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=4.826e^-2)
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	0.07275

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2213 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
2R	9476276	2R_9476276_SNP [dm3] 2R_13588771_SNP [dm6]	G	C	6.591e^-7	0.553	INTRON CG6191 & 1 other
2L	2488138	2L_2488138_SNP [dm3] 2L_2488138_SNP [dm6]	T	A	7.999e^-7	0.553	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
X	18466485	X_18466485_SNP [dm3] X_18572452_SNP [dm6]	G	A	1.078e^-6	0.553	UTR_3_PRIME Bx DOWNSTREAM Bx
2L	2488114	2L_2488114_SNP [dm3] 2L_2488114_SNP [dm6]	T	A	1.189e^-6	0.553	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
3L	16553341	3L_16553341_SNP [dm3] 3L_16560241_SNP [dm6]	G	T	1.586e^-6	0.553	INTERGENIC
2L	7490336	2L_7490336_SNP [dm3] 2L_7490336_SNP [dm6]	C	T	2.187e^-6	0.553	INTRON Ziz
2R	9459482	2R_9459482_SNP [dm3] 2R_13571977_SNP [dm6]	A	G	2.283e^-6	0.553	INTRON CG42807	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad
X	6880579	X_6880579_SNP [dm3] X_6986546_SNP [dm6]	G	T	2.550e^-6	0.553	UTR_5_PRIME bou UPSTREAM ogre INTRON ogre	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_run mE1_TFBS_sens mE1_TFBS_Trl
3R	14675777	3R_14675777_SNP [dm3] 3R_18850055_SNP [dm6]	T	A	3.035e^-6	0.553	UPSTREAM CG18208 DOWNSTREAM CR45633 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	10764650	3R_10764650_SNP [dm3] 3R_14938928_SNP [dm6]	A	G	3.077e^-6	0.553	INTERGENIC
2R	18233644	2R_18233644_SNP [dm3] 2R_22346139_SNP [dm6]	C	T	3.244e^-6	0.553	NON_SYNONYMOUS_CODING Liprin-gamma INTRON Liprin-gamma
2L	13745473	2L_13745473_SNP [dm3] 2L_13745473_SNP [dm6]	C	G	4.685e^-6	0.653	INTERGENIC
3R	10904075	3R_10904075_SNP [dm3] 3R_15078353_SNP [dm6]	G	A	5.135e^-6	0.653	DOWNSTREAM CG6974 & 1 other INTERGENIC
3L	15899276	3L_15899276_SNP [dm3] 3L_15906176_SNP [dm6]	C	G	5.989e^-6	0.653	SYNONYMOUS_CODING sff
3L	10801737	3L_10801737_SNP [dm3] 3L_10808637_SNP [dm6]	G	A	6.096e^-6	0.653	INTERGENIC
3L	15899108	3L_15899108_SNP [dm3] 3L_15906008_SNP [dm6]	T	C	6.703e^-6	0.653	SYNONYMOUS_CODING sff
2L	2488122	2L_2488122_SNP [dm3] 2L_2488122_SNP [dm6]	T	A	6.739e^-6	0.653	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
3L	9340497	3L_9340497_INS [dm3] 3L_9347397_INS [dm6]	CA	ATTT	6.822e^-6	0.653	DOWNSTREAM PGRP-LC INTRON PGRP-LC
2L	2488108	2L_2488108_SNP [dm3] 2L_2488108_SNP [dm6]	T	G	6.833e^-6	0.653	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
2R	2051002	2R_2051002_SNP [dm3] 2R_6163497_SNP [dm6]	A	C	7.331e^-6	0.653	UPSTREAM tRNA:K2:42Ac DOWNSTREAM tRNA:N5:42Aa INTRON EcR	transposable element FlyBase
2L	2488106	2L_2488106_SNP [dm3] 2L_2488106_SNP [dm6]	G	A	7.974e^-6	0.653	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
3L	9340486	3L_9340486_SNP [dm3] 3L_9347386_SNP [dm6]	A	G	8.710e^-6	0.653	DOWNSTREAM PGRP-LC INTRON PGRP-LC
2L	20146604	2L_20146604_SNP [dm3] 2L_20146604_SNP [dm6]	G	A	8.893e^-6	0.653	INTERGENIC
