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=6.268e^-21)
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	<2e-16

Kruskal-Wallis test

Covariate	χ²	p-value
In_3R_P	6.8609	0.0324
In_3R_K	18.0426	0.0001
In_3R_Mo	6.9753	0.0306

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3784 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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Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	473509	3L_473509_INS [dm3] 3L_473509_INS [dm6]	C	CTTTTC	2.617e^-8	0.049	INTRON klar
3R	15891270	3R_15891270_SNP [dm3] 3R_20065548_SNP [dm6]	C	T	5.522e^-8	0.052	INTERGENIC
3R	15892162	3R_15892162_SNP [dm3] 3R_20066440_SNP [dm6]	A	G	1.121e^-7	0.054	INTERGENIC
3R	15886276	3R_15886276_SNP [dm3] 3R_20060554_SNP [dm6]	A	G	1.567e^-7	0.054	UPSTREAM CG4390 INTERGENIC
3R	15891264	3R_15891264_SNP [dm3] 3R_20065542_SNP [dm6]	G	A	1.600e^-7	0.054	INTERGENIC
3R	15893343	3R_15893343_INS [dm3] 3R_20067621_INS [dm6]	A	AG	1.812e^-7	0.054	INTERGENIC
X	16679364	X_16679364_DEL [dm3] X_16785331_DEL [dm6]	CGGATGTTTCTGAACGCAAA...	C	2.033e^-7	0.054	UTR_3_PRIME CG9609 DOWNSTREAM mRpL22
3R	15892199	3R_15892199_SNP [dm3] 3R_20066477_SNP [dm6]	T	G	2.435e^-7	0.055	INTERGENIC
3R	15892115	3R_15892115_SNP [dm3] 3R_20066393_SNP [dm6]	T	A	3.492e^-7	0.055	INTERGENIC
3R	15892179	3R_15892179_SNP [dm3] 3R_20066457_SNP [dm6]	A	T	3.528e^-7	0.055	INTERGENIC
3R	10628531	3R_10628531_SNP [dm3] 3R_14802809_SNP [dm6]	C	A	3.648e^-7	0.055	SYNONYMOUS_CODING CG14857
X	7599741	X_7599741_DEL [dm3] X_7705708_DEL [dm6]	AAA	A	3.860e^-7	0.055	UPSTREAM CHES-1-like INTRON CHES-1-like	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	15890913	3R_15890913_SNP [dm3] 3R_20065191_SNP [dm6]	T	C	3.942e^-7	0.055	INTERGENIC
3R	15892122	3R_15892122_SNP [dm3] 3R_20066400_SNP [dm6]	T	A	4.296e^-7	0.055	INTERGENIC
3R	15892176	3R_15892176_SNP [dm3] 3R_20066454_SNP [dm6]	T	C	5.011e^-7	0.055	INTERGENIC
3R	15881347	3R_15881347_SNP [dm3] 3R_20055625_SNP [dm6]	G	C	5.061e^-7	0.055	DOWNSTREAM CG4390 INTRON CG17193
3R	15892071	3R_15892071_INS [dm3] 3R_20066349_INS [dm6]	A	AA	5.295e^-7	0.055	INTERGENIC
3R	15892161	3R_15892161_SNP [dm3] 3R_20066439_SNP [dm6]	A	G	5.349e^-7	0.055	INTERGENIC
3L	18329829	3L_18329829_INS [dm3] 3L_18336729_INS [dm6]	T	TT	5.565e^-7	0.055	INTERGENIC
3R	15892155	3R_15892155_SNP [dm3] 3R_20066433_SNP [dm6]	G	A	6.400e^-7	0.058	INTERGENIC
3R	15888186	3R_15888186_SNP [dm3] 3R_20062464_SNP [dm6]	C	A	7.886e^-7	0.058	INTERGENIC
3R	15882905	3R_15882905_SNP [dm3] 3R_20057183_SNP [dm6]	G	T	8.075e^-7	0.058	SYNONYMOUS_CODING CG4390 UPSTREAM mdlc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	8397999	X_8397999_DEL [dm3] X_8503966_DEL [dm6]	TT	T	8.258e^-7	0.058	INTRON CG33181
