.270e^-5	0.512	INTRON Rbp6
3R	3373694	3R_3373694_SNP [dm3] 3R_7547972_SNP [dm6]	G	A	2.337e^-5	0.512	SYNONYMOUS_CODING alpha-Est1
3L	17337163	3L_17337163_SNP [dm3] 3L_17344063_SNP [dm6]	G	T	2.340e^-5	0.512	DOWNSTREAM Mip INTRON brv2
3R	3589744	3R_3589744_SNP [dm3] 3R_7764022_SNP [dm6]	G	A	2.343e^-5	0.512	DOWNSTREAM Sp7 INTERGENIC
X	10863770	X_10863770_SNP [dm3] X_10969737_SNP [dm6]	T	C	2.347e^-5	0.512	INTRON CG42339
3R	19188115	3R_19188115_SNP [dm3] 3R_23362393_SNP [dm6]	C	T	2.364e^-5	0.512	SYNONYMOUS_CODING CG4408	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	17337299	3L_17337299_SNP [dm3] 3L_17344199_SNP [dm6]	G	A	2.387e^-5	0.512	SYNONYMOUS_CODING brv2 DOWNSTREAM Mip
3R	3506594	3R_3506594_SNP [dm3] 3R_7680872_SNP [dm6]	G	A	2.427e^-5	0.512	INTRON Nlg1
3L	9604899	3L_9604899_DEL [dm3] 3L_9611799_DEL [dm6]	GT	G	2.451e^-5	0.512	SPLICE_SITE_REGION CG3280 INTRON CG3280
2R	11511098	2R_11511098_SNP [dm3] 2R_15623593_SNP [dm6]	A	G	2.460e^-5	0.512	INTRON CG42524	TF binding site mE1_TFBS_chinmo
3L	12556215	3L_12556215_SNP [dm3] 3L_12563115_SNP [dm6]	T	C	2.461e^-5	0.512	INTRON sowah	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	7184972	3L_7184972_SNP [dm3] 3L_7191872_SNP [dm6]	G	A	2.518e^-5	0.512	INTERGENIC
2L	6110853	2L_6110853_SNP [dm3] 2L_6110853_SNP [dm6]	G	C	2.539e^-5	0.512	INTRON stai
2L	3485581	2L_3485581_SNP [dm3] 2L_3485581_SNP [dm6]	C	T	2.582e^-5	0.512	INTRON CG15414
3L	13685780	3L_13685780_SNP [dm3] 3L_13692680_SNP [dm6]	T	C	2.611e^-5	0.512	INTRON bru-3
2L	804780	2L_804780_SNP [dm3] 2L_804780_SNP [dm6]	A	T	2.625e^-5	0.512	INTERGENIC	TF binding site mE1_TFBS_HSA
X	9419068	X_9419068_SNP [dm3] X_9525035_SNP [dm6]	T	C	2.637e^-5	0.512	INTRON CG32700
3L	11417987	3L_11417987_SNP [dm3] 3L_11424887_SNP [dm6]	A	C	2.666e^-5	0.512	UPSTREAM CG7560 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr
3L	4681182	3L_4681182_SNP [dm3] 3L_4681182_SNP [dm6]	A	T	2.701e^-5	0.512	INTRON axo
3L	4681184	3L_4681184_SNP [dm3] 3L_4681184_SNP [dm6]	A	T	2.701e^-5	0.512	INTRON axo
2L	7270672	2L_7270672_SNP [dm3] 2L_7270672_SNP [dm6]	T	C	2.708e^-5	0.512	INTRON Wnt4
2L	18522257	2L_18522257_SNP [dm3] 2L_18522257_SNP [dm6]	G	A	2.721e^-5	0.512	INTRON CG10211
3R	3490105	3R_3490105_SNP [dm3] 3R_7664383_SNP [dm6]	C	A	2.735e^-5	0.512	INTRON Nlg1
3L	7184949	3L_7184949_SNP [dm3] 3L_7191849_SNP [dm6]	T	G	2.773e^-5	0.512	INTERGENIC
X	2997323	X_2997323_SNP [dm3] X_3103290_SNP [dm6]	T	C	2.811e^-5	0.512	INTRON kirre
X	8258448	X_8258448_SNP [dm3] X_8364415_SNP [dm6]	G	T	2.821e^-5	0.512	INTRON nAChRalpha3

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By genomic position
Variant impact
Gene name

Microbiota_OTU090 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results