2R	8133130	2R_8133130_SNP [dm3] 2R_12245625_SNP [dm6]	G	C	9.167e^-6	0.653	UPSTREAM CG43244 INTERGENIC
3L	9340493	3L_9340493_SNP [dm3] 3L_9347393_SNP [dm6]	C	A	9.208e^-6	0.653	DOWNSTREAM PGRP-LC INTRON PGRP-LC
2L	5943563	2L_5943563_SNP [dm3] 2L_5943563_SNP [dm6]	A	G	9.763e^-6	0.653	UPSTREAM Gpdh & 1 other DOWNSTREAM CR45289 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_kn mE1_TFBS_Trl
3R	20017063	3R_20017063_SNP [dm3] 3R_24191341_SNP [dm6]	A	G	1.028e^-5	0.653	INTRON jnj
3R	20017058	3R_20017058_SNP [dm3] 3R_24191336_SNP [dm6]	C	T	1.033e^-5	0.653	INTRON jnj
3L	9340505	3L_9340505_SNP [dm3] 3L_9347405_SNP [dm6]	T	C	1.064e^-5	0.653	DOWNSTREAM PGRP-LC INTRON PGRP-LC
2L	2488081	2L_2488081_SNP [dm3] 2L_2488081_SNP [dm6]	A	T	1.087e^-5	0.653	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
3L	15899551	3L_15899551_SNP [dm3] 3L_15906451_SNP [dm6]	T	C	1.145e^-5	0.653	INTRON sff
3L	6068385	3L_6068385_SNP [dm3] 3L_6075285_SNP [dm6]	G	C	1.188e^-5	0.653	UPSTREAM CG6610 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_sens
3L	9340483	3L_9340483_SNP [dm3] 3L_9347383_SNP [dm6]	T	C	1.212e^-5	0.653	DOWNSTREAM PGRP-LC INTRON PGRP-LC
3L	9340464	3L_9340464_SNP [dm3] 3L_9347364_SNP [dm6]	C	T	1.264e^-5	0.653	DOWNSTREAM PGRP-LC INTRON PGRP-LC
3L	9340466	3L_9340466_DEL [dm3] 3L_9347366_DEL [dm6]	TT	T	1.264e^-5	0.653	DOWNSTREAM PGRP-LC INTRON PGRP-LC
3L	21767823	3L_21767823_SNP [dm3] 3L_21774723_SNP [dm6]	T	A	1.281e^-5	0.653	UPSTREAM CG42552 INTRON CG42689
2L	21927458	2L_21927458_SNP [dm3] 2L_21927458_SNP [dm6]	T	C	1.288e^-5	0.653	INTERGENIC	transposable element FlyBase
2L	20146645	2L_20146645_SNP [dm3] 2L_20146645_SNP [dm6]	C	T	1.404e^-5	0.655	INTERGENIC
2L	5943559	2L_5943559_DEL [dm3] 2L_5943559_DEL [dm6]	TAG	A	1.435e^-5	0.655	UPSTREAM Gpdh & 1 other DOWNSTREAM CR45289 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_kn mE1_TFBS_Trl
X	14666137	X_14666137_INS [dm3] X_14772104_INS [dm6]	T	TCAGTT	1.472e^-5	0.655	INTERGENIC
2L	5943728	2L_5943728_SNP [dm3] 2L_5943728_SNP [dm6]	C	A	1.479e^-5	0.655	UTR_5_PRIME Gpdh UPSTREAM Gpdh & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl
2L	2488072	2L_2488072_INS [dm3] 2L_2488072_INS [dm6]	T	TCTT	1.502e^-5	0.655	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
2R	8133171	2R_8133171_SNP [dm3] 2R_12245666_SNP [dm6]	C	T	1.503e^-5	0.655	UPSTREAM CG43244 INTERGENIC
3R	15755513	3R_15755513_SNP [dm3] 3R_19929791_SNP [dm6]	A	G	1.606e^-5	0.684	UTR_3_PRIME Hs6st	TF binding site BDTNP1_TFBS_dl
3L	9339346	3L_9339346_DEL [dm3] 3L_9346246_DEL [dm6]	GTC	AA	1.727e^-5	0.707	UTR_3_PRIME PGRP-LC INTRON PGRP-LC
3R	20017323	3R_20017323_SNP [dm3] 3R_24191601_SNP [dm6]	C	T	1.753e^-5	0.707	NON_SYNONYMOUS_CODING jnj
3L	7111439	3L_7111439_SNP [dm3] 3L_7118339_SNP [dm6]	C	T	1.790e^-5	0.707	SYNONYMOUS_CODING form3	TF binding site mE1_TFBS_chinmo
3L	9340575	3L_9340575_SNP [dm3] 3L_9347475_SNP [dm6]	T	C	1.809e^-5	0.707	DOWNSTREAM PGRP-LC INTRON PGRP-LC