X	19436752	X_19436752_INS [dm3] X_19542719_INS [dm6]	T	TCCTATAATAAAGT...	9.207e^-7	0.058	INTRON CG32532
3R	15890792	3R_15890792_SNP [dm3] 3R_20065070_SNP [dm6]	T	G	9.559e^-7	0.058	INTERGENIC
3L	14908900	3L_14908900_DEL [dm3] 3L_14915800_DEL [dm6]	AA	A	9.607e^-7	0.058	INTRON DCX-EMAP
3R	15875928	3R_15875928_SNP [dm3] 3R_20050206_SNP [dm6]	T	G	9.795e^-7	0.058	INTRON CG17193
3R	15876004	3R_15876004_SNP [dm3] 3R_20050282_SNP [dm6]	G	C	9.849e^-7	0.058	INTRON CG17193
3R	15891978	3R_15891978_SNP [dm3] 3R_20066256_SNP [dm6]	A	T	1.014e^-6	0.058	INTERGENIC
3R	15877779	3R_15877779_SNP [dm3] 3R_20052057_SNP [dm6]	T	A	1.015e^-6	0.058	INTRON CG17193	TF binding site BDTNP1_TFBS_twi
3R	15876056	3R_15876056_SNP [dm3] 3R_20050334_SNP [dm6]	T	A	1.038e^-6	0.058	INTRON CG17193
3L	4981535	3L_4981535_DEL [dm3] 3L_4981535_DEL [dm6]	GG	G	1.100e^-6	0.058	UPSTREAM CG17030 INTRON Con EXON CR45685	TF binding site mE1_TFBS_HSA
3R	15891982	3R_15891982_SNP [dm3] 3R_20066260_SNP [dm6]	G	C	1.124e^-6	0.058	INTERGENIC
3R	15881456	3R_15881456_SNP [dm3] 3R_20055734_SNP [dm6]	G	T	1.148e^-6	0.058	UTR_5_PRIME CG17193 DOWNSTREAM CG4390
2R	10715588	2R_10715588_SNP [dm3] 2R_14828083_SNP [dm6]	A	T	1.156e^-6	0.058	INTERGENIC
3R	15891906	3R_15891906_SNP [dm3] 3R_20066184_SNP [dm6]	G	T	1.187e^-6	0.058	INTERGENIC
3L	14675527	3L_14675527_DEL [dm3] 3L_14682427_DEL [dm6]	ATTTTTCA	A	1.207e^-6	0.058	INTRON ome
3R	15892266	3R_15892266_SNP [dm3] 3R_20066544_SNP [dm6]	G	A	1.213e^-6	0.058	INTERGENIC
3R	15892120	3R_15892120_SNP [dm3] 3R_20066398_SNP [dm6]	T	A	1.238e^-6	0.058	INTERGENIC
3R	15892378	3R_15892378_SNP [dm3] 3R_20066656_SNP [dm6]	T	A	1.241e^-6	0.058	INTERGENIC
3R	15890709	3R_15890709_SNP [dm3] 3R_20064987_SNP [dm6]	G	A	1.292e^-6	0.058	INTERGENIC
X	7600034	X_7600034_DEL [dm3] X_7706001_DEL [dm6]	TT	T	1.319e^-6	0.058	INTRON CHES-1-like	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	15892036	3R_15892036_SNP [dm3] 3R_20066314_SNP [dm6]	A	G	1.338e^-6	0.058	INTERGENIC
3R	15891876	3R_15891876_SNP [dm3] 3R_20066154_SNP [dm6]	T	A	1.398e^-6	0.058	INTERGENIC
3L	14909030	3L_14909030_SNP [dm3] 3L_14915930_SNP [dm6]	G	T	1.453e^-6	0.058	INTRON DCX-EMAP
3R	15892073	3R_15892073_SNP [dm3] 3R_20066351_SNP [dm6]	C	G	1.457e^-6	0.058	INTERGENIC
3R	15892521	3R_15892521_SNP [dm3] 3R_20066799_SNP [dm6]	G	A	1.468e^-6	0.058	INTERGENIC
3R	17165416	3R_17165416_DEL [dm3] 3R_21339694_DEL [dm6]	TGTGTGT	T	1.486e^-6	0.058	INTRON CG16791	TF binding site BDTNP1_TFBS_dl
3R	15892451	3R_15892451_SNP [dm3] 3R_20066729_SNP [dm6]	G	T	1.800e^-6	0.069	INTERGENIC
3R	15888896	3R_15888896_SNP [dm3] 3R_20063174_SNP [dm6]	A	C	1.957e^-6	0.073	INTERGENIC
