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=4.911e^-6)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT 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	0.01292
In_2L_t	0.06027

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2226 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
3L	23033953	3L_23033953_SNP [dm3] 3L_23040853_SNP [dm6]	T	A	2.001e^-6	0.832	DOWNSTREAM nrm INTERGENIC
3L	4377238	3L_4377238_SNP [dm3] 3L_4377238_SNP [dm6]	A	T	2.789e^-6	0.832	DOWNSTREAM CR44360 INTRON DopEcR
3R	25210851	3R_25210851_SNP [dm3] 3R_29385129_SNP [dm6]	C	A	2.929e^-6	0.832	INTRON Ptp99A
X	13351507	X_13351507_SNP [dm3] X_13457474_SNP [dm6]	T	C	3.108e^-6	0.832	NON_SYNONYMOUS_CODING CG34324 INTRON Neto
3R	21311871	3R_21311871_SNP [dm3] 3R_25486149_SNP [dm6]	C	T	3.541e^-6	0.832	UTR_3_PRIME Dhap-at DOWNSTREAM CG42488 & 1 other	TF binding site mE1_TFBS_cad
3R	9884122	3R_9884122_SNP [dm3] 3R_14058400_SNP [dm6]	A	C	4.073e^-6	0.832	INTRON foxo
3L	23141225	3L_23141225_SNP [dm3] 3L_23148125_SNP [dm6]	C	T	4.249e^-6	0.832	NON_SYNONYMOUS_CODING CG32350
3L	5523009	3L_5523009_SNP [dm3] 3L_5529909_SNP [dm6]	A	T	4.498e^-6	0.832	UPSTREAM Lkr INTERGENIC
3R	11543653	3R_11543653_SNP [dm3] 3R_15717931_SNP [dm6]	G	C	5.033e^-6	0.832	INTERGENIC
2L	16782112	2L_16782112_SNP [dm3] 2L_16782112_SNP [dm6]	T	C	5.789e^-6	0.832	INTRON Mhc	TF binding site mE1_TFBS_chinmo
2L	16782062	2L_16782062_SNP [dm3] 2L_16782062_SNP [dm6]	G	A	6.629e^-6	0.832	INTRON Mhc	TF binding site mE1_TFBS_chinmo
3R	25210781	3R_25210781_SNP [dm3] 3R_29385059_SNP [dm6]	C	T	7.040e^-6	0.832	INTRON Ptp99A
2L	16781974	2L_16781974_DEL [dm3] 2L_16781974_DEL [dm6]	GG	A	7.463e^-6	0.832	INTRON Mhc	TF binding site mE1_TFBS_chinmo
3R	21486240	3R_21486240_SNP [dm3] 3R_25660518_SNP [dm6]	G	A	8.566e^-6	0.832	INTRON Tnks	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	25210808	3R_25210808_INS [dm3] 3R_29385086_INS [dm6]	C	CACC	8.870e^-6	0.832	INTRON Ptp99A
3L	8675181	3L_8675181_SNP [dm3] 3L_8682081_SNP [dm6]	G	A	9.487e^-6	0.832	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
2L	16782103	2L_16782103_SNP [dm3] 2L_16782103_SNP [dm6]	T	A	9.886e^-6	0.832	INTRON Mhc	TF binding site mE1_TFBS_chinmo
3L	18819641	3L_18819641_SNP [dm3] 3L_18826541_SNP [dm6]	T	C	9.940e^-6	0.832	SYNONYMOUS_CODING Cat	TF binding site mE1_TFBS_chinmo
3L	4700971	3L_4700971_SNP [dm3] 3L_4700971_SNP [dm6]	C	A	1.037e^-5	0.832	INTRON RhoGEF64C
3R	5443035	3R_5443035_SNP [dm3] 3R_9617313_SNP [dm6]	A	G	1.044e^-5	0.832	INTRON CG8312
3R	5366433	3R_5366433_SNP [dm3] 3R_9540711_SNP [dm6]	A	T	1.047e^-5	0.832	SYNONYMOUS_CODING mura	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	10930521	3L_10930521_DEL [dm3] 3L_10937421_DEL [dm6]	AAG	A	1.172e^-5	0.832	INTERGENIC
3L	10930525	3L_10930525_INS [dm3] 3L_10937425_INS [dm6]	T	TAATTAA	1.172e^-5	0.832	INTERGENIC
3L	5771288	3L_5771288_SNP [dm3] 3L_5778188_SNP [dm6]	A	G	1.227e^-5	0.832	SYNONYMOUS_CODING Myt1 UPSTREAM vito
