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=3.735e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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_P	0.0506834

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

445 significant hits at p-value < 0.001.

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
2L	10862309	2L_10862309_SNP [dm3] 2L_10862309_SNP [dm6]	A	G	2.351e^-4	0.807	DOWNSTREAM Stam EXON CR43807
2L	13111121	2L_13111121_SNP [dm3] 2L_13111121_SNP [dm6]	T	C	2.351e^-4	0.807	INTERGENIC
2L	13688810	2L_13688810_SNP [dm3] 2L_13688810_SNP [dm6]	A	C	2.351e^-4	0.807	INTRON CG31814
2L	14418378	2L_14418378_SNP [dm3] 2L_14418378_SNP [dm6]	G	A	2.351e^-4	0.807	INTERGENIC
2L	14418395	2L_14418395_SNP [dm3] 2L_14418395_SNP [dm6]	A	T	2.351e^-4	0.807	INTERGENIC
2L	14418401	2L_14418401_SNP [dm3] 2L_14418401_SNP [dm6]	A	G	2.351e^-4	0.807	INTERGENIC
2L	14428386	2L_14428386_SNP [dm3] 2L_14428386_SNP [dm6]	T	C	2.351e^-4	0.807	DOWNSTREAM CR44732 INTERGENIC	TF binding site mE1_TFBS_cnc
2L	1563000	2L_1563000_SNP [dm3] 2L_1563000_SNP [dm6]	G	A	2.351e^-4	0.807	INTRON haf	TF binding site mE1_TFBS_inv
2L	1563037	2L_1563037_SNP [dm3] 2L_1563037_SNP [dm6]	C	A	2.351e^-4	0.807	INTRON haf	TF binding site mE1_TFBS_inv
2L	15769414	2L_15769414_SNP [dm3] 2L_15769414_SNP [dm6]	T	C	2.351e^-4	0.807	SYNONYMOUS_CODING Ku80
2L	18621207	2L_18621207_SNP [dm3] 2L_18621207_SNP [dm6]	G	T	2.351e^-4	0.807	INTRON MESR3	TF binding site mE1_TFBS_HSA mE1_TFBS_zfh1
2L	19948693	2L_19948693_SNP [dm3] 2L_19948693_SNP [dm6]	A	G	2.351e^-4	0.807	INTRON sick	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	19948707	2L_19948707_INS [dm3] 2L_19948707_INS [dm6]	T	TT	2.351e^-4	0.807	INTRON sick	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	22034519	2L_22034519_SNP [dm3] 2L_22034519_SNP [dm6]	T	C	2.351e^-4	0.807	DOWNSTREAM CR45335 INTERGENIC
2L	22080935	2L_22080935_SNP [dm3] 2L_22080935_SNP [dm6]	T	C	2.351e^-4	0.807	DOWNSTREAM ttm3 INTERGENIC
2L	22085395	2L_22085395_SNP [dm3] 2L_22085395_SNP [dm6]	C	A	2.351e^-4	0.807	INTERGENIC
2L	22095948	2L_22095948_SNP [dm3] 2L_22095948_SNP [dm6]	A	G	2.351e^-4	0.807	INTERGENIC
2L	3156949	2L_3156949_SNP [dm3] 2L_3156949_SNP [dm6]	G	A	2.351e^-4	0.807	INTRON Mad
2L	5814382	2L_5814382_SNP [dm3] 2L_5814382_SNP [dm6]	T	C	2.351e^-4	0.807	INTERGENIC
2L	7215199	2L_7215199_SNP [dm3] 2L_7215199_SNP [dm6]	T	G	2.351e^-4	0.807	INTRON CG13784
2R	11850411	2R_11850411_SNP [dm3] 2R_15962906_SNP [dm6]	T	C	2.351e^-4	0.807	INTRON Strn-Mlck	TF binding site mE1_TFBS_cad
2R	12187970	2R_12187970_SNP [dm3] 2R_16300465_SNP [dm6]	T	A	2.351e^-4	0.807	EXON CR45232
2R	13648653	2R_13648653_SNP [dm3] 2R_17761148_SNP [dm6]	A	C	2.351e^-4	0.807	UTR_5_PRIME CG5009 DOWNSTREAM HLH54F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_en mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl mE1_TFBS_Ubx
