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=8.765e^-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_K	0.06702

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1885 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	17347546	2R_17347546_SNP [dm3] 2R_21460041_SNP [dm6]	G	A	3.757e^-6	0.894	INTRON Sdc
2L	18438982	2L_18438982_SNP [dm3] 2L_18438982_SNP [dm6]	G	A	4.417e^-6	0.894	INTERGENIC
3R	22279691	3R_22279691_SNP [dm3] 3R_26453969_SNP [dm6]	C	T	4.524e^-6	0.894	UPSTREAM CG43117 INTRON CG5447
2R	13782100	2R_13782100_SNP [dm3] 2R_17894595_SNP [dm6]	A	T	4.584e^-6	0.894	UPSTREAM CG14491 & 1 other INTRON Elk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3L	723422	3L_723422_DEL [dm3] 3L_723422_DEL [dm6]	AGT	TC	5.102e^-6	0.894	INTERGENIC
2L	15835955	2L_15835955_SNP [dm3] 2L_15835955_SNP [dm6]	G	A	5.366e^-6	0.894	UPSTREAM CG18518 DOWNSTREAM CR31822 INTERGENIC
2L	15835953	2L_15835953_SNP [dm3] 2L_15835953_SNP [dm6]	C	T	5.534e^-6	0.894	UPSTREAM CG18518 DOWNSTREAM CR31822 INTERGENIC
2L	15835967	2L_15835967_SNP [dm3] 2L_15835967_SNP [dm6]	A	C	5.534e^-6	0.894	UPSTREAM CG18518 DOWNSTREAM CR31822 INTERGENIC
2L	1094208	2L_1094208_SNP [dm3] 2L_1094208_SNP [dm6]	G	T	5.548e^-6	0.894	INTRON CG4629
2L	12133058	2L_12133058_SNP [dm3] 2L_12133058_SNP [dm6]	G	C	6.164e^-6	0.894	INTRON rho-6	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	15835962	2L_15835962_SNP [dm3] 2L_15835962_SNP [dm6]	T	C	6.543e^-6	0.894	UPSTREAM CG18518 DOWNSTREAM CR31822 INTERGENIC
2L	7671355	2L_7671355_SNP [dm3] 2L_7671355_SNP [dm6]	G	C	7.639e^-6	0.894	INTRON Slob & 1 other
2L	15837656	2L_15837656_DEL [dm3] 2L_15837656_DEL [dm6]	CTGTGGAGA	C	7.688e^-6	0.894	UPSTREAM CR31822 INTERGENIC
2L	16797261	2L_16797261_SNP [dm3] 2L_16797261_SNP [dm6]	G	T	8.258e^-6	0.894	NON_SYNONYMOUS_CODING Ugt36Bb	TF binding site mE1_TFBS_sens
2L	1094117	2L_1094117_SNP [dm3] 2L_1094117_SNP [dm6]	C	T	8.552e^-6	0.894	INTRON CG4629
2L	7673232	2L_7673232_SNP [dm3] 2L_7673232_SNP [dm6]	A	G	9.219e^-6	0.894	INTRON Slob & 1 other
3L	1866267	3L_1866267_SNP [dm3] 3L_1866267_SNP [dm6]	T	A	9.588e^-6	0.894	INTRON CG12025	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3R	3408950	3R_3408950_SNP [dm3] 3R_7583228_SNP [dm6]	A	C	1.003e^-5	0.894	INTRON CG34127
2L	2612034	2L_2612034_SNP [dm3] 2L_2612034_SNP [dm6]	G	C	1.038e^-5	0.894	DOWNSTREAM CG15395 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	4661225	2R_4661225_SNP [dm3] 2R_8773720_SNP [dm6]	A	T	1.188e^-5	0.894	INTERGENIC
X	17025680	X_17025680_SNP [dm3] X_17131647_SNP [dm6]	G	T	1.206e^-5	0.894	INTRON CG5004
2R	1179199	2R_1179199_SNP [dm3] 2R_5291694_SNP [dm6]	C	A	1.217e^-5	0.894	INTRON d4	transposable element FlyBase
2L	9272908	2L_9272908_SNP [dm3] 2L_9272908_SNP [dm6]	G	A	1.294e^-5	0.894	INTRON Ggamma30A	TF binding site mE1_TFBS_Trl
2L	9272983	2L_9272983_SNP [dm3] 2L_9272983_SNP [dm6]	T	A	1.294e^-5	0.894	INTRON Ggamma30A	TF binding site mE1_TFBS_Trl
