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=6.341e^-2)
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
wolba	0.0435

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

31 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

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	11375326	2L_11375326_SNP [dm3] 2L_11375326_SNP [dm6]	A	C	4.472e^-8	0.004	INTERGENIC	regulatory region REDfly_CRMs
2L	11641084	2L_11641084_SNP [dm3] 2L_11641084_SNP [dm6]	A	G	4.472e^-8	0.004	INTERGENIC
2L	21279486	2L_21279486_SNP [dm3] 2L_21279486_SNP [dm6]	A	T	4.472e^-8	0.004	INTRON CG8671
2L	6516660	2L_6516660_SNP [dm3] 2L_6516660_SNP [dm6]	T	G	4.472e^-8	0.004	INTRON CG31637	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
2L	6735888	2L_6735888_SNP [dm3] 2L_6735888_SNP [dm6]	C	A	4.472e^-8	0.004	UTR_3_PRIME TTLL3B DOWNSTREAM TTLL3A
2L	7486664	2L_7486664_SNP [dm3] 2L_7486664_SNP [dm6]	G	T	4.472e^-8	0.004	INTRON Ziz
2L	9419357	2L_9419357_SNP [dm3] 2L_9419357_SNP [dm6]	G	T	4.472e^-8	0.004	INTRON Mco1
2R	3917166	2R_3917166_SNP [dm3] 2R_8029661_SNP [dm6]	C	T	4.472e^-8	0.004	UPSTREAM CR43724 EXON CR43724	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	12106924	3L_12106924_SNP [dm3] 3L_12113824_SNP [dm6]	G	A	4.472e^-8	0.004	INTERGENIC
3L	12106930	3L_12106930_SNP [dm3] 3L_12113830_SNP [dm6]	A	C	4.472e^-8	0.004	INTERGENIC
3L	22633389	3L_22633389_SNP [dm3] 3L_22640289_SNP [dm6]	G	A	4.472e^-8	0.004	INTERGENIC
3L	8573308	3L_8573308_SNP [dm3] 3L_8580208_SNP [dm6]	T	C	4.472e^-8	0.004	INTRON CG43078
3R	16726316	3R_16726316_SNP [dm3] 3R_20900594_SNP [dm6]	C	T	4.472e^-8	0.004	INTERGENIC
3R	3203595	3R_3203595_SNP [dm3] 3R_7377873_SNP [dm6]	A	G	4.472e^-8	0.004	INTERGENIC	TF binding site mE1_TFBS_HSA
X	16768229	X_16768229_SNP [dm3] X_16874196_SNP [dm6]	T	C	4.472e^-8	0.004	INTRON CG13003
X	22172400	X_22172400_SNP [dm3] X_22770564_SNP [dm6]	C	T	4.472e^-8	0.004	INTRON CR44997	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	5253026	X_5253026_SNP [dm3] X_5358993_SNP [dm6]	T	A	4.472e^-8	0.004	INTRON SK
2L	5445417	2L_5445417_SNP [dm3] 2L_5445417_SNP [dm6]	T	G	6.324e^-8	0.004	INTERGENIC
2L	9418260	2L_9418260_SNP [dm3] 2L_9418260_SNP [dm6]	G	A	6.324e^-8	0.004	INTRON Mco1
2L	9418262	2L_9418262_SNP [dm3] 2L_9418262_SNP [dm6]	G	A	6.324e^-8	0.004	INTRON Mco1
2R	10838857	2R_10838857_SNP [dm3] 2R_14951352_SNP [dm6]	G	T	6.324e^-8	0.004	UPSTREAM aPKC INTRON aPKC	TF binding site mE1_TFBS_HSA mE1_TFBS_run
2R	5226824	2R_5226824_SNP [dm3] 2R_9339319_SNP [dm6]	C	A	6.324e^-8	0.004	INTRON CG13954 & 1 other
X	21283843	X_21283843_INS [dm3] X_21412816_INS [dm6]	T	TATATT	6.324e^-8	0.004	INTERGENIC
2L	10479793	2L_10479793_SNP [dm3] 2L_10479793_SNP [dm6]	C	G	4.429e^-6	0.206	INTRON RluA-2	TF binding site BDTNP1_TFBS_dl
2L	11083661	2L_11083661_SNP [dm3] 2L_11083661_SNP [dm6]	G	C	4.429e^-6	0.206	UTR_3_PRIME AstCC
2L	3687367	2L_3687367_SNP [dm3] 2L_3687367_SNP [dm6]	T	C	4.429e^-6	0.206	INTRON CG34340
2R	19961908	2R_19961908_INS [dm3] 2R_24074385_INS [dm6]	G	GATCAGATCGAG...	4.429e^-6	0.206	UPSTREAM Mlp60A DOWNSTREAM CG3209 INTERGENIC
3R	14363573	3R_14363573_SNP [dm3] 3R_18537851_SNP [dm6]	G	C	4.429e^-6	0.206	INTRON fru
3R	25631799	3R_25631799_SNP [dm3] 3R_29806077_SNP [dm6]	C	A	4.429e^-6	0.206	NON_SYNONYMOUS_CODING ncd UPSTREAM ca	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3R	4964313	3R_4964313_SNP [dm3] 3R_9138591_SNP [dm6]	C	T	4.429e^-6	0.206	INTRON pum	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	9927543	3R_9927543_SNP [dm3] 3R_14101821_SNP [dm6]	C	A	4.429e^-6	0.206	INTRON PK1-R	TF binding site mE1_TFBS_cad

By genomic position
Variant impact
Gene name

cg14380C phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results