2R	13648988	2R_13648988_SNP [dm3] 2R_17761483_SNP [dm6]	G	A	2.351e^-4	0.807	DOWNSTREAM HLH54F INTRON CG5009	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
2R	13649079	2R_13649079_SNP [dm3] 2R_17761574_SNP [dm6]	T	A	2.351e^-4	0.807	INTRON CG5009	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
2R	13649123	2R_13649123_SNP [dm3] 2R_17761618_SNP [dm6]	G	A	2.351e^-4	0.807	INTRON CG5009	TF binding site mE1_TFBS_sens
2R	13649129	2R_13649129_SNP [dm3] 2R_17761624_SNP [dm6]	T	G	2.351e^-4	0.807	INTRON CG5009	TF binding site mE1_TFBS_sens
2R	13649195	2R_13649195_SNP [dm3] 2R_17761690_SNP [dm6]	C	T	2.351e^-4	0.807	INTRON CG5009
2R	13649215	2R_13649215_SNP [dm3] 2R_17761710_SNP [dm6]	T	C	2.351e^-4	0.807	INTRON CG5009
2R	13649218	2R_13649218_SNP [dm3] 2R_17761713_SNP [dm6]	A	G	2.351e^-4	0.807	INTRON CG5009
2R	13649743	2R_13649743_SNP [dm3] 2R_17762238_SNP [dm6]	G	T	2.351e^-4	0.807	NON_SYNONYMOUS_CODING CG5009
2R	14586469	2R_14586469_SNP [dm3] 2R_18698964_SNP [dm6]	G	A	2.351e^-4	0.807	INTRON Sik3
2R	5840258	2R_5840258_SNP [dm3] 2R_9952753_SNP [dm6]	T	G	2.351e^-4	0.807	INTRON Mef2
2R	6373997	2R_6373997_SNP [dm3] 2R_10486492_SNP [dm6]	A	G	2.351e^-4	0.807	DOWNSTREAM lola INTRON lola	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	9811915	2R_9811915_SNP [dm3] 2R_13924410_SNP [dm6]	A	G	2.351e^-4	0.807	INTRON shot	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_Trl
2R	9971232	2R_9971232_SNP [dm3] 2R_14083727_SNP [dm6]	T	C	2.351e^-4	0.807	INTRON Prosap
2R	9979343	2R_9979343_SNP [dm3] 2R_14091838_SNP [dm6]	G	C	2.351e^-4	0.807	DOWNSTREAM CG42287 & 1 other INTRON Prosap
3L	1280296	3L_1280296_DEL [dm3] 3L_1280296_DEL [dm6]	AA	A	2.351e^-4	0.807	INTRON CG32333
3L	1280382	3L_1280382_SNP [dm3] 3L_1280382_SNP [dm6]	A	G	2.351e^-4	0.807	INTRON CG32333
3L	1280527	3L_1280527_SNP [dm3] 3L_1280527_SNP [dm6]	C	A	2.351e^-4	0.807	INTRON CG32333
3L	1364567	3L_1364567_SNP [dm3] 3L_1364567_SNP [dm6]	A	G	2.351e^-4	0.807	INTRON Ptp61F	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_tll mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	1386222	3L_1386222_SNP [dm3] 3L_1386222_SNP [dm6]	T	A	2.351e^-4	0.807	NON_SYNONYMOUS_CODING ru INTRON Ptp61F	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3L	13891658	3L_13891658_SNP [dm3] 3L_13898558_SNP [dm6]	A	T	2.351e^-4	0.807	INTRON dysc
3L	13891673	3L_13891673_SNP [dm3] 3L_13898573_SNP [dm6]	A	C	2.351e^-4	0.807	INTRON dysc
3L	13891789	3L_13891789_SNP [dm3] 3L_13898689_SNP [dm6]	A	C	2.351e^-4	0.807	INTRON dysc
3L	13891794	3L_13891794_SNP [dm3] 3L_13898694_SNP [dm6]	A	G	2.351e^-4	0.807	INTRON dysc
3L	13891827	3L_13891827_SNP [dm3] 3L_13898727_SNP [dm6]	G	C	2.351e^-4	0.807	INTRON dysc
3L	13891861	3L_13891861_SNP [dm3] 3L_13898761_SNP [dm6]	T	A	2.351e^-4	0.807	INTRON dysc
3L	16046615	3L_16046615_SNP [dm3] 3L_16053515_SNP [dm6]	C	T	2.351e^-4	0.807	SYNONYMOUS_CODING Mbs	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	2029776	3L_2029776_SNP [dm3] 3L_2029776_SNP [dm6]	G	A	2.351e^-4	0.807	INTERGENIC
