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=3.037e^-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

2299 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
X	467798	X_467798_SNP [dm3] X_573765_SNP [dm6]	A	T	3.988e^-6	0.657	INTRON Appl
2L	5887991	2L_5887991_SNP [dm3] 2L_5887991_SNP [dm6]	A	G	5.516e^-6	0.657	UPSTREAM CR44578 & 1 other INTERGENIC
3L	4510693	3L_4510693_SNP [dm3] 3L_4510693_SNP [dm6]	A	C	5.880e^-6	0.657	DOWNSTREAM Tie INTERGENIC
X	19037553	X_19037553_SNP [dm3] X_19143520_SNP [dm6]	A	C	6.092e^-6	0.657	UTR_3_PRIME RhoGAP18B
2L	6958889	2L_6958889_SNP [dm3] 2L_6958889_SNP [dm6]	T	C	6.430e^-6	0.657	SYNONYMOUS_CODING CG3430 DOWNSTREAM Atac1
3R	7089271	3R_7089271_DEL [dm3] 3R_11263549_DEL [dm6]	CT	C	6.526e^-6	0.657	INTERGENIC
2L	8737357	2L_8737357_SNP [dm3] 2L_8737357_SNP [dm6]	A	T	6.820e^-6	0.657	INTRON raw
3R	7089275	3R_7089275_DEL [dm3] 3R_11263553_DEL [dm6]	GCCCCGCACCATGATTTCAG...	G	7.521e^-6	0.657	INTERGENIC
3L	8598259	3L_8598259_SNP [dm3] 3L_8605159_SNP [dm6]	C	T	7.793e^-6	0.657	INTRON CG6282	TF binding site BDTNP1_TFBS_dl
3R	16616922	3R_16616922_SNP [dm3] 3R_20791200_SNP [dm6]	C	T	8.397e^-6	0.657	INTRON Syp
3L	4511269	3L_4511269_SNP [dm3] 3L_4511269_SNP [dm6]	A	G	8.456e^-6	0.657	SYNONYMOUS_CODING Tie	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
2R	14138975	2R_14138975_SNP [dm3] 2R_18251470_SNP [dm6]	C	G	8.470e^-6	0.657	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	7855979	3R_7855979_SNP [dm3] 3R_12030257_SNP [dm6]	T	G	8.785e^-6	0.657	SYNONYMOUS_CODING CG31358 UTR_5_PRIME CG42505 & 1 other
3L	4510654	3L_4510654_SNP [dm3] 3L_4510654_SNP [dm6]	T	A	9.650e^-6	0.657	DOWNSTREAM Tie INTERGENIC
3L	4511272	3L_4511272_SNP [dm3] 3L_4511272_SNP [dm6]	G	A	9.762e^-6	0.657	SYNONYMOUS_CODING Tie	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
3L	15763843	3L_15763843_SNP [dm3] 3L_15770743_SNP [dm6]	C	T	9.986e^-6	0.657	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	19259131	X_19259131_SNP [dm3] X_19365098_SNP [dm6]	C	T	1.021e^-5	0.657	INTRON kek5
2R	16992686	2R_16992686_SNP [dm3] 2R_21105181_SNP [dm6]	T	G	1.025e^-5	0.657	INTRON ktub	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	465935	X_465935_SNP [dm3] X_571902_SNP [dm6]	G	A	1.057e^-5	0.657	SYNONYMOUS_CODING Appl	TF binding site mE1_TFBS_sens
2R	14138980	2R_14138980_SNP [dm3] 2R_18251475_SNP [dm6]	T	A	1.066e^-5	0.657	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	468920	X_468920_SNP [dm3] X_574887_SNP [dm6]	T	A	1.091e^-5	0.657	INTRON Appl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
3R	7821876	3R_7821876_SNP [dm3] 3R_11996154_SNP [dm6]	A	T	1.128e^-5	0.657	INTRON Tk
3R	7833573	3R_7833573_SNP [dm3] 3R_12007851_SNP [dm6]	T	C	1.128e^-5	0.657	UTR_3_PRIME KLHL18 DOWNSTREAM KLHL18
3R	7833808	3R_7833808_SNP [dm3] 3R_12008086_SNP [dm6]	C	A	1.128e^-5	0.657	DOWNSTREAM KLHL18 INTRON KLHL18
3R	7847530	3R_7847530_SNP [dm3] 3R_12021808_SNP [dm6]	A	G	1.139e^-5	0.657	INTERGENIC