3R	13580403	3R_13580403_INS [dm3] 3R_17754681_INS [dm6]	G	GAG	1.900e^-5	0.713	INTRON TyrR
X	9107596	X_9107596_SNP [dm3] X_9213563_SNP [dm6]	T	G	1.932e^-5	0.713	INTERGENIC
2L	7536029	2L_7536029_SNP [dm3] 2L_7536029_SNP [dm6]	A	G	1.982e^-5	0.713	INTRON RapGAP1	TF binding site mE1_TFBS_cad
3R	20016930	3R_20016930_SNP [dm3] 3R_24191208_SNP [dm6]	T	A	2.002e^-5	0.713	SYNONYMOUS_CODING jnj
2R	7499421	2R_7499421_INS [dm3] 2R_11611916_INS [dm6]	G	GG	2.017e^-5	0.713	INTRON tou	TF binding site BDTNP1_TFBS_dl
3L	9340534	3L_9340534_INS [dm3] 3L_9347434_INS [dm6]	A	ATTGTA	2.151e^-5	0.731	DOWNSTREAM PGRP-LC INTRON PGRP-LC
2R	9251317	2R_9251317_SNP [dm3] 2R_13363812_SNP [dm6]	G	A	2.171e^-5	0.731	UPSTREAM CR45312 INTERGENIC
3R	20017195	3R_20017195_SNP [dm3] 3R_24191473_SNP [dm6]	T	C	2.184e^-5	0.731	NON_SYNONYMOUS_CODING jnj
3L	16529565	3L_16529565_SNP [dm3] 3L_16536465_SNP [dm6]	G	C	2.522e^-5	0.771	INTRON CG43373
3L	9340509	3L_9340509_INS [dm3] 3L_9347409_INS [dm6]	T	CACATACACATATTAATTGA...	2.540e^-5	0.771	DOWNSTREAM PGRP-LC INTRON PGRP-LC
3L	2292874	3L_2292874_SNP [dm3] 3L_2292874_SNP [dm6]	A	G	2.609e^-5	0.771	INTRON MsR2
3L	10801819	3L_10801819_SNP [dm3] 3L_10808719_SNP [dm6]	A	T	2.615e^-5	0.771	INTERGENIC
2L	855323	2L_855323_SNP [dm3] 2L_855323_SNP [dm6]	G	A	2.615e^-5	0.771	UPSTREAM CG13949 DOWNSTREAM kraken INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2R	8133105	2R_8133105_SNP [dm3] 2R_12245600_SNP [dm6]	A	C	2.625e^-5	0.771	UPSTREAM CG43244 INTERGENIC
2R	5797495	2R_5797495_SNP [dm3] 2R_9909990_SNP [dm6]	G	A	2.637e^-5	0.771	SYNONYMOUS_CODING FMRFa UPSTREAM Etf-QO	TF binding site mE1_TFBS_chinmo
X	9107598	X_9107598_SNP [dm3] X_9213565_SNP [dm6]	A	T	2.689e^-5	0.771	INTERGENIC
2R	18143041	2R_18143041_SNP [dm3] 2R_22255536_SNP [dm6]	T	G	2.730e^-5	0.771	INTRON dve	TF binding site mE1_TFBS_sens
2R	18230934	2R_18230934_SNP [dm3] 2R_22343429_SNP [dm6]	C	T	2.778e^-5	0.771	INTRON Liprin-gamma
X	12079989	X_12079989_SNP [dm3] X_12185956_SNP [dm6]	C	G	2.817e^-5	0.771	INTRON Ten-a
3L	9336947	3L_9336947_SNP [dm3] 3L_9343847_SNP [dm6]	C	T	2.826e^-5	0.771	UPSTREAM PGRP-LC INTRON PGRP-LC
3L	506087	3L_506087_SNP [dm3] 3L_506087_SNP [dm6]	G	A	2.837e^-5	0.771	INTRON klar	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_ttk mE1_TFBS_zfh1
2L	21913750	2L_21913750_SNP [dm3] 2L_21913750_SNP [dm6]	A	T	3.001e^-5	0.798	DOWNSTREAM CG31600 INTERGENIC
X	9246963	X_9246963_SNP [dm3] X_9352930_SNP [dm6]	A	G	3.024e^-5	0.798	INTRON CG34449
3R	18797071	3R_18797071_SNP [dm3] 3R_22971349_SNP [dm6]	C	A	3.064e^-5	0.798	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	5796778	2R_5796778_SNP [dm3] 2R_9909273_SNP [dm6]	C	T	3.131e^-5	0.804	SYNONYMOUS_CODING FMRFa	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	20017110	3R_20017110_SNP [dm3] 3R_24191388_SNP [dm6]	C	T	3.232e^-5	0.809	NON_SYNONYMOUS_CODING jnj
3L	10803166	3L_10803166_SNP [dm3] 3L_10810066_SNP [dm6]	A	T	3.333e^-5	0.809	INTERGENIC