3L	2683494	3L_2683494_SNP [dm3] 3L_2683494_SNP [dm6]	A	G	2.351e^-4	0.807	INTRON Fife
3L	991991	3L_991991_SNP [dm3] 3L_991991_SNP [dm6]	A	G	2.351e^-4	0.807	UTR_3_PRIME Glut1 DOWNSTREAM Glut1
X	16579981	X_16579981_SNP [dm3] X_16685948_SNP [dm6]	T	G	2.351e^-4	0.807	INTRON Sep4
X	16580007	X_16580007_SNP [dm3] X_16685974_SNP [dm6]	G	C	2.351e^-4	0.807	INTRON Sep4
X	16580020	X_16580020_SNP [dm3] X_16685987_SNP [dm6]	C	T	2.351e^-4	0.807	INTRON Sep4
X	16961004	X_16961004_SNP [dm3] X_17066971_SNP [dm6]	T	A	2.351e^-4	0.807	UPSTREAM CG45002 DOWNSTREAM CG43077 INTERGENIC
X	16961137	X_16961137_SNP [dm3] X_17067104_SNP [dm6]	A	G	2.351e^-4	0.807	UPSTREAM CG45002 DOWNSTREAM CG43077 INTERGENIC
X	16961156	X_16961156_SNP [dm3] X_17067123_SNP [dm6]	G	A	2.351e^-4	0.807	UPSTREAM CG45002 DOWNSTREAM CG43077 INTERGENIC
X	16961209	X_16961209_SNP [dm3] X_17067176_SNP [dm6]	A	T	2.351e^-4	0.807	UPSTREAM CG45002 DOWNSTREAM CG43077 INTERGENIC
X	17622059	X_17622059_SNP [dm3] X_17728026_SNP [dm6]	C	T	2.351e^-4	0.807	INTRON CG42684
X	20455847	X_20455847_SNP [dm3] X_20584820_SNP [dm6]	T	C	2.351e^-4	0.807	INTERGENIC
X	21162507	X_21162507_SNP [dm3] X_21291480_SNP [dm6]	T	C	2.351e^-4	0.807	SYNONYMOUS_CODING CG1494 DOWNSTREAM CG1718	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	2287980	X_2287980_SNP [dm3] X_2393947_SNP [dm6]	G	A	2.351e^-4	0.807	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd mE1_TFBS_HSA
X	2469577	X_2469577_SNP [dm3] X_2575544_SNP [dm6]	T	A	2.351e^-4	0.807	INTRON Pdfr
X	2469747	X_2469747_SNP [dm3] X_2575714_SNP [dm6]	C	T	2.351e^-4	0.807	SYNONYMOUS_CODING Pdfr
X	2675799	X_2675799_INS [dm3] X_2781766_INS [dm6]	T	TT	2.351e^-4	0.807	INTRON kirre	TF binding site mE1_TFBS_chinmo
X	2882205	X_2882205_SNP [dm3] X_2988172_SNP [dm6]	C	T	2.351e^-4	0.807	UPSTREAM kirre INTRON kirre	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
X	6646564	X_6646564_SNP [dm3] X_6752531_SNP [dm6]	C	T	2.351e^-4	0.807	INTRON CG14439
X	8427384	X_8427384_SNP [dm3] X_8533351_SNP [dm6]	G	A	2.351e^-4	0.807	INTRON Nrg	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	10883230	3L_10883230_SNP [dm3] 3L_10890130_SNP [dm6]	A	G	2.589e^-4	0.807	INTRON Cpr67Fa1
3L	10927644	3L_10927644_SNP [dm3] 3L_10934544_SNP [dm6]	C	T	2.589e^-4	0.807	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	10927647	3L_10927647_SNP [dm3] 3L_10934547_SNP [dm6]	C	T	2.589e^-4	0.807	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	19181120	3L_19181120_SNP [dm3] 3L_19188020_SNP [dm6]	C	A	2.835e^-4	0.807	INTRON fz2
2R	17341439	2R_17341439_SNP [dm3] 2R_21453934_SNP [dm6]	C	G	3.070e^-4	0.807	INTRON Sdc	TF binding site BDTNP1_TFBS_dl
3L	10434419	3L_10434419_SNP [dm3] 3L_10441319_SNP [dm6]	C	A	3.070e^-4	0.807	INTERGENIC
3L	10437614	3L_10437614_SNP [dm3] 3L_10444514_SNP [dm6]	T	A	3.070e^-4	0.807	INTERGENIC