3R	7856485	3R_7856485_SNP [dm3] 3R_12030763_SNP [dm6]	A	C	1.139e^-5	0.657	INTRON CG31358 & 2 others
3R	7878994	3R_7878994_SNP [dm3] 3R_12053272_SNP [dm6]	A	T	1.139e^-5	0.657	INTERGENIC
3R	7882462	3R_7882462_SNP [dm3] 3R_12056740_SNP [dm6]	C	T	1.139e^-5	0.657	INTERGENIC
2R	17153259	2R_17153259_SNP [dm3] 2R_21265754_SNP [dm6]	A	G	1.159e^-5	0.657	SYNONYMOUS_CODING CG30391 DOWNSTREAM CG30393 INTRON Rgk3
3L	4510450	3L_4510450_SNP [dm3] 3L_4510450_SNP [dm6]	T	C	1.175e^-5	0.657	DOWNSTREAM Tie INTERGENIC
3R	7827966	3R_7827966_SNP [dm3] 3R_12002244_SNP [dm6]	A	G	1.203e^-5	0.657	INTRON Tk & 1 other
3R	7841534	3R_7841534_SNP [dm3] 3R_12015812_SNP [dm6]	G	A	1.213e^-5	0.657	SYNONYMOUS_CODING CG3313 DOWNSTREAM GCC185	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3R	7856690	3R_7856690_SNP [dm3] 3R_12030968_SNP [dm6]	C	G	1.214e^-5	0.657	INTRON CG31358 & 2 others
2R	9240476	2R_9240476_SNP [dm3] 2R_13352971_SNP [dm6]	A	G	1.252e^-5	0.657	DOWNSTREAM CG17048 INTRON CR44206
3L	10839515	3L_10839515_SNP [dm3] 3L_10846415_SNP [dm6]	A	C	1.288e^-5	0.657	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Kr mE1_TFBS_Trl
3L	8598288	3L_8598288_SNP [dm3] 3L_8605188_SNP [dm6]	A	G	1.310e^-5	0.657	INTRON CG6282	TF binding site BDTNP1_TFBS_dl
3R	12493888	3R_12493888_SNP [dm3] 3R_16668166_SNP [dm6]	T	G	1.344e^-5	0.657	INTRON Ubx	TF binding site mE1_TFBS_HSA
3R	7865038	3R_7865038_SNP [dm3] 3R_12039316_SNP [dm6]	A	G	1.373e^-5	0.657	INTERGENIC
2L	8507662	2L_8507662_SNP [dm3] 2L_8507662_SNP [dm6]	A	T	1.390e^-5	0.657	UPSTREAM Dh31 INTERGENIC
X	468919	X_468919_SNP [dm3] X_574886_SNP [dm6]	C	T	1.402e^-5	0.657	SPLICE_SITE_REGION Appl INTRON Appl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
2R	11416864	2R_11416864_SNP [dm3] 2R_15529359_SNP [dm6]	A	T	1.592e^-5	0.696	INTRON Khc-73	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	10789201	3L_10789201_SNP [dm3] 3L_10796101_SNP [dm6]	C	G	1.603e^-5	0.696	DOWNSTREAM CR44546 INTERGENIC
2L	4044015	2L_4044015_SNP [dm3] 2L_4044015_SNP [dm6]	C	G	1.697e^-5	0.696	INTRON ed
3L	4510169	3L_4510169_SNP [dm3] 3L_4510169_SNP [dm6]	A	T	1.758e^-5	0.696	DOWNSTREAM Tie INTERGENIC
3R	14320182	3R_14320182_SNP [dm3] 3R_18494460_SNP [dm6]	C	T	1.766e^-5	0.696	INTRON fru
2L	16126312	2L_16126312_SNP [dm3] 2L_16126312_SNP [dm6]	T	G	1.815e^-5	0.696	INTERGENIC
2R	10631248	2R_10631248_SNP [dm3] 2R_14743743_SNP [dm6]	A	G	1.815e^-5	0.696	INTRON CG12858	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	12145182	2L_12145182_SNP [dm3] 2L_12145182_SNP [dm6]	A	G	1.823e^-5	0.696	UTR_5_PRIME CG31760
3L	4178234	3L_4178234_SNP [dm3] 3L_4178234_SNP [dm6]	G	T	1.914e^-5	0.696	UTR_5_PRIME Teh4 DOWNSTREAM Teh2 INTRON CG18675
3L	10839701	3L_10839701_SNP [dm3] 3L_10846601_SNP [dm6]	G	A	1.933e^-5	0.696	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_Kr
3R	10138932	3R_10138932_SNP [dm3] 3R_14313210_SNP [dm6]	G	A	1.944e^-5	0.696	SYNONYMOUS_CODING CG31321
3L	4510237	3L_4510237_SNP [dm3] 3L_4510237_SNP [dm6]	A	C	1.961e^-5	0.696	DOWNSTREAM Tie INTERGENIC