2L	2612016	2L_2612016_SNP [dm3] 2L_2612016_SNP [dm6]	A	G	1.311e^-5	0.894	DOWNSTREAM CG15395 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	2612033	2L_2612033_SNP [dm3] 2L_2612033_SNP [dm6]	T	A	1.311e^-5	0.894	DOWNSTREAM CG15395 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	2611942	2L_2611942_SNP [dm3] 2L_2611942_SNP [dm6]	A	T	1.361e^-5	0.894	DOWNSTREAM CG15395 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	7671459	2L_7671459_SNP [dm3] 2L_7671459_SNP [dm6]	T	C	1.409e^-5	0.894	INTRON Slob & 1 other
3L	9248790	3L_9248790_SNP [dm3] 3L_9255690_SNP [dm6]	T	A	1.481e^-5	0.894	INTRON GluRIB
3L	9248812	3L_9248812_SNP [dm3] 3L_9255712_SNP [dm6]	A	G	1.481e^-5	0.894	INTRON GluRIB
2R	8308944	2R_8308944_SNP [dm3] 2R_12421439_SNP [dm6]	G	A	1.534e^-5	0.894	SYNONYMOUS_CODING CG8834	TF binding site mE1_TFBS_cad
3L	1866320	3L_1866320_SNP [dm3] 3L_1866320_SNP [dm6]	T	C	1.718e^-5	0.894	INTRON CG12025	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3L	13370427	3L_13370427_SNP [dm3] 3L_13377327_SNP [dm6]	C	T	1.741e^-5	0.894	UPSTREAM CG14111 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	17347548	2R_17347548_SNP [dm3] 2R_21460043_SNP [dm6]	T	G	1.808e^-5	0.894	INTRON Sdc
X	3984887	X_3984887_SNP [dm3] X_4090854_SNP [dm6]	T	A	1.815e^-5	0.894	UTR_3_PRIME CG43689 DOWNSTREAM CG43689	TF binding site mE1_TFBS_cad
2L	2612017	2L_2612017_SNP [dm3] 2L_2612017_SNP [dm6]	A	C	1.818e^-5	0.894	DOWNSTREAM CG15395 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	20146803	2L_20146803_SNP [dm3] 2L_20146803_SNP [dm6]	T	A	1.829e^-5	0.894	INTERGENIC
3L	10822338	3L_10822338_SNP [dm3] 3L_10829238_SNP [dm6]	T	G	1.848e^-5	0.894	INTERGENIC
2R	8309297	2R_8309297_SNP [dm3] 2R_12421792_SNP [dm6]	G	A	1.864e^-5	0.894	INTRON CG8834	TF binding site mE1_TFBS_cad
3L	2938083	3L_2938083_SNP [dm3] 3L_2938083_SNP [dm6]	C	T	1.939e^-5	0.907	INTRON Shab
2R	4161144	2R_4161144_SNP [dm3] 2R_8273639_SNP [dm6]	A	T	2.088e^-5	0.927	INTERGENIC
2R	8308950	2R_8308950_SNP [dm3] 2R_12421445_SNP [dm6]	G	A	2.166e^-5	0.927	SYNONYMOUS_CODING CG8834	TF binding site mE1_TFBS_cad
3L	13370514	3L_13370514_SNP [dm3] 3L_13377414_SNP [dm6]	G	A	2.178e^-5	0.927	UPSTREAM CG14111 INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2L	1094207	2L_1094207_SNP [dm3] 2L_1094207_SNP [dm6]	T	A	2.181e^-5	0.927	INTRON CG4629
3L	2937979	3L_2937979_SNP [dm3] 3L_2937979_SNP [dm6]	C	T	2.557e^-5	0.966	INTRON Shab
2R	15390051	2R_15390051_SNP [dm3] 2R_19502546_SNP [dm6]	A	G	2.685e^-5	0.966	UPSTREAM CG11007 INTERGENIC
2L	7671918	2L_7671918_SNP [dm3] 2L_7671918_SNP [dm6]	T	C	2.766e^-5	0.966	INTRON Slob & 1 other
2L	734294	2L_734294_SNP [dm3] 2L_734294_SNP [dm6]	A	G	2.810e^-5	0.966	INTERGENIC
2R	9558416	2R_9558416_SNP [dm3] 2R_13670911_SNP [dm6]	T	C	2.824e^-5	0.966	SYNONYMOUS_CODING CG18368 DOWNSTREAM CR45031 INTRON fas
2R	5523689	2R_5523689_SNP [dm3] 2R_9636184_SNP [dm6]	C	A	2.839e^-5	0.966	DOWNSTREAM CR44070 INTRON Mmp2
2L	7779244	2L_7779244_SNP [dm3] 2L_7779244_SNP [dm6]	C	G	2.871e^-5	0.966	UPSTREAM Uro INTERGENIC
