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=1.500e^-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_2L_t	0.02206
In_2R_NS	0.03396

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.2841	0.0712

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

57 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	16572540	2L_16572540_SNP [dm3] 2L_16572540_SNP [dm6]	A	C	4.214e^-4	0.287	INTRON CG42389
2L	20321239	2L_20321239_SNP [dm3] 2L_20321239_SNP [dm6]	A	G	4.214e^-4	0.287	INTRON spir
2L	20348382	2L_20348382_SNP [dm3] 2L_20348382_SNP [dm6]	A	T	4.214e^-4	0.287	UTR_3_PRIME spir DOWNSTREAM La
2L	7442026	2L_7442026_MNP [dm3] 2L_7442026_MNP [dm6]	TTC	GGA	4.214e^-4	0.287	INTRON CG5973
2L	9175899	2L_9175899_SNP [dm3] 2L_9175899_SNP [dm6]	G	T	4.214e^-4	0.287	UPSTREAM tai INTRON tai	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2L	9188435	2L_9188435_DEL [dm3] 2L_9188435_DEL [dm6]	TA	T	4.214e^-4	0.287	INTRON tai
2R	18399972	2R_18399972_SNP [dm3] 2R_22512467_SNP [dm6]	T	G	4.214e^-4	0.287	INTRON px	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
2R	18887422	2R_18887422_SNP [dm3] 2R_22999899_SNP [dm6]	G	C	4.214e^-4	0.287	INTRON twi
2R	3374988	2R_3374988_SNP [dm3] 2R_7487483_SNP [dm6]	A	G	4.214e^-4	0.287	INTRON wech	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_Kr
2R	3377790	2R_3377790_SNP [dm3] 2R_7490285_SNP [dm6]	T	A	4.214e^-4	0.287	UPSTREAM wech DOWNSTREAM Coop INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	3377804	2R_3377804_SNP [dm3] 2R_7490299_SNP [dm6]	A	T	4.214e^-4	0.287	UPSTREAM wech DOWNSTREAM Coop INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	6932024	2R_6932024_SNP [dm3] 2R_11044519_SNP [dm6]	G	A	4.214e^-4	0.287	INTRON luna	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2R	7821441	2R_7821441_SNP [dm3] 2R_11933936_SNP [dm6]	C	T	4.214e^-4	0.287	INTERGENIC
3L	11311664	3L_11311664_SNP [dm3] 3L_11318564_SNP [dm6]	G	T	4.214e^-4	0.287	INTERGENIC	TF binding site mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Kr
3L	1854718	3L_1854718_SNP [dm3] 3L_1854718_SNP [dm6]	T	G	4.214e^-4	0.287	UTR_5_PRIME CG13936
3L	19560805	3L_19560805_SNP [dm3] 3L_19567705_SNP [dm6]	G	A	4.214e^-4	0.287	UTR_3_PRIME Shal DOWNSTREAM Shal
3L	20759308	3L_20759308_SNP [dm3] 3L_20766208_SNP [dm6]	T	C	4.214e^-4	0.287	INTERGENIC
3L	6127504	3L_6127504_SNP [dm3] 3L_6134404_SNP [dm6]	T	C	4.214e^-4	0.287	UPSTREAM Lcp65Ag2 DOWNSTREAM Lcp65Ag1 INTERGENIC
3L	7945586	3L_7945586_INS [dm3] 3L_7952486_INS [dm6]	C	CT	4.214e^-4	0.287	DOWNSTREAM exex INTERGENIC	TF binding site mE1_TFBS_cad
3R	11003394	3R_11003394_INS [dm3] 3R_15177672_INS [dm6]	A	AA	4.214e^-4	0.287	UTR_3_PRIME Mf INTRON Gyc88E & 1 other
3R	8811032	3R_8811032_SNP [dm3] 3R_12985310_SNP [dm6]	A	G	4.214e^-4	0.287	UTR_3_PRIME Paip2 UPSTREAM CG31342 DOWNSTREAM Paip2
X	11750839	X_11750839_SNP [dm3] X_11856806_SNP [dm6]	T	A	4.214e^-4	0.287	INTRON ATP7	TF binding site mE1_TFBS_HSA
X	12679515	X_12679515_DEL [dm3] X_12785482_DEL [dm6]	AAACTTATAAAGATTAATAT...	A	4.214e^-4	0.287	UPSTREAM CG32647 DOWNSTREAM Pde9 INTERGENIC	TF binding site mE1_TFBS_kn
X	15289659	X_15289659_SNP [dm3] X_15395626_SNP [dm6]	G	A	4.214e^-4	0.287	INTRON Cngl	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	15289678	X_15289678_SNP [dm3] X_15395645_SNP [dm6]	C	T	4.214e^-4	0.287	INTRON Cngl	TF binding site mE1_TFBS_sbb
X	16413828	X_16413828_INS [dm3] X_16519795_INS [dm6]	G	GGG	4.214e^-4	0.287	INTRON para
