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=8.310e^-4)
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
In_2L_t	0.05405

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1794 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
2L	2488138	2L_2488138_SNP [dm3] 2L_2488138_SNP [dm6]	T	A	8.257e^-7	0.809	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
3L	6542226	3L_6542226_SNP [dm3] 3L_6549126_SNP [dm6]	A	T	1.359e^-6	0.809	UTR_3_PRIME sfl
2L	2488114	2L_2488114_SNP [dm3] 2L_2488114_SNP [dm6]	T	A	1.480e^-6	0.809	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
X	6880579	X_6880579_SNP [dm3] X_6986546_SNP [dm6]	G	T	2.676e^-6	0.809	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
2R	2051002	2R_2051002_SNP [dm3] 2R_6163497_SNP [dm6]	A	C	2.824e^-6	0.809	UPSTREAM tRNA:K2:42Ac DOWNSTREAM tRNA:N5:42Aa INTRON EcR	transposable element FlyBase
3L	8615750	3L_8615750_SNP [dm3] 3L_8622650_SNP [dm6]	T	C	3.127e^-6	0.809	SYNONYMOUS_CODING GAPsec DOWNSTREAM S-Lap2	TF binding site mE1_TFBS_sens
2L	2488122	2L_2488122_SNP [dm3] 2L_2488122_SNP [dm6]	T	A	4.031e^-6	0.809	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
3R	14675777	3R_14675777_SNP [dm3] 3R_18850055_SNP [dm6]	T	A	4.110e^-6	0.809	UPSTREAM CG18208 DOWNSTREAM CR45633 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	13745473	2L_13745473_SNP [dm3] 2L_13745473_SNP [dm6]	C	G	4.318e^-6	0.809	INTERGENIC
3L	7111439	3L_7111439_SNP [dm3] 3L_7118339_SNP [dm6]	C	T	4.574e^-6	0.809	SYNONYMOUS_CODING form3	TF binding site mE1_TFBS_chinmo
3L	6068385	3L_6068385_SNP [dm3] 3L_6075285_SNP [dm6]	G	C	4.806e^-6	0.809	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
2R	8133130	2R_8133130_SNP [dm3] 2R_12245625_SNP [dm6]	G	C	5.611e^-6	0.809	UPSTREAM CG43244 INTERGENIC
2L	21061321	2L_21061321_SNP [dm3] 2L_21061321_SNP [dm6]	T	G	5.945e^-6	0.809	INTRON CG9265
2R	8133171	2R_8133171_SNP [dm3] 2R_12245666_SNP [dm6]	C	T	6.171e^-6	0.809	UPSTREAM CG43244 INTERGENIC
3L	10230591	3L_10230591_SNP [dm3] 3L_10237491_SNP [dm6]	G	A	6.478e^-6	0.809	DOWNSTREAM CR44542 INTERGENIC
2R	19585638	2R_19585638_SNP [dm3] 2R_23698115_SNP [dm6]	C	A	6.902e^-6	0.809	UTR_5_PRIME mRpL43 UPSTREAM CG30183 DOWNSTREAM CG4091	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
2R	9459482	2R_9459482_SNP [dm3] 2R_13571977_SNP [dm6]	A	G	7.403e^-6	0.817	INTRON CG42807	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_cad
2L	2488108	2L_2488108_SNP [dm3] 2L_2488108_SNP [dm6]	T	G	8.492e^-6	0.874	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
2L	2488106	2L_2488106_SNP [dm3] 2L_2488106_SNP [dm6]	G	A	9.534e^-6	0.874	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
X	18466485	X_18466485_SNP [dm3] X_18572452_SNP [dm6]	G	A	9.674e^-6	0.874	UTR_3_PRIME Bx DOWNSTREAM Bx
3R	23480872	3R_23480872_SNP [dm3] 3R_27655150_SNP [dm6]	C	T	9.794e^-6	0.874	INTRON tau
2L	22322001	2L_22322001_SNP [dm3] 2L_22322001_SNP [dm6]	C	T	1.178e^-5	0.968	INTRON CG17018	transposable element FlyBase
X	5208441	X_5208441_SNP [dm3] X_5314408_SNP [dm6]	G	C	1.188e^-5	0.968	NON_SYNONYMOUS_CODING CG4198 DOWNSTREAM CG15930	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	10764650	3R_10764650_SNP [dm3] 3R_14938928_SNP [dm6]	A	G	1.398e^-5	0.976	INTERGENIC
3L	16553341	3L_16553341_SNP [dm3] 3L_16560241_SNP [dm6]	G	T	1.429e^-5	0.976	INTERGENIC