3L	17909708	3L_17909708_SNP [dm3] 3L_17916608_SNP [dm6]	A	G	1.287e^-5	0.832	INTERGENIC
3L	9777329	3L_9777329_SNP [dm3] 3L_9784229_SNP [dm6]	T	G	1.515e^-5	0.832	SYNONYMOUS_CODING CG8177	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	4880023	2L_4880023_SNP [dm3] 2L_4880023_SNP [dm6]	G	A	1.534e^-5	0.832	INTRON Cf2
3L	4377231	3L_4377231_SNP [dm3] 3L_4377231_SNP [dm6]	G	A	1.546e^-5	0.832	DOWNSTREAM CR44360 INTRON DopEcR
2L	3388550	2L_3388550_SNP [dm3] 2L_3388550_SNP [dm6]	T	G	1.596e^-5	0.832	UPSTREAM Sfp23F & 2 others INTERGENIC
3L	12612853	3L_12612853_SNP [dm3] 3L_12619753_SNP [dm6]	A	C	1.615e^-5	0.832	SYNONYMOUS_CODING caup	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	4377232	3L_4377232_SNP [dm3] 3L_4377232_SNP [dm6]	C	A	1.730e^-5	0.832	DOWNSTREAM CR44360 INTRON DopEcR
3L	23048784	3L_23048784_SNP [dm3] 3L_23055684_SNP [dm6]	T	C	1.833e^-5	0.832	INTERGENIC
3L	4701038	3L_4701038_SNP [dm3] 3L_4701038_SNP [dm6]	C	A	1.844e^-5	0.832	INTRON RhoGEF64C
3R	11543738	3R_11543738_SNP [dm3] 3R_15718016_SNP [dm6]	C	T	1.857e^-5	0.832	INTERGENIC
3R	10373679	3R_10373679_SNP [dm3] 3R_14547957_SNP [dm6]	C	G	1.903e^-5	0.832	INTRON Pde6
3L	4709865	3L_4709865_SNP [dm3] 3L_4709865_SNP [dm6]	T	C	2.018e^-5	0.832	UTR_5_PRIME CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4709870	3L_4709870_SNP [dm3] 3L_4709870_SNP [dm6]	A	C	2.018e^-5	0.832	UTR_5_PRIME CG13712 INTRON RhoGEF64C	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	16782100	2L_16782100_SNP [dm3] 2L_16782100_SNP [dm6]	A	C	2.085e^-5	0.832	INTRON Mhc	TF binding site mE1_TFBS_chinmo
2L	7209272	2L_7209272_SNP [dm3] 2L_7209272_SNP [dm6]	T	A	2.120e^-5	0.832	INTRON CG13784
X	2698884	X_2698884_SNP [dm3] X_2804851_SNP [dm6]	A	C	2.189e^-5	0.832	INTRON kirre	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	14141249	2R_14141249_SNP [dm3] 2R_18253744_SNP [dm6]	C	T	2.271e^-5	0.832	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	18364980	3L_18364980_SNP [dm3] 3L_18371880_SNP [dm6]	C	T	2.312e^-5	0.832	INTERGENIC
3R	21681629	3R_21681629_SNP [dm3] 3R_25855907_SNP [dm6]	C	G	2.330e^-5	0.832	UPSTREAM CG5890 INTERGENIC
2L	4505507	2L_4505507_SNP [dm3] 2L_4505507_SNP [dm6]	G	A	2.382e^-5	0.832	SYNONYMOUS_CODING dp INTRON dp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3L	7533468	3L_7533468_SNP [dm3] 3L_7540368_SNP [dm6]	T	C	2.429e^-5	0.832	SYNONYMOUS_CODING CG32374 UPSTREAM CG16998 DOWNSTREAM lqf
3L	7330950	3L_7330950_SNP [dm3] 3L_7337850_SNP [dm6]	T	C	2.436e^-5	0.832	NON_SYNONYMOUS_CODING eco	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	12818569	2R_12818569_SNP [dm3] 2R_16931064_SNP [dm6]	T	C	2.524e^-5	0.832	INTRON Pkc53E
3R	24205174	3R_24205174_SNP [dm3] 3R_28379452_SNP [dm6]	A	G	2.579e^-5	0.832	INTERGENIC
3R	21681620	3R_21681620_SNP [dm3] 3R_25855898_SNP [dm6]	A	G	2.589e^-5	0.832	UPSTREAM CG5890 INTERGENIC