X	18130173	X_18130173_SNP [dm3] X_18236140_SNP [dm6]	T	A	4.214e^-4	0.287	INTERGENIC
X	19668673	X_19668673_INS [dm3] X_19774640_INS [dm6]	A	AA	4.214e^-4	0.287	INTRON vfl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens
X	5248145	X_5248145_DEL [dm3] X_5354112_DEL [dm6]	ACA	A	4.214e^-4	0.287	INTRON SK
X	9070407	X_9070407_SNP [dm3] X_9176374_SNP [dm6]	C	A	4.214e^-4	0.287	UTR_3_PRIME mei-P26
2L	16381922	2L_16381922_SNP [dm3] 2L_16381922_SNP [dm6]	G	C	7.605e^-4	0.287	INTERGENIC
2L	7839640	2L_7839640_SNP [dm3] 2L_7839640_SNP [dm6]	G	A	7.605e^-4	0.287	UPSTREAM CG14537 DOWNSTREAM CR43100 INTERGENIC
2L	7839641	2L_7839641_SNP [dm3] 2L_7839641_SNP [dm6]	C	A	7.605e^-4	0.287	UPSTREAM CG14537 DOWNSTREAM CR43100 INTERGENIC
2L	951498	2L_951498_SNP [dm3] 2L_951498_SNP [dm6]	G	A	7.605e^-4	0.287	INTRON CG4341	TF binding site mE1_TFBS_chinmo
2R	10100843	2R_10100843_SNP [dm3] 2R_14213338_SNP [dm6]	A	C	7.605e^-4	0.287	UPSTREAM Sox15 INTERGENIC
2R	10287247	2R_10287247_SNP [dm3] 2R_14399742_SNP [dm6]	T	G	7.605e^-4	0.287	INTERGENIC
2R	11495628	2R_11495628_SNP [dm3] 2R_15608123_SNP [dm6]	C	T	7.605e^-4	0.287	INTERGENIC
2R	14116133	2R_14116133_SNP [dm3] 2R_18228628_SNP [dm6]	G	T	7.605e^-4	0.287	DOWNSTREAM CR45310 EXON CR45311
2R	15377632	2R_15377632_SNP [dm3] 2R_19490127_SNP [dm6]	G	A	7.605e^-4	0.287	SYNONYMOUS_CODING Oseg6
2R	15668500	2R_15668500_INS [dm3] 2R_19780995_INS [dm6]	G	GTAGAC	7.605e^-4	0.287	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	15679356	2R_15679356_SNP [dm3] 2R_19791851_SNP [dm6]	C	A	7.605e^-4	0.287	INTERGENIC
2R	18933657	2R_18933657_SNP [dm3] 2R_23046134_SNP [dm6]	C	T	7.605e^-4	0.287	START_GAINED twi UTR_5_PRIME twi UPSTREAM twi	regulatory region FlyBase REDfly_CRMs silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	7700397	2R_7700397_SNP [dm3] 2R_11812892_SNP [dm6]	A	T	7.605e^-4	0.287	UTR_3_PRIME ths DOWNSTREAM ths
3L	10834562	3L_10834562_SNP [dm3] 3L_10841462_SNP [dm6]	A	C	7.605e^-4	0.287	INTERGENIC	TF binding site BDTNP1_TFBS_da
3L	11771126	3L_11771126_SNP [dm3] 3L_11778026_SNP [dm6]	T	C	7.605e^-4	0.287	INTRON Pi3K68D & 1 other	TF binding site mE1_TFBS_cad
3L	13002729	3L_13002729_SNP [dm3] 3L_13009629_SNP [dm6]	A	G	7.605e^-4	0.287	SYNONYMOUS_CODING CG11261 DOWNSTREAM CG14117
3L	13687363	3L_13687363_SNP [dm3] 3L_13694263_SNP [dm6]	C	T	7.605e^-4	0.287	INTRON bru-3
3L	18052931	3L_18052931_SNP [dm3] 3L_18059831_SNP [dm6]	T	G	7.605e^-4	0.287	UTR_5_PRIME Eip75B UPSTREAM Eip75B
3L	3777227	3L_3777227_DEL [dm3] 3L_3777227_DEL [dm6]	AACAGAGGCGGA...	A	7.605e^-4	0.287	INTRON CG32264
3L	3865027	3L_3865027_SNP [dm3] 3L_3865027_SNP [dm6]	C	G	7.605e^-4	0.287	UPSTREAM CR45379 INTERGENIC
3L	4593366	3L_4593366_SNP [dm3] 3L_4593366_SNP [dm6]	G	T	7.605e^-4	0.287	UTR_3_PRIME Src64B
3L	7405064	3L_7405064_INS [dm3] 3L_7411964_INS [dm6]	G	AT	7.605e^-4	0.287	INTERGENIC
3R	13966217	3R_13966217_SNP [dm3] 3R_18140495_SNP [dm6]	A	C	7.605e^-4	0.287	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	27813328	3R_27813328_SNP [dm3] 3R_31987606_SNP [dm6]	T	A	7.605e^-4	0.287	INTRON CG2003 & 1 other
3R	27887147	3R_27887147_DEL [dm3] 3R_32061425_DEL [dm6]	TGAT	T	7.605e^-4	0.287	INTRON Map205
X	19097764	X_19097764_SNP [dm3] X_19203731_SNP [dm6]	T	C	7.605e^-4	0.287	SYNONYMOUS_CODING Ulp1
X	19098141	X_19098141_SNP [dm3] X_19204108_SNP [dm6]	G	T	7.605e^-4	0.287	SYNONYMOUS_CODING Ulp1

By genomic position
Variant impact
Gene name

TyrRP phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results