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=8.948e^-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_K	0.02214

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2216 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
X	2670126	X_2670126_SNP [dm3] X_2776093_SNP [dm6]	T	G	1.332e^-8	0.025	INTRON kirre
X	2670124	X_2670124_SNP [dm3] X_2776091_SNP [dm6]	A	T	3.414e^-8	0.032	INTRON kirre
2L	13237450	2L_13237450_SNP [dm3] 2L_13237450_SNP [dm6]	G	A	6.614e^-8	0.041	INTRON CG5867
X	2670119	X_2670119_DEL [dm3] X_2776086_DEL [dm6]	AGCC	A	9.220e^-8	0.043	INTRON kirre
2L	13237369	2L_13237369_SNP [dm3] 2L_13237369_SNP [dm6]	A	C	8.986e^-7	0.319	INTRON CG5867
2L	13237366	2L_13237366_SNP [dm3] 2L_13237366_SNP [dm6]	T	A	1.021e^-6	0.319	INTRON CG5867
2R	17596515	2R_17596515_SNP [dm3] 2R_21709010_SNP [dm6]	T	A	1.549e^-6	0.409	DOWNSTREAM CG30403 INTRON HmgD EXON CR44749	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2R	20204293	2R_20204293_SNP [dm3] 2R_24316770_SNP [dm6]	A	G	1.788e^-6	0.409	INTERGENIC
2L	13237377	2L_13237377_SNP [dm3] 2L_13237377_SNP [dm6]	G	A	1.965e^-6	0.409	INTRON CG5867
X	14364751	X_14364751_SNP [dm3] X_14470718_SNP [dm6]	G	A	3.079e^-6	0.537	INTERGENIC
3L	13769604	3L_13769604_SNP [dm3] 3L_13776504_SNP [dm6]	C	A	3.379e^-6	0.537	INTRON bru-3
3L	2008057	3L_2008057_SNP [dm3] 3L_2008057_SNP [dm6]	A	T	3.477e^-6	0.537	DOWNSTREAM CR44535 INTERGENIC
3L	18947292	3L_18947292_SNP [dm3] 3L_18954192_SNP [dm6]	A	C	3.725e^-6	0.537	INTRON CG6836
2R	2051002	2R_2051002_SNP [dm3] 2R_6163497_SNP [dm6]	A	C	4.213e^-6	0.564	UPSTREAM tRNA:K2:42Ac DOWNSTREAM tRNA:N5:42Aa INTRON EcR	transposable element FlyBase
3L	497117	3L_497117_SNP [dm3] 3L_497117_SNP [dm6]	C	G	7.162e^-6	0.719	INTRON klar
3L	15932347	3L_15932347_SNP [dm3] 3L_15939247_SNP [dm6]	A	G	7.453e^-6	0.719	INTRON Pka-C3
3L	22779791	3L_22779791_INS [dm3] 3L_22786691_INS [dm6]	T	TAT	7.789e^-6	0.719	UTR_3_PRIME SPoCk
2L	20330061	2L_20330061_SNP [dm3] 2L_20330061_SNP [dm6]	T	G	7.985e^-6	0.719	INTRON spir
3L	17280378	3L_17280378_SNP [dm3] 3L_17287278_SNP [dm6]	C	T	8.796e^-6	0.719	INTERGENIC
2R	9078171	2R_9078171_DEL [dm3] 2R_13190666_DEL [dm6]	ACAGA	A	9.091e^-6	0.719	UPSTREAM seq & 2 others INTRON Kdm4B	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_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	13769605	3L_13769605_SNP [dm3] 3L_13776505_SNP [dm6]	T	A	9.869e^-6	0.719	INTRON bru-3
2L	4546212	2L_4546212_SNP [dm3] 2L_4546212_SNP [dm6]	G	C	1.028e^-5	0.719	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	19398242	2R_19398242_SNP [dm3] 2R_23510719_SNP [dm6]	C	G	1.035e^-5	0.719	DOWNSTREAM CG3906 INTERGENIC
3L	1997139	3L_1997139_SNP [dm3] 3L_1997139_SNP [dm6]	T	C	1.083e^-5	0.719	INTERGENIC