3R	15892601	3R_15892601_SNP [dm3] 3R_20066879_SNP [dm6]	G	A	2.107e^-6	0.078	INTERGENIC
3R	15875781	3R_15875781_SNP [dm3] 3R_20050059_SNP [dm6]	A	G	2.152e^-6	0.078	INTRON CG17193
3R	15875755	3R_15875755_SNP [dm3] 3R_20050033_SNP [dm6]	G	A	2.280e^-6	0.08	INTRON CG17193
3R	15892640	3R_15892640_SNP [dm3] 3R_20066918_SNP [dm6]	A	G	2.352e^-6	0.08	INTERGENIC
3R	13262235	3R_13262235_INS [dm3] 3R_17436513_INS [dm6]	T	TCT	2.387e^-6	0.08	INTRON CG5873
3R	15892011	3R_15892011_SNP [dm3] 3R_20066289_SNP [dm6]	A	T	2.409e^-6	0.08	INTERGENIC
X	11097583	X_11097583_INS [dm3] X_11203550_INS [dm6]	A	AGAATTTA	2.421e^-6	0.08	DOWNSTREAM CG11106 INTERGENIC
2L	12281357	2L_12281357_INS [dm3] 2L_12281357_INS [dm6]	G	GTGGGCAG	2.584e^-6	0.081	INTRON aret
3R	15875900	3R_15875900_SNP [dm3] 3R_20050178_SNP [dm6]	T	G	2.628e^-6	0.081	INTRON CG17193
3R	15877862	3R_15877862_SNP [dm3] 3R_20052140_SNP [dm6]	C	T	2.637e^-6	0.081	INTRON CG17193	TF binding site BDTNP1_TFBS_twi
X	17628810	X_17628810_SNP [dm3] X_17734777_SNP [dm6]	C	A	2.657e^-6	0.081	UTR_5_PRIME CG42684 INTRON CG42684	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	15877860	3R_15877860_SNP [dm3] 3R_20052138_SNP [dm6]	C	A	2.667e^-6	0.081	INTRON CG17193	TF binding site BDTNP1_TFBS_twi
3R	15891134	3R_15891134_SNP [dm3] 3R_20065412_SNP [dm6]	A	G	2.788e^-6	0.082	INTERGENIC
3R	9552543	3R_9552543_DEL [dm3] 3R_13726821_DEL [dm6]	TAAATG	T	2.798e^-6	0.082	INTRON CG34383
3R	15887041	3R_15887041_SNP [dm3] 3R_20061319_SNP [dm6]	A	G	2.897e^-6	0.084	INTERGENIC
3R	15892611	3R_15892611_INS [dm3] 3R_20066889_INS [dm6]	A	AT	3.108e^-6	0.088	INTERGENIC
3R	15887107	3R_15887107_SNP [dm3] 3R_20061385_SNP [dm6]	A	G	3.130e^-6	0.088	INTERGENIC
3R	15882866	3R_15882866_SNP [dm3] 3R_20057144_SNP [dm6]	G	A	3.413e^-6	0.094	SYNONYMOUS_CODING CG4390 UPSTREAM mdlc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	15894982	3R_15894982_SNP [dm3] 3R_20069260_SNP [dm6]	T	C	3.454e^-6	0.094	INTERGENIC
3R	15890714	3R_15890714_SNP [dm3] 3R_20064992_SNP [dm6]	G	A	3.541e^-6	0.095	INTERGENIC
3L	6519178	3L_6519178_SNP [dm3] 3L_6526078_SNP [dm6]	A	G	3.792e^-6	0.1	INTRON sfl
X	17605826	X_17605826_INS [dm3] X_17711793_INS [dm6]	A	AGCTAAATATTA...	3.918e^-6	0.102	INTRON CG42684	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	15892694	3R_15892694_SNP [dm3] 3R_20066972_SNP [dm6]	T	C	4.074e^-6	0.104	INTERGENIC
3R	9552564	3R_9552564_DEL [dm3] 3R_13726842_DEL [dm6]	AGTCT	A	4.099e^-6	0.104	INTRON CG34383
3R	15880819	3R_15880819_SNP [dm3] 3R_20055097_SNP [dm6]	T	A	4.183e^-6	0.104	INTRON CG17193
3R	9552551	3R_9552551_DEL [dm3] 3R_13726829_DEL [dm6]	TG	T	4.263e^-6	0.104	INTRON CG34383
3R	15892579	3R_15892579_SNP [dm3] 3R_20066857_SNP [dm6]	A	G	4.366e^-6	0.104	INTERGENIC