X	12086255	X_12086255_INS [dm3] X_12192222_INS [dm6]	G	GAG	3.360e^-5	0.809	INTRON Ten-a
2R	20374772	2R_20374772_SNP [dm3] 2R_24487249_SNP [dm6]	T	C	3.377e^-5	0.809	INTRON CG13579	TF binding site mE1_TFBS_cad
3R	25906671	3R_25906671_SNP [dm3] 3R_30080949_SNP [dm6]	C	A	3.459e^-5	0.809	INTRON sima
2L	22322001	2L_22322001_SNP [dm3] 2L_22322001_SNP [dm6]	C	T	3.489e^-5	0.809	INTRON CG17018	transposable element FlyBase
3L	9338028	3L_9338028_SNP [dm3] 3L_9344928_SNP [dm6]	C	A	3.509e^-5	0.809	SYNONYMOUS_CODING PGRP-LC
X	14819025	X_14819025_INS [dm3] X_14924992_INS [dm6]	T	TCT	3.643e^-5	0.809	UPSTREAM Flo2 INTRON Flo2
3L	1325184	3L_1325184_SNP [dm3] 3L_1325184_SNP [dm6]	G	A	3.646e^-5	0.809	UTR_5_PRIME Myo61F UPSTREAM CR45166 INTRON Myo61F	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	18793607	3R_18793607_DEL [dm3] 3R_22967885_DEL [dm6]	ATTCGGCGGTAATTAGA...	A	3.739e^-5	0.809	DOWNSTREAM Tpl94D INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
3R	10199285	3R_10199285_SNP [dm3] 3R_14373563_SNP [dm6]	G	A	3.898e^-5	0.809	UPSTREAM NK7.1 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	6772294	3L_6772294_SNP [dm3] 3L_6779194_SNP [dm6]	C	G	3.946e^-5	0.809	INTERGENIC	enhancer mE1_CBP_Enhancers regulatory region REDfly_CRMs
X	14666160	X_14666160_SNP [dm3] X_14772127_SNP [dm6]	G	A	3.992e^-5	0.809	INTERGENIC
X	16813089	X_16813089_SNP [dm3] X_16919056_SNP [dm6]	C	T	3.997e^-5	0.809	INTRON CG4928
3R	14676991	3R_14676991_DEL [dm3] 3R_18851269_DEL [dm6]	CG	T	4.069e^-5	0.809	UPSTREAM CR45633 DOWNSTREAM CG31226 INTERGENIC
3L	13366747	3L_13366747_SNP [dm3] 3L_13373647_SNP [dm6]	T	C	4.109e^-5	0.809	INTERGENIC
2L	7490357	2L_7490357_SNP [dm3] 2L_7490357_SNP [dm6]	A	G	4.134e^-5	0.809	INTRON Ziz
2L	7492255	2L_7492255_SNP [dm3] 2L_7492255_SNP [dm6]	A	T	4.227e^-5	0.809	INTRON Ziz	TF binding site BDTNP1_TFBS_dl
2R	8133273	2R_8133273_DEL [dm3] 2R_12245768_DEL [dm6]	ACT	A	4.255e^-5	0.809	DOWNSTREAM CR44315 INTERGENIC
2L	10814349	2L_10814349_SNP [dm3] 2L_10814349_SNP [dm6]	A	G	4.359e^-5	0.809	INTRON Nos
2L	7548086	2L_7548086_SNP [dm3] 2L_7548086_SNP [dm6]	A	G	4.376e^-5	0.809	INTRON RapGAP1
X	908567	X_908567_SNP [dm3] X_1014534_SNP [dm6]	C	G	4.392e^-5	0.809	UTR_3_PRIME CG11638 INTRON su_w[a]_
X	14442170	X_14442170_SNP [dm3] X_14548137_SNP [dm6]	A	C	4.428e^-5	0.809	INTERGENIC
2R	18145505	2R_18145505_DEL [dm3] 2R_22258000_DEL [dm6]	GG	G	4.441e^-5	0.809	INTRON dve	TF binding site mE1_TFBS_chinmo
2L	15363185	2L_15363185_SNP [dm3] 2L_15363185_SNP [dm6]	G	T	4.579e^-5	0.809	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	14676984	3R_14676984_SNP [dm3] 3R_18851262_SNP [dm6]	C	T	4.672e^-5	0.809	UPSTREAM CR45633 DOWNSTREAM CG31226 INTERGENIC
X	18466521	X_18466521_SNP [dm3] X_18572488_SNP [dm6]	C	T	4.777e^-5	0.809	UTR_3_PRIME Bx DOWNSTREAM Bx

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Missing results

By genomic position
Variant impact
Gene name

Unique_TEs phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results