2L	4521364	2L_4521364_SNP [dm3] 2L_4521364_SNP [dm6]	G	T	1.089e^-5	0.719	INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	13237509	2L_13237509_SNP [dm3] 2L_13237509_SNP [dm6]	A	T	1.109e^-5	0.719	INTRON CG5867
2R	1405874	2R_1405874_SNP [dm3] 2R_5518369_SNP [dm6]	T	C	1.145e^-5	0.719	UPSTREAM CG30438 INTRON CG30438	transposable element FlyBase
2R	20309172	2R_20309172_SNP [dm3] 2R_24421649_SNP [dm6]	C	G	1.281e^-5	0.719	INTRON prom	TF binding site mE1_TFBS_chinmo
3L	16471811	3L_16471811_SNP [dm3] 3L_16478711_SNP [dm6]	A	C	1.304e^-5	0.719	INTRON CG33158 & 1 other
3L	17280234	3L_17280234_SNP [dm3] 3L_17287134_SNP [dm6]	T	G	1.343e^-5	0.719	INTERGENIC
3L	13769601	3L_13769601_SNP [dm3] 3L_13776501_SNP [dm6]	T	G	1.369e^-5	0.719	INTRON bru-3
3L	11187867	3L_11187867_SNP [dm3] 3L_11194767_SNP [dm6]	C	T	1.383e^-5	0.719	INTRON GlcAT-P	TF binding site BDTNP1_TFBS_twi
3L	5600030	3L_5600030_DEL [dm3] 3L_5606930_DEL [dm6]	AC	A	1.388e^-5	0.719	UTR_3_PRIME mthl2 DOWNSTREAM Eaf6
2R	17203370	2R_17203370_SNP [dm3] 2R_21315865_SNP [dm6]	G	A	1.449e^-5	0.719	SYNONYMOUS_CODING CG9485	TF binding site mE1_TFBS_cad
3R	25463438	3R_25463438_SNP [dm3] 3R_29637716_SNP [dm6]	A	G	1.470e^-5	0.719	INTRON Dop1R2
X	13844759	X_13844759_SNP [dm3] X_13950726_SNP [dm6]	C	A	1.520e^-5	0.719	INTRON mamo
2R	12489138	2R_12489138_SNP [dm3] 2R_16601633_SNP [dm6]	G	A	1.543e^-5	0.719	INTRON CG8303
3L	13769594	3L_13769594_SNP [dm3] 3L_13776494_SNP [dm6]	A	T	1.585e^-5	0.719	INTRON bru-3
X	14371574	X_14371574_SNP [dm3] X_14477541_SNP [dm6]	G	T	1.600e^-5	0.719	INTRON CG9411
X	13844763	X_13844763_INS [dm3] X_13950730_INS [dm6]	C	ATGGA	1.640e^-5	0.719	INTRON mamo
2R	3908588	2R_3908588_SNP [dm3] 2R_8021083_SNP [dm6]	C	T	1.808e^-5	0.719	EXON CR45267	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	5600033	3L_5600033_SNP [dm3] 3L_5606933_SNP [dm6]	A	T	1.812e^-5	0.719	UTR_3_PRIME mthl2 DOWNSTREAM Eaf6
2L	2740559	2L_2740559_SNP [dm3] 2L_2740559_SNP [dm6]	C	T	1.838e^-5	0.719	SYNONYMOUS_CODING Hrs UPSTREAM Hrs DOWNSTREAM CG31689	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	4546687	2L_4546687_SNP [dm3] 2L_4546687_SNP [dm6]	A	G	1.851e^-5	0.719	NON_SYNONYMOUS_CODING dp INTRON dp
2L	13236984	2L_13236984_SNP [dm3] 2L_13236984_SNP [dm6]	A	G	1.857e^-5	0.719	INTRON CG5867
2L	4190517	2L_4190517_SNP [dm3] 2L_4190517_SNP [dm6]	C	G	1.874e^-5	0.719	INTRON CG3714	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	1608271	2L_1608271_SNP [dm3] 2L_1608271_SNP [dm6]	C	T	1.876e^-5	0.719	UTR_3_PRIME haf INTRON CG31935
2L	20330020	2L_20330020_SNP [dm3] 2L_20330020_SNP [dm6]	G	A	1.877e^-5	0.719	INTRON spir
2L	13237005	2L_13237005_INS [dm3] 2L_13237005_INS [dm6]	A	ATCTCTAAAAGTTA...	1.879e^-5	0.719	INTRON CG5867