2L	9271018	2L_9271018_INS [dm3] 2L_9271018_INS [dm6]	T	TT	3.069e^-5	0.966	INTRON Ggamma30A	TF binding site mE1_TFBS_HSA
2L	1365901	2L_1365901_SNP [dm3] 2L_1365901_SNP [dm6]	T	C	3.070e^-5	0.966	INTERGENIC
3L	1867021	3L_1867021_SNP [dm3] 3L_1867021_SNP [dm6]	T	G	3.118e^-5	0.966	INTRON CG12025	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3L	13282598	3L_13282598_SNP [dm3] 3L_13289498_SNP [dm6]	G	T	3.141e^-5	0.966	INTERGENIC
2L	3670683	2L_3670683_SNP [dm3] 2L_3670683_SNP [dm6]	G	A	3.239e^-5	0.966	UPSTREAM Sfp24Bb & 1 other INTRON CG34340
2L	12134290	2L_12134290_SNP [dm3] 2L_12134290_SNP [dm6]	T	G	3.373e^-5	0.966	UPSTREAM rho-6 INTERGENIC
2R	19404101	2R_19404101_SNP [dm3] 2R_23516578_SNP [dm6]	C	G	3.438e^-5	0.966	INTERGENIC
X	14378295	X_14378295_SNP [dm3] X_14484262_SNP [dm6]	C	T	3.447e^-5	0.966	INTERGENIC
3L	9225504	3L_9225504_SNP [dm3] 3L_9232404_SNP [dm6]	A	G	3.473e^-5	0.966	INTERGENIC	TF binding site mE1_TFBS_inv
2L	1093321	2L_1093321_SNP [dm3] 2L_1093321_SNP [dm6]	A	G	3.500e^-5	0.966	INTRON CG4629
3L	1866871	3L_1866871_SNP [dm3] 3L_1866871_SNP [dm6]	T	A	3.519e^-5	0.966	INTRON CG12025	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2L	1093320	2L_1093320_SNP [dm3] 2L_1093320_SNP [dm6]	C	T	3.531e^-5	0.966	INTRON CG4629
2R	19144240	2R_19144240_SNP [dm3] 2R_23256717_SNP [dm6]	G	A	3.554e^-5	0.966	INTERGENIC
X	10058312	X_10058312_SNP [dm3] X_10164279_SNP [dm6]	A	G	3.594e^-5	0.966	INTRON CR44894 & 1 other
2R	3921028	2R_3921028_SNP [dm3] 2R_8033523_SNP [dm6]	T	C	3.773e^-5	0.966	INTRON Optix
2L	7654316	2L_7654316_SNP [dm3] 2L_7654316_SNP [dm6]	C	G	3.852e^-5	0.966	INTRON Slob
2L	7654319	2L_7654319_INS [dm3] 2L_7654319_INS [dm6]	C	GATAAGT	3.852e^-5	0.966	INTRON Slob
2L	7654322	2L_7654322_SNP [dm3] 2L_7654322_SNP [dm6]	C	A	3.852e^-5	0.966	INTRON Slob
2L	12134104	2L_12134104_SNP [dm3] 2L_12134104_SNP [dm6]	A	C	3.889e^-5	0.966	UPSTREAM rho-6 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	6732478	2R_6732478_SNP [dm3] 2R_10844973_SNP [dm6]	T	A	4.046e^-5	0.966	UPSTREAM CG30015 INTRON CG30015	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	15835782	2L_15835782_SNP [dm3] 2L_15835782_SNP [dm6]	A	G	4.175e^-5	0.966	UPSTREAM CG18518 DOWNSTREAM CR31822 INTERGENIC
2L	7671257	2L_7671257_SNP [dm3] 2L_7671257_SNP [dm6]	A	G	4.278e^-5	0.966	INTRON Slob & 1 other
2L	20229722	2L_20229722_SNP [dm3] 2L_20229722_SNP [dm6]	C	T	4.350e^-5	0.966	INTERGENIC
2R	6773704	2R_6773704_SNP [dm3] 2R_10886199_SNP [dm6]	G	A	4.381e^-5	0.966	UPSTREAM CG30020 DOWNSTREAM mir-1008 INTRON CG18004	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo
2L	16805633	2L_16805633_SNP [dm3] 2L_16805633_SNP [dm6]	T	G	4.430e^-5	0.966	INTRON CG13280 & 1 other
2L	7780034	2L_7780034_SNP [dm3] 2L_7780034_SNP [dm6]	T	C	4.496e^-5	0.966	UPSTREAM Uro INTERGENIC
2L	15837667	2L_15837667_SNP [dm3] 2L_15837667_SNP [dm6]	A	G	4.543e^-5	0.966	UPSTREAM CR31822 INTERGENIC