3L	13841879	3L_13841879_SNP [dm3] 3L_13848779_SNP [dm6]	T	G	3.070e^-4	0.807	INTRON Hml
3L	13841907	3L_13841907_SNP [dm3] 3L_13848807_SNP [dm6]	G	C	3.070e^-4	0.807	INTRON Hml
3L	16745156	3L_16745156_SNP [dm3] 3L_16752056_SNP [dm6]	T	C	3.070e^-4	0.807	INTERGENIC
3L	16745720	3L_16745720_SNP [dm3] 3L_16752620_SNP [dm6]	C	T	3.070e^-4	0.807	INTERGENIC
3L	6652287	3L_6652287_SNP [dm3] 3L_6659187_SNP [dm6]	A	G	3.070e^-4	0.807	INTERGENIC
3L	6652427	3L_6652427_SNP [dm3] 3L_6659327_SNP [dm6]	A	G	3.070e^-4	0.807	INTERGENIC
3L	6652505	3L_6652505_SNP [dm3] 3L_6659405_SNP [dm6]	G	C	3.070e^-4	0.807	INTERGENIC
3L	6652611	3L_6652611_SNP [dm3] 3L_6659511_SNP [dm6]	T	G	3.070e^-4	0.807	INTERGENIC
3L	6652628	3L_6652628_SNP [dm3] 3L_6659528_SNP [dm6]	C	T	3.070e^-4	0.807	INTERGENIC
3L	6652661	3L_6652661_SNP [dm3] 3L_6659561_SNP [dm6]	C	T	3.070e^-4	0.807	INTERGENIC
3L	6652806	3L_6652806_SNP [dm3] 3L_6659706_SNP [dm6]	A	T	3.070e^-4	0.807	INTERGENIC
3L	7775706	3L_7775706_SNP [dm3] 3L_7782606_SNP [dm6]	T	A	3.070e^-4	0.807	INTRON CG32369	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	9058388	3L_9058388_SNP [dm3] 3L_9065288_SNP [dm6]	A	G	3.070e^-4	0.807	INTRON Argk	TF binding site mE1_TFBS_bab1
3L	9058450	3L_9058450_SNP [dm3] 3L_9065350_SNP [dm6]	T	C	3.070e^-4	0.807	INTRON Argk	TF binding site mE1_TFBS_bab1
3L	9216939	3L_9216939_SNP [dm3] 3L_9223839_SNP [dm6]	G	C	3.070e^-4	0.807	INTERGENIC
3L	9383766	3L_9383766_SNP [dm3] 3L_9390666_SNP [dm6]	T	C	3.070e^-4	0.807	SYNONYMOUS_CODING CG4080	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	9883782	3L_9883782_DEL [dm3] 3L_9890682_DEL [dm6]	AACTAATGTG	A	3.070e^-4	0.807	INTRON CalpB	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	9887281	3L_9887281_SNP [dm3] 3L_9894181_SNP [dm6]	T	C	3.070e^-4	0.807	SYNONYMOUS_CODING CG14164 START_GAINED CG6709 UTR_5_PRIME CG6709 UPSTREAM CG6709 DOWNSTREAM CalpB & 1 other
X	18739809	X_18739809_SNP [dm3] X_18845776_SNP [dm6]	G	A	3.070e^-4	0.807	SYNONYMOUS_CODING CG34422 DOWNSTREAM CG7280	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	6984632	2L_6984632_SNP [dm3] 2L_6984632_SNP [dm6]	G	A	3.222e^-4	0.807	SYNONYMOUS_CODING uif	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	16961245	X_16961245_SNP [dm3] X_17067212_SNP [dm6]	A	T	3.222e^-4	0.807	UPSTREAM CG45002 DOWNSTREAM CG43077 INTERGENIC
2R	13650490	2R_13650490_SNP [dm3] 2R_17762985_SNP [dm6]	T	G	3.578e^-4	0.807	SYNONYMOUS_CODING CG5009
X	4472906	X_4472906_SNP [dm3] X_4578873_SNP [dm6]	T	A	3.608e^-4	0.807	INTRON CR32773
2R	12675026	2R_12675026_SNP [dm3] 2R_16787521_SNP [dm6]	T	G	3.759e^-4	0.807	INTRON CG5522

Showing 1 to 100 of 445 entries

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Missing results

By genomic position
Variant impact
Gene name

Pa14 LT50 (Wang et al 2017) phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results