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=2.851e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

35 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	3121166	2L_3121166_SNP [dm3] 2L_3121166_SNP [dm6]	G	A	8.909e^-4	0.531	INTRON toc
2L	4811254	2L_4811254_SNP [dm3] 2L_4811254_SNP [dm6]	T	C	8.909e^-4	0.531	DOWNSTREAM CR45297 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_en mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl mE1_TFBS_Ubx mE1_TFBS_zfh1
2L	6549932	2L_6549932_SNP [dm3] 2L_6549932_SNP [dm6]	T	A	8.909e^-4	0.531	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2R	10304536	2R_10304536_SNP [dm3] 2R_14417031_SNP [dm6]	G	T	8.909e^-4	0.531	INTERGENIC
2R	11456147	2R_11456147_SNP [dm3] 2R_15568642_SNP [dm6]	A	T	8.909e^-4	0.531	UPSTREAM CG30466 DOWNSTREAM Cdk5 INTRON Flo1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA
2R	13833804	2R_13833804_SNP [dm3] 2R_17946299_SNP [dm6]	G	A	8.909e^-4	0.531	INTERGENIC
2R	1410778	2R_1410778_SNP [dm3] 2R_5523273_SNP [dm6]	C	A	8.909e^-4	0.531	INTRON CG30438	transposable element FlyBase
2R	14331739	2R_14331739_SNP [dm3] 2R_18444234_SNP [dm6]	G	C	8.909e^-4	0.531	INTRON slim
2R	15280962	2R_15280962_SNP [dm3] 2R_19393457_SNP [dm6]	G	A	8.909e^-4	0.531	SYNONYMOUS_CODING SdhA	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	17305364	2R_17305364_INS [dm3] 2R_21417859_INS [dm6]	A	ACA	8.909e^-4	0.531	UPSTREAM Sdc INTRON Sdc
2R	17311801	2R_17311801_SNP [dm3] 2R_21424296_SNP [dm6]	A	G	8.909e^-4	0.531	INTRON Sdc
2R	18554560	2R_18554560_SNP [dm3] 2R_22667055_SNP [dm6]	A	C	8.909e^-4	0.531	UPSTREAM CG30273 & 2 others DOWNSTREAM CG42867 & 1 other INTERGENIC	TF binding site mE1_TFBS_cad
2R	18883206	2R_18883206_SNP [dm3] 2R_22995683_SNP [dm6]	C	A	8.909e^-4	0.531	INTRON twi & 1 other
2R	19901920	2R_19901920_SNP [dm3] 2R_24014397_SNP [dm6]	T	G	8.909e^-4	0.531	UPSTREAM Unc-89 DOWNSTREAM CG4324 INTERGENIC
2R	2784153	2R_2784153_SNP [dm3] 2R_6896648_SNP [dm6]	T	C	8.909e^-4	0.531	INTRON CG30158	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	5567018	2R_5567018_SNP [dm3] 2R_9679513_SNP [dm6]	T	C	8.909e^-4	0.531	INTRON Mmp2
2R	6867164	2R_6867164_SNP [dm3] 2R_10979659_SNP [dm6]	A	T	8.909e^-4	0.531	UTR_3_PRIME luna
2R	9046809	2R_9046809_SNP [dm3] 2R_13159304_SNP [dm6]	G	T	8.909e^-4	0.531	UPSTREAM TppII & 1 other INTRON CG34439	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13839176	3L_13839176_SNP [dm3] 3L_13846076_SNP [dm6]	G	A	8.909e^-4	0.531	UTR_5_PRIME Hml DOWNSTREAM Tsp68C	TF binding site mE1_TFBS_bab1
3L	13953935	3L_13953935_SNP [dm3] 3L_13960835_SNP [dm6]	A	C	8.909e^-4	0.531	INTRON CG32137
3L	14105191	3L_14105191_SNP [dm3] 3L_14112091_SNP [dm6]	A	C	8.909e^-4	0.531	DOWNSTREAM Sox21b INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_zfh1
3L	1754577	3L_1754577_SNP [dm3] 3L_1754577_SNP [dm6]	C	T	8.909e^-4	0.531	UTR_5_PRIME Cht2 INTRON Cht2
3L	17736192	3L_17736192_SNP [dm3] 3L_17743092_SNP [dm6]	G	C	8.909e^-4	0.531	DOWNSTREAM CG7460 INTRON Ccn
3L	17736200	3L_17736200_SNP [dm3] 3L_17743100_SNP [dm6]	A	C	8.909e^-4	0.531	DOWNSTREAM CG7460 INTRON Ccn
3L	1927755	3L_1927755_SNP [dm3] 3L_1927755_SNP [dm6]	G	T	8.909e^-4	0.531	INTRON Dbx	TF binding site mE1_TFBS_chinmo
3L	2838159	3L_2838159_SNP [dm3] 3L_2838159_SNP [dm6]	A	T	8.909e^-4	0.531	INTRON CG43444
3L	4503344	3L_4503344_SNP [dm3] 3L_4503344_SNP [dm6]	A	G	8.909e^-4	0.531	SYNONYMOUS_CODING NT1 DOWNSTREAM NT1
3L	5407565	3L_5407565_SNP [dm3] 3L_5414465_SNP [dm6]	C	A	8.909e^-4	0.531	INTERGENIC
3L	762561	3L_762561_SNP [dm3] 3L_762561_SNP [dm6]	A	G	8.909e^-4	0.531	INTERGENIC	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_eve mE1_TFBS_HSA mE1_TFBS_sens
3L	7841292	3L_7841292_SNP [dm3] 3L_7848192_SNP [dm6]	G	A	8.909e^-4	0.531	INTRON Pdp1	regulatory region REDfly_CRMs TF binding site mE1_TFBS_Trl
X	16861279	X_16861279_SNP [dm3] X_16967246_SNP [dm6]	C	T	8.909e^-4	0.531	INTRON CG9086	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_zfh1
X	21875578	X_21875578_SNP [dm3] X_22473742_SNP [dm6]	G	A	8.909e^-4	0.531	UTR_5_PRIME CG14618	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
X	2932500	X_2932500_SNP [dm3] X_3038467_SNP [dm6]	C	A	8.909e^-4	0.531	INTRON kirre
X	8837993	X_8837993_SNP [dm3] X_8943960_SNP [dm6]	G	A	8.909e^-4	0.531	INTRON rdgA
X	9684790	X_9684790_SNP [dm3] X_9790757_SNP [dm6]	C	A	8.909e^-4	0.531	INTRON CG32698	TF binding site BDTNP1_TFBS_twi

By genomic position
Variant impact
Gene name

Interaction_Estimate phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results