2R	5221235	2R_5221235_SNP [dm3] 2R_9333730_SNP [dm6]	A	C	1.995e^-5	0.725	INTRON CG13954 & 1 other
3L	17280374	3L_17280374_SNP [dm3] 3L_17287274_SNP [dm6]	T	C	2.013e^-5	0.725	INTERGENIC
3L	11618712	3L_11618712_SNP [dm3] 3L_11625612_SNP [dm6]	C	T	2.040e^-5	0.725	SPLICE_SITE_REGION CG6083 UPSTREAM PCID2 INTRON CG6083
2R	1974249	2R_1974249_SNP [dm3] 2R_6086744_SNP [dm6]	T	G	2.059e^-5	0.725	INTERGENIC
2L	8788718	2L_8788718_SNP [dm3] 2L_8788718_SNP [dm6]	A	G	2.212e^-5	0.725	INTERGENIC	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
X	21511037	X_21511037_SNP [dm3] X_21640010_SNP [dm6]	C	T	2.222e^-5	0.725	INTERGENIC
2L	13237507	2L_13237507_SNP [dm3] 2L_13237507_SNP [dm6]	T	G	2.275e^-5	0.725	INTRON CG5867
3L	7185336	3L_7185336_SNP [dm3] 3L_7192236_SNP [dm6]	T	G	2.327e^-5	0.725	INTERGENIC
2L	3432256	2L_3432256_SNP [dm3] 2L_3432256_SNP [dm6]	G	T	2.355e^-5	0.725	INTERGENIC
X	5482737	X_5482737_SNP [dm3] X_5588704_SNP [dm6]	A	G	2.383e^-5	0.725	INTERGENIC	TF binding site mE1_TFBS_inv
2L	17180166	2L_17180166_SNP [dm3] 2L_17180166_SNP [dm6]	A	T	2.408e^-5	0.725	UPSTREAM Gr36c DOWNSTREAM Gr36b INTERGENIC
2L	4170733	2L_4170733_SNP [dm3] 2L_4170733_SNP [dm6]	G	C	2.415e^-5	0.725	INTERGENIC
3L	9708125	3L_9708125_SNP [dm3] 3L_9715025_SNP [dm6]	C	A	2.436e^-5	0.725	INTRON vsg	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_zfh1
X	15865050	X_15865050_INS [dm3] X_15971017_INS [dm6]	C	CC	2.471e^-5	0.725	INTRON mmd	TF binding site mE1_TFBS_HSA
X	15865052	X_15865052_SNP [dm3] X_15971019_SNP [dm6]	C	A	2.552e^-5	0.725	INTRON mmd	TF binding site mE1_TFBS_HSA
2R	12807372	2R_12807372_SNP [dm3] 2R_16919867_SNP [dm6]	T	A	2.555e^-5	0.725	INTERGENIC
2L	14213476	2L_14213476_SNP [dm3] 2L_14213476_SNP [dm6]	G	C	2.593e^-5	0.725	INTRON Dyrk2
2L	16650643	2L_16650643_SNP [dm3] 2L_16650643_SNP [dm6]	G	A	2.637e^-5	0.725	INTRON CG42389
2R	4148737	2R_4148737_SNP [dm3] 2R_8261232_SNP [dm6]	C	G	2.696e^-5	0.725	UTR_5_PRIME CG2291 DOWNSTREAM CG14759 INTRON CG2291
2R	14767049	2R_14767049_SNP [dm3] 2R_18879544_SNP [dm6]	T	C	2.716e^-5	0.725	INTRON sano	TF binding site BDTNP1_TFBS_dl
3L	5600035	3L_5600035_SNP [dm3] 3L_5606935_SNP [dm6]	A	T	2.727e^-5	0.725	UTR_3_PRIME mthl2 DOWNSTREAM Eaf6
2L	1603540	2L_1603540_SNP [dm3] 2L_1603540_SNP [dm6]	C	T	2.783e^-5	0.725	SYNONYMOUS_CODING haf INTRON CG31935
3L	17298851	3L_17298851_SNP [dm3] 3L_17305751_SNP [dm6]	T	C	2.819e^-5	0.725	INTERGENIC
3L	7621457	3L_7621457_SNP [dm3] 3L_7628357_SNP [dm6]	T	G	2.823e^-5	0.725	INTRON CG33275
2R	16968938	2R_16968938_SNP [dm3] 2R_21081433_SNP [dm6]	G	A	2.865e^-5	0.725	INTRON Treh
3L	6291176	3L_6291176_SNP [dm3] 3L_6298076_SNP [dm6]	G	A	2.900e^-5	0.725	INTERGENIC	TF binding site mE1_TFBS_cad