2L	10207344	2L_10207344_SNP [dm3] 2L_10207344_SNP [dm6]	T	A	2.019e^-5	0.696	SYNONYMOUS_CODING CG5731 UPSTREAM CG5734	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_ttk
X	3319195	X_3319195_DEL [dm3] X_3425162_DEL [dm6]	CGAAA	C	2.071e^-5	0.696	INTRON CR44999 & 1 other
3L	4178141	3L_4178141_SNP [dm3] 3L_4178141_SNP [dm6]	A	T	2.084e^-5	0.696	UTR_5_PRIME Teh4 DOWNSTREAM Teh2 INTRON CG18675
2L	5087615	2L_5087615_SNP [dm3] 2L_5087615_SNP [dm6]	C	G	2.084e^-5	0.696	INTRON pgant5
3L	4178215	3L_4178215_SNP [dm3] 3L_4178215_SNP [dm6]	G	A	2.189e^-5	0.696	UTR_5_PRIME Teh4 DOWNSTREAM Teh2 INTRON CG18675
3L	13122446	3L_13122446_SNP [dm3] 3L_13129346_SNP [dm6]	G	C	2.275e^-5	0.696	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	12699380	2L_12699380_SNP [dm3] 2L_12699380_SNP [dm6]	G	A	2.295e^-5	0.696	SYNONYMOUS_CODING CG17036 DOWNSTREAM PICK1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
3R	14643332	3R_14643332_SNP [dm3] 3R_18817610_SNP [dm6]	C	G	2.405e^-5	0.696	INTRON CG18208
3R	22882230	3R_22882230_SNP [dm3] 3R_27056508_SNP [dm6]	T	C	2.431e^-5	0.696	INTRON RYa-R	TF binding site mE1_TFBS_inv
X	19259130	X_19259130_SNP [dm3] X_19365097_SNP [dm6]	A	G	2.448e^-5	0.696	INTRON kek5
3L	10839517	3L_10839517_SNP [dm3] 3L_10846417_SNP [dm6]	C	G	2.486e^-5	0.696	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Kr mE1_TFBS_Trl
3L	4113673	3L_4113673_SNP [dm3] 3L_4113673_SNP [dm6]	A	G	2.506e^-5	0.696	SYNONYMOUS_CODING Ack DOWNSTREAM Chd64	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	12134359	2L_12134359_SNP [dm3] 2L_12134359_SNP [dm6]	C	T	2.520e^-5	0.696	UPSTREAM rho-6 INTERGENIC	TF binding site mE1_TFBS_Trl
3L	4510651	3L_4510651_SNP [dm3] 3L_4510651_SNP [dm6]	A	G	2.544e^-5	0.696	DOWNSTREAM Tie INTERGENIC
3R	21520393	3R_21520393_SNP [dm3] 3R_25694671_SNP [dm6]	A	G	2.546e^-5	0.696	INTERGENIC
2R	15699384	2R_15699384_SNP [dm3] 2R_19811879_SNP [dm6]	G	A	2.565e^-5	0.696	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	9687286	3R_9687286_SNP [dm3] 3R_13861564_SNP [dm6]	A	G	2.582e^-5	0.696	INTERGENIC
3L	14722708	3L_14722708_SNP [dm3] 3L_14729608_SNP [dm6]	C	T	2.624e^-5	0.696	DOWNSTREAM CG13473 INTRON ome
3L	7904086	3L_7904086_SNP [dm3] 3L_7910986_SNP [dm6]	A	T	2.686e^-5	0.696	INTRON pbl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	7872565	3R_7872565_SNP [dm3] 3R_12046843_SNP [dm6]	G	A	2.690e^-5	0.696	INTERGENIC
2L	6187849	2L_6187849_SNP [dm3] 2L_6187849_SNP [dm6]	C	A	2.798e^-5	0.696	INTRON CG34380	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
X	21934277	X_21934277_SNP [dm3] X_22532441_SNP [dm6]	T	C	2.930e^-5	0.696	SYNONYMOUS_CODING S6kII INTRON CG17600
3R	16324107	3R_16324107_SNP [dm3] 3R_20498385_SNP [dm6]	C	T	3.001e^-5	0.696	INTERGENIC
3L	4510079	3L_4510079_SNP [dm3] 3L_4510079_SNP [dm6]	A	T	3.037e^-5	0.696	DOWNSTREAM Tie INTERGENIC