2L	15837669	2L_15837669_DEL [dm3] 2L_15837669_DEL [dm6]	AT	A	4.543e^-5	0.966	UPSTREAM CR31822 INTERGENIC
2L	16802836	2L_16802836_SNP [dm3] 2L_16802836_SNP [dm6]	G	A	4.557e^-5	0.966	SYNONYMOUS_CODING CG13280	TF binding site mE1_TFBS_chinmo
3L	13367397	3L_13367397_DEL [dm3] 3L_13374297_DEL [dm6]	ACAGGTTTTTCCCACTTTTG...	A	4.638e^-5	0.966	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	7671796	2L_7671796_SNP [dm3] 2L_7671796_SNP [dm6]	G	A	4.667e^-5	0.966	INTRON Slob & 1 other
2R	15383318	2R_15383318_SNP [dm3] 2R_19495813_SNP [dm6]	A	G	4.667e^-5	0.966	SYNONYMOUS_CODING hpo	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	22456463	3R_22456463_SNP [dm3] 3R_26630741_SNP [dm6]	C	G	4.764e^-5	0.966	SYNONYMOUS_CODING TwdlJ	TF binding site mE1_TFBS_chinmo
3R	13425689	3R_13425689_SNP [dm3] 3R_17599967_SNP [dm6]	T	G	4.774e^-5	0.966	INTERGENIC
2R	19144239	2R_19144239_SNP [dm3] 2R_23256716_SNP [dm6]	A	C	4.804e^-5	0.966	INTERGENIC
2R	15383819	2R_15383819_SNP [dm3] 2R_19496314_SNP [dm6]	A	T	5.022e^-5	0.966	SYNONYMOUS_CODING hpo	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	17077478	2L_17077478_SNP [dm3] 2L_17077478_SNP [dm6]	T	A	5.048e^-5	0.966	INTERGENIC
2R	15389964	2R_15389964_SNP [dm3] 2R_19502459_SNP [dm6]	T	C	5.049e^-5	0.966	UPSTREAM CG11007 INTERGENIC
2L	13543760	2L_13543760_SNP [dm3] 2L_13543760_SNP [dm6]	G	A	5.235e^-5	0.966	DOWNSTREAM CG16853 INTRON B4	transposable element FlyBase
2R	10539113	2R_10539113_SNP [dm3] 2R_14651608_SNP [dm6]	A	G	5.326e^-5	0.966	INTERGENIC
2R	8307699	2R_8307699_SNP [dm3] 2R_12420194_SNP [dm6]	T	C	5.333e^-5	0.966	UPSTREAM CG42782 DOWNSTREAM CG8834 INTRON CG8834
2R	8309803	2R_8309803_SNP [dm3] 2R_12422298_SNP [dm6]	A	C	5.333e^-5	0.966	UPSTREAM CG8520 INTRON CG8834	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	15835747	2L_15835747_SNP [dm3] 2L_15835747_SNP [dm6]	G	A	5.344e^-5	0.966	UPSTREAM CG18518 DOWNSTREAM CR31822 INTERGENIC
3L	13367367	3L_13367367_SNP [dm3] 3L_13374267_SNP [dm6]	A	C	5.357e^-5	0.966	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	6011825	2L_6011825_SNP [dm3] 2L_6011825_SNP [dm6]	G	A	5.402e^-5	0.966	SYNONYMOUS_CODING CG9098 START_GAINED CG9098 UTR_5_PRIME CG9098 UPSTREAM CG9098	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	6773710	2R_6773710_SNP [dm3] 2R_10886205_SNP [dm6]	T	C	5.459e^-5	0.966	UPSTREAM CG30020 DOWNSTREAM mir-1008 INTRON CG18004	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo
3L	513391	3L_513391_SNP [dm3] 3L_513391_SNP [dm6]	T	A	5.496e^-5	0.966	INTRON klar
2R	8282022	2R_8282022_SNP [dm3] 2R_12394517_SNP [dm6]	G	T	5.510e^-5	0.966	NON_SYNONYMOUS_CODING Or49a SPLICE_SITE_REGION Or49a UPSTREAM CG30048
2L	1789815	2L_1789815_SNP [dm3] 2L_1789815_SNP [dm6]	C	T	5.535e^-5	0.966	NON_SYNONYMOUS_CODING Gr22d DOWNSTREAM Gr22c	TF binding site mE1_TFBS_HSA mE1_TFBS_sens

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By genomic position
Variant impact
Gene name

FBS phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results