2R	14767655	2R_14767655_SNP [dm3] 2R_18880150_SNP [dm6]	T	A	3.100e^-5	0.765	INTRON sano
2R	6634600	2R_6634600_SNP [dm3] 2R_10747095_SNP [dm6]	C	T	3.238e^-5	0.774	INTRON CG33144
3R	25520272	3R_25520272_SNP [dm3] 3R_29694550_SNP [dm6]	T	C	3.249e^-5	0.774	INTRON dmrt99B
2R	2445086	2R_2445086_SNP [dm3] 2R_6557581_SNP [dm6]	T	A	3.291e^-5	0.774	INTRON jing
3R	5831143	3R_5831143_SNP [dm3] 3R_10005421_SNP [dm6]	G	A	3.360e^-5	0.774	SYNONYMOUS_CODING Mical UTR_3_PRIME Mical	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_inv
3R	9830596	3R_9830596_SNP [dm3] 3R_14004874_SNP [dm6]	C	T	3.452e^-5	0.774	INTRON rdx
X	19185275	X_19185275_SNP [dm3] X_19291242_SNP [dm6]	A	C	3.467e^-5	0.774	INTRON CG8034
3L	10237066	3L_10237066_SNP [dm3] 3L_10243966_SNP [dm6]	C	G	3.515e^-5	0.774	NON_SYNONYMOUS_CODING Or67c UPSTREAM CR44541
3L	5600037	3L_5600037_INS [dm3] 3L_5606937_INS [dm6]	G	GAA	3.517e^-5	0.774	UTR_3_PRIME mthl2 DOWNSTREAM Eaf6
3L	1196905	3L_1196905_SNP [dm3] 3L_1196905_SNP [dm6]	G	T	3.554e^-5	0.774	INTRON Aplip1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	6634598	2R_6634598_SNP [dm3] 2R_10747093_SNP [dm6]	T	C	3.633e^-5	0.774	INTRON CG33144
3L	2118136	3L_2118136_INS [dm3] 3L_2118136_INS [dm6]	C	CCCCAAGAGCAG...	3.662e^-5	0.774	INTRON zormin
X	8835028	X_8835028_SNP [dm3] X_8940995_SNP [dm6]	A	G	3.696e^-5	0.774	INTRON rdgA
X	15865063	X_15865063_SNP [dm3] X_15971030_SNP [dm6]	T	C	3.724e^-5	0.774	INTRON mmd	TF binding site mE1_TFBS_HSA
X	2691554	X_2691554_SNP [dm3] X_2797521_SNP [dm6]	G	T	3.777e^-5	0.774	INTRON kirre
3L	13509969	3L_13509969_SNP [dm3] 3L_13516869_SNP [dm6]	C	A	3.838e^-5	0.774	NON_SYNONYMOUS_CODING CG10710 DOWNSTREAM Liprin-beta	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	19381763	2R_19381763_SNP [dm3] 2R_23494240_SNP [dm6]	G	C	3.864e^-5	0.774	INTERGENIC
2L	16655186	2L_16655186_SNP [dm3] 2L_16655186_SNP [dm6]	G	T	3.894e^-5	0.774	INTRON CG42389
3L	1997206	3L_1997206_SNP [dm3] 3L_1997206_SNP [dm6]	T	C	3.908e^-5	0.774	INTERGENIC
3L	5600068	3L_5600068_INS [dm3] 3L_5606968_INS [dm6]	C	CCGTCACTTCATGATAAATA...	3.950e^-5	0.774	UTR_3_PRIME mthl2 DOWNSTREAM Eaf6
3L	3451077	3L_3451077_INS [dm3] 3L_3451077_INS [dm6]	C	CCCCTCC	3.997e^-5	0.774	INTRON eIF5B
X	3803309	X_3803309_SNP [dm3] X_3909276_SNP [dm6]	A	G	4.062e^-5	0.774	INTRON CG42541
3L	15932295	3L_15932295_SNP [dm3] 3L_15939195_SNP [dm6]	G	A	4.109e^-5	0.774	INTRON Pka-C3
X	15161323	X_15161323_SNP [dm3] X_15267290_SNP [dm6]	C	T	4.148e^-5	0.774	INTERGENIC
3L	18943582	3L_18943582_SNP [dm3] 3L_18950482_SNP [dm6]	G	A	4.206e^-5	0.774	UPSTREAM CG6836 INTERGENIC

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By genomic position
Variant impact
Gene name

Mitochon_Breadth_Cov phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results