3R	15815337	3R_15815337_INS [dm3] 3R_19989615_INS [dm6]	C	CTTTTCCATCCAAATGTATA...	4.386e^-6	0.104	INTRON Hs6st
3L	6793188	3L_6793188_SNP [dm3] 3L_6800088_SNP [dm6]	C	A	4.393e^-6	0.104	INTERGENIC	enhancer mE1_CBP_Enhancers
3R	15893334	3R_15893334_SNP [dm3] 3R_20067612_SNP [dm6]	A	T	4.511e^-6	0.104	INTERGENIC
2L	16614018	2L_16614018_INS [dm3] 2L_16614018_INS [dm6]	T	TT	4.592e^-6	0.104	INTRON CG42389
3R	15892009	3R_15892009_SNP [dm3] 3R_20066287_SNP [dm6]	C	T	4.598e^-6	0.104	INTERGENIC
3L	18503519	3L_18503519_INS [dm3] 3L_18510419_INS [dm6]	G	GGGT	4.663e^-6	0.104	INTERGENIC	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
2L	5955959	2L_5955959_SNP [dm3] 2L_5955959_SNP [dm6]	G	A	4.742e^-6	0.104	SYNONYMOUS_CODING CG13999 DOWNSTREAM CG9044 & 1 other
3R	15875906	3R_15875906_SNP [dm3] 3R_20050184_SNP [dm6]	G	A	4.752e^-6	0.104	INTRON CG17193
3R	15875812	3R_15875812_SNP [dm3] 3R_20050090_SNP [dm6]	C	A	4.768e^-6	0.104	INTRON CG17193
X	11479413	X_11479413_SNP [dm3] X_11585380_SNP [dm6]	C	G	4.811e^-6	0.104	NON_SYNONYMOUS_CODING nod UPSTREAM CR43217	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9552554	3R_9552554_DEL [dm3] 3R_13726832_DEL [dm6]	TAAA	T	5.123e^-6	0.109	INTRON CG34383
2R	20348873	2R_20348873_MNP [dm3] 2R_24461350_MNP [dm6]	TGG	AAA	5.244e^-6	0.111	INTRON CG13579
3L	18552944	3L_18552944_DEL [dm3] 3L_18559844_DEL [dm6]	ACTTTG	A	5.423e^-6	0.113	UPSTREAM AstC-R1 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	15892593	3R_15892593_SNP [dm3] 3R_20066871_SNP [dm6]	G	T	5.844e^-6	0.12	INTERGENIC
3R	10628425	3R_10628425_SNP [dm3] 3R_14802703_SNP [dm6]	C	A	6.055e^-6	0.123	INTRON CG14857
3R	9552529	3R_9552529_SNP [dm3] 3R_13726807_SNP [dm6]	T	G	6.120e^-6	0.123	INTRON CG34383
3R	15892624	3R_15892624_DEL [dm3] 3R_20066902_DEL [dm6]	TG	T	6.214e^-6	0.123	INTERGENIC
X	7266024	X_7266024_SNP [dm3] X_7371991_SNP [dm6]	G	A	6.261e^-6	0.123	INTRON CG1677 & 1 other	TF binding site mE1_TFBS_HSA
3R	15877380	3R_15877380_SNP [dm3] 3R_20051658_SNP [dm6]	T	A	6.324e^-6	0.123	INTRON CG17193	TF binding site BDTNP1_TFBS_twi
3R	15892304	3R_15892304_SNP [dm3] 3R_20066582_SNP [dm6]	C	T	6.373e^-6	0.123	INTERGENIC
3R	15877888	3R_15877888_SNP [dm3] 3R_20052166_SNP [dm6]	C	G	6.476e^-6	0.124	INTRON CG17193	TF binding site BDTNP1_TFBS_twi
3R	15877845	3R_15877845_SNP [dm3] 3R_20052123_SNP [dm6]	C	T	6.933e^-6	0.13	INTRON CG17193	TF binding site BDTNP1_TFBS_twi
3R	5764164	3R_5764164_DEL [dm3] 3R_9938442_DEL [dm6]	AACTC	A	6.948e^-6	0.13	INTRON Glut4EF	TF binding site mE1_TFBS_cad

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Missing results

By genomic position
Variant impact
Gene name

pc_SegregVariants_3L phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results