2R	16090909	2R_16090909_SNP [dm3] 2R_20203404_SNP [dm6]	C	A	2.621e^-5	0.832	INTERGENIC
3L	16137545	3L_16137545_SNP [dm3] 3L_16144445_SNP [dm6]	A	C	2.627e^-5	0.832	UPSTREAM CG5151 & 1 other INTRON CG5151
3L	990355	3L_990355_SNP [dm3] 3L_990355_SNP [dm6]	A	C	2.641e^-5	0.832	SYNONYMOUS_CODING Glut1 UTR_3_PRIME Glut1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	21681623	3R_21681623_SNP [dm3] 3R_25855901_SNP [dm6]	T	C	2.663e^-5	0.832	UPSTREAM CG5890 INTERGENIC
2L	8262214	2L_8262214_SNP [dm3] 2L_8262214_SNP [dm6]	G	A	2.667e^-5	0.832	SYNONYMOUS_CODING Btk29A
3L	15055734	3L_15055734_SNP [dm3] 3L_15062634_SNP [dm6]	T	C	2.714e^-5	0.832	UPSTREAM CG13460 & 1 other INTRON Sytbeta
3L	7331186	3L_7331186_SNP [dm3] 3L_7338086_SNP [dm6]	C	T	2.757e^-5	0.832	NON_SYNONYMOUS_CODING eco	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	12538816	3L_12538816_SNP [dm3] 3L_12545716_SNP [dm6]	T	C	2.958e^-5	0.832	INTRON sowah
3R	5648003	3R_5648003_SNP [dm3] 3R_9822281_SNP [dm6]	A	G	2.974e^-5	0.832	DOWNSTREAM CG34302 INTERGENIC
3L	23115613	3L_23115613_SNP [dm3] 3L_23122513_SNP [dm6]	G	A	3.089e^-5	0.832	INTERGENIC	transposable element FlyBase
2L	15627004	2L_15627004_SNP [dm3] 2L_15627004_SNP [dm6]	A	G	3.273e^-5	0.832	INTERGENIC
2L	10521858	2L_10521858_SNP [dm3] 2L_10521858_SNP [dm6]	T	C	3.356e^-5	0.832	INTERGENIC
2L	13313637	2L_13313637_SNP [dm3] 2L_13313637_SNP [dm6]	C	A	3.366e^-5	0.832	INTRON CG43778	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	13113053	X_13113053_SNP [dm3] X_13219020_SNP [dm6]	G	T	3.389e^-5	0.832	INTRON mew
3R	17618570	3R_17618570_SNP [dm3] 3R_21792848_SNP [dm6]	A	G	3.422e^-5	0.832	INTRON CASK	TF binding site mE1_TFBS_cad
2R	14303713	2R_14303713_SNP [dm3] 2R_18416208_SNP [dm6]	G	C	3.448e^-5	0.832	SYNONYMOUS_CODING Dp1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	12391762	X_12391762_SNP [dm3] X_12497729_SNP [dm6]	T	G	3.532e^-5	0.832	INTRON CG2556 EXON snoRNA:Me18S-G894
2L	5502830	2L_5502830_SNP [dm3] 2L_5502830_SNP [dm6]	A	G	3.567e^-5	0.832	INTERGENIC
3L	17027644	3L_17027644_SNP [dm3] 3L_17034544_SNP [dm6]	G	A	3.584e^-5	0.832	UPSTREAM CR43250 INTERGENIC
3L	995863	3L_995863_SNP [dm3] 3L_995863_SNP [dm6]	G	T	3.671e^-5	0.832	DOWNSTREAM trio & 1 other INTERGENIC
3L	23148368	3L_23148368_SNP [dm3] 3L_23155268_SNP [dm6]	A	C	3.697e^-5	0.832	INTERGENIC	transposable element FlyBase
2R	18078525	2R_18078525_SNP [dm3] 2R_22191020_SNP [dm6]	C	A	3.712e^-5	0.832	SYNONYMOUS_CODING Swim	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	16293730	2L_16293730_SNP [dm3] 2L_16293730_SNP [dm6]	A	T	3.726e^-5	0.832	UPSTREAM CG13258 & 2 others INTERGENIC
3L	15943355	3L_15943355_SNP [dm3] 3L_15950255_SNP [dm6]	G	A	3.847e^-5	0.832	INTRON Pka-C3
3R	16233661	3R_16233661_SNP [dm3] 3R_20407939_SNP [dm6]	A	G	3.876e^-5	0.832	UPSTREAM CG10881 & 1 other INTRON Gfrl
3R	5651025	3R_5651025_SNP [dm3] 3R_9825303_SNP [dm6]	C	G	3.877e^-5	0.832	UPSTREAM CR42858 DOWNSTREAM Teh1 INTERGENIC	TF binding site mE1_TFBS_cad