3R	22882499	3R_22882499_SNP [dm3] 3R_27056777_SNP [dm6]	G	A	3.069e^-5	0.696	SPLICE_SITE_REGION RYa-R INTRON RYa-R	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	10839419	3L_10839419_SNP [dm3] 3L_10846319_SNP [dm6]	A	G	3.107e^-5	0.696	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
2R	10135727	2R_10135727_SNP [dm3] 2R_14248222_SNP [dm6]	C	A	3.126e^-5	0.696	SYNONYMOUS_CODING Mdr50
3L	4178099	3L_4178099_SNP [dm3] 3L_4178099_SNP [dm6]	T	C	3.129e^-5	0.696	UTR_5_PRIME Teh4 DOWNSTREAM Teh2 INTRON CG18675
3L	10839718	3L_10839718_SNP [dm3] 3L_10846618_SNP [dm6]	T	G	3.151e^-5	0.696	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_Kr
3R	18808791	3R_18808791_SNP [dm3] 3R_22983069_SNP [dm6]	G	A	3.200e^-5	0.696	SYNONYMOUS_CODING Nha2
3R	7876476	3R_7876476_SNP [dm3] 3R_12050754_SNP [dm6]	G	A	3.309e^-5	0.696	INTERGENIC
3L	2867646	3L_2867646_SNP [dm3] 3L_2867646_SNP [dm6]	C	T	3.321e^-5	0.696	INTRON CG43444	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	7870290	3R_7870290_SNP [dm3] 3R_12044568_SNP [dm6]	A	T	3.346e^-5	0.696	INTERGENIC
3R	7871953	3R_7871953_SNP [dm3] 3R_12046231_SNP [dm6]	A	G	3.346e^-5	0.696	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	7880771	3R_7880771_SNP [dm3] 3R_12055049_SNP [dm6]	C	G	3.346e^-5	0.696	INTERGENIC
3L	4158298	3L_4158298_SNP [dm3] 3L_4158298_SNP [dm6]	G	C	3.349e^-5	0.696	INTRON nab	TF binding site BDTNP1_TFBS_dl
3R	12260571	3R_12260571_SNP [dm3] 3R_16434849_SNP [dm6]	T	C	3.448e^-5	0.696	UPSTREAM CG14881 DOWNSTREAM CG17565 INTERGENIC
3R	9853016	3R_9853016_SNP [dm3] 3R_14027294_SNP [dm6]	C	T	3.467e^-5	0.696	INTRON rdx	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	12268816	3R_12268816_SNP [dm3] 3R_16443094_SNP [dm6]	A	G	3.493e^-5	0.696	UPSTREAM CG14882 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA
2L	9133443	2L_9133443_SNP [dm3] 2L_9133443_SNP [dm6]	A	T	3.504e^-5	0.696	INTRON CG32982
2L	10207407	2L_10207407_SNP [dm3] 2L_10207407_SNP [dm6]	A	G	3.523e^-5	0.696	SYNONYMOUS_CODING CG5731 UPSTREAM CG5734	TF binding site mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_ttk
3L	10789198	3L_10789198_SNP [dm3] 3L_10796098_SNP [dm6]	C	T	3.547e^-5	0.696	DOWNSTREAM CR44546 INTERGENIC
3L	10789209	3L_10789209_SNP [dm3] 3L_10796109_SNP [dm6]	T	A	3.564e^-5	0.696	DOWNSTREAM CR44546 INTERGENIC
3L	10789218	3L_10789218_MNP [dm3] 3L_10796118_MNP [dm6]	AAA	TTT	3.564e^-5	0.696	DOWNSTREAM CR44546 INTERGENIC
2R	12833592	2R_12833592_SNP [dm3] 2R_16946087_SNP [dm6]	T	C	3.726e^-5	0.703	SYNONYMOUS_CODING CG15614 DOWNSTREAM Pkc53E & 1 other	TF binding site mE1_TFBS_HSA
2L	6966042	2L_6966042_INS [dm3] 2L_6966042_INS [dm6]	T	TTGTACATT	3.731e^-5	0.703	DOWNSTREAM smt3 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3L	3953888	3L_3953888_SNP [dm3] 3L_3953888_SNP [dm6]	C	G	3.731e^-5	0.703	DOWNSTREAM CG12605 INTERGENIC
2L	5888020	2L_5888020_SNP [dm3] 2L_5888020_SNP [dm6]	T	G	3.813e^-5	0.703	UPSTREAM CR44578 & 1 other INTERGENIC

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By genomic position
Variant impact
Gene name

W6 Vial 3 ascension (cm) phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results