3R	11006745	3R_11006745_SNP [dm3] 3R_15181023_SNP [dm6]	G	C	3.884e^-5	0.832	UPSTREAM Mf INTRON Gyc88E & 1 other
3R	7520788	3R_7520788_SNP [dm3] 3R_11695066_SNP [dm6]	G	A	3.979e^-5	0.832	UPSTREAM Fer3 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
3L	2680513	3L_2680513_SNP [dm3] 3L_2680513_SNP [dm6]	A	C	4.002e^-5	0.832	INTRON Fife
2R	9330075	2R_9330075_SNP [dm3] 2R_13442570_SNP [dm6]	A	G	4.067e^-5	0.832	DOWNSTREAM cnn INTRON cnn	TF binding site mE1_TFBS_cad
3L	23019124	3L_23019124_SNP [dm3] 3L_23026024_SNP [dm6]	T	A	4.178e^-5	0.832	NON_SYNONYMOUS_CODING nrm INTRON nrm	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	13439981	2L_13439981_SNP [dm3] 2L_13439981_SNP [dm6]	C	T	4.218e^-5	0.832	DOWNSTREAM Tehao INTRON CG42784 EXON CR45683
3L	4701112	3L_4701112_SNP [dm3] 3L_4701112_SNP [dm6]	T	C	4.225e^-5	0.832	INTRON RhoGEF64C
X	12090730	X_12090730_SNP [dm3] X_12196697_SNP [dm6]	T	A	4.264e^-5	0.832	INTRON Ten-a
3R	15363310	3R_15363310_SNP [dm3] 3R_19537588_SNP [dm6]	G	A	4.285e^-5	0.832	INTRON Dys
3L	18240799	3L_18240799_SNP [dm3] 3L_18247699_SNP [dm6]	C	T	4.301e^-5	0.832	INTERGENIC
2L	15617846	2L_15617846_SNP [dm3] 2L_15617846_SNP [dm6]	T	C	4.302e^-5	0.832	UTR_3_PRIME CG11865
3R	16176619	3R_16176619_SNP [dm3] 3R_20350897_SNP [dm6]	T	G	4.331e^-5	0.832	INTERGENIC
X	17394889	X_17394889_SNP [dm3] X_17500856_SNP [dm6]	A	T	4.419e^-5	0.832	INTRON CG43658
2R	10228102	2R_10228102_INS [dm3] 2R_14340597_INS [dm6]	A	ACCCCTGCGAA...	4.441e^-5	0.832	INTRON Shroom
3L	12538817	3L_12538817_SNP [dm3] 3L_12545717_SNP [dm6]	C	T	4.471e^-5	0.832	INTRON sowah
3R	11596080	3R_11596080_SNP [dm3] 3R_15770358_SNP [dm6]	A	T	4.627e^-5	0.832	INTERGENIC
3L	995306	3L_995306_SNP [dm3] 3L_995306_SNP [dm6]	A	C	4.721e^-5	0.832	SYNONYMOUS_CODING CG12038 DOWNSTREAM trio	TF binding site mE1_TFBS_cad
2R	8294112	2R_8294112_SNP [dm3] 2R_12406607_SNP [dm6]	T	C	4.731e^-5	0.832	UTR_3_PRIME Cpr49Af DOWNSTREAM Cpr49Af
X	14685801	X_14685801_SNP [dm3] X_14791768_SNP [dm6]	C	T	4.772e^-5	0.832	NON_SYNONYMOUS_CODING rut INTRON rut	TF binding site mE1_TFBS_chinmo
3L	17909009	3L_17909009_SNP [dm3] 3L_17915909_SNP [dm6]	A	T	4.865e^-5	0.832	INTERGENIC	transposable element FlyBase
3L	17909057	3L_17909057_SNP [dm3] 3L_17915957_SNP [dm6]	G	A	4.865e^-5	0.832	INTERGENIC	transposable element FlyBase
3L	17244979	3L_17244979_SNP [dm3] 3L_17251879_SNP [dm6]	T	C	4.924e^-5	0.832	DOWNSTREAM CG6497 INTRON CR43870
2R	12968077	2R_12968077_SNP [dm3] 2R_17080572_SNP [dm6]	G	A	4.979e^-5	0.832	INTRON CG30460
3L	5523021	3L_5523021_SNP [dm3] 3L_5529921_SNP [dm6]	C	T	5.000e^-5	0.832	UPSTREAM Lkr INTERGENIC
3R	9883898	3R_9883898_DEL [dm3] 3R_14058176_DEL [dm6]	CTAAATTCGATTCGAATCTA...	C	5.023e^-5	0.832	INTRON foxo

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By genomic position
Variant impact
Gene name

idx_Surv_10MeHg_CAFF phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results