X	18719096	X_18719096_SNP [dm3] X_18825063_SNP [dm6]	G	A	1.480e^-5	0.976	SYNONYMOUS_CODING CG42450	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	10230695	3L_10230695_SNP [dm3] 3L_10237595_SNP [dm6]	G	A	1.555e^-5	0.976	DOWNSTREAM CR44542 INTERGENIC
X	14646736	X_14646736_SNP [dm3] X_14752703_SNP [dm6]	T	C	1.601e^-5	0.976	INTERGENIC
2R	8133105	2R_8133105_SNP [dm3] 2R_12245600_SNP [dm6]	A	C	1.740e^-5	0.976	UPSTREAM CG43244 INTERGENIC
2R	9476276	2R_9476276_SNP [dm3] 2R_13588771_SNP [dm6]	G	C	1.793e^-5	0.976	INTRON CG6191 & 1 other
3L	10230626	3L_10230626_SNP [dm3] 3L_10237526_SNP [dm6]	C	T	1.796e^-5	0.976	DOWNSTREAM CR44542 INTERGENIC
2L	7363705	2L_7363705_SNP [dm3] 2L_7363705_SNP [dm6]	G	A	1.806e^-5	0.976	UTR_5_PRIME Wnt10
3L	16731035	3L_16731035_SNP [dm3] 3L_16737935_SNP [dm6]	G	A	1.868e^-5	0.976	SYNONYMOUS_CODING CG9701	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	16731038	3L_16731038_SNP [dm3] 3L_16737938_SNP [dm6]	T	C	1.926e^-5	0.976	SYNONYMOUS_CODING CG9701	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	12260774	2R_12260774_SNP [dm3] 2R_16373269_SNP [dm6]	G	T	1.936e^-5	0.976	INTERGENIC
2R	6799802	2R_6799802_SNP [dm3] 2R_10912297_SNP [dm6]	T	C	1.991e^-5	0.976	INTERGENIC
2L	7363621	2L_7363621_SNP [dm3] 2L_7363621_SNP [dm6]	C	A	2.133e^-5	0.976	UTR_5_PRIME Wnt10
2L	1591117	2L_1591117_SNP [dm3] 2L_1591117_SNP [dm6]	T	A	2.146e^-5	0.976	INTRON haf
X	9107596	X_9107596_SNP [dm3] X_9213563_SNP [dm6]	T	G	2.181e^-5	0.976	INTERGENIC
X	5237780	X_5237780_SNP [dm3] X_5343747_SNP [dm6]	C	T	2.236e^-5	0.976	INTRON SK
2L	1284517	2L_1284517_DEL [dm3] 2L_1284517_DEL [dm6]	GACATGG	G	2.269e^-5	0.976	INTRON robo3
2L	10814383	2L_10814383_SNP [dm3] 2L_10814383_SNP [dm6]	T	A	2.271e^-5	0.976	INTRON Nos
2R	8133273	2R_8133273_DEL [dm3] 2R_12245768_DEL [dm6]	ACT	A	2.447e^-5	0.976	DOWNSTREAM CR44315 INTERGENIC
2L	2488072	2L_2488072_INS [dm3] 2L_2488072_INS [dm6]	T	TCTT	2.659e^-5	0.976	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
X	18717963	X_18717963_DEL [dm3] X_18823930_DEL [dm6]	TT	T	2.731e^-5	0.976	INTRON CG42450
X	9107598	X_9107598_SNP [dm3] X_9213565_SNP [dm6]	A	T	2.740e^-5	0.976	INTERGENIC
3R	25906671	3R_25906671_SNP [dm3] 3R_30080949_SNP [dm6]	C	A	2.788e^-5	0.976	INTRON sima
3L	1325184	3L_1325184_SNP [dm3] 3L_1325184_SNP [dm6]	G	A	2.841e^-5	0.976	UTR_5_PRIME Myo61F UPSTREAM CR45166 INTRON Myo61F	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
X	14223693	X_14223693_SNP [dm3] X_14329660_SNP [dm6]	A	G	2.847e^-5	0.976	INTRON dpr8
3R	25907851	3R_25907851_SNP [dm3] 3R_30082129_SNP [dm6]	C	A	2.885e^-5	0.976	INTRON sima
2L	2488081	2L_2488081_SNP [dm3] 2L_2488081_SNP [dm6]	A	T	2.936e^-5	0.976	DOWNSTREAM Slh INTERGENIC	enhancer FlyBase
2L	1591089	2L_1591089_SNP [dm3] 2L_1591089_SNP [dm6]	G	C	3.234e^-5	0.976	INTRON haf
X	15327425	X_15327425_SNP [dm3] X_15433392_SNP [dm6]	A	T	3.449e^-5	0.976	INTRON Cngl	transposable element FlyBase
3R	18390916	3R_18390916_SNP [dm3] 3R_22565194_SNP [dm6]	A	T	3.507e^-5	0.976	INTERGENIC
3R	18792563	3R_18792563_SNP [dm3] 3R_22966841_SNP [dm6]	C	T	3.518e^-5	0.976	SYNONYMOUS_CODING Tpl94D	TF binding site mE1_TFBS_cad
3R	10904075	3R_10904075_SNP [dm3] 3R_15078353_SNP [dm6]	G	A	3.532e^-5	0.976	DOWNSTREAM CG6974 & 1 other INTERGENIC
2R	7835809	2R_7835809_SNP [dm3] 2R_11948304_SNP [dm6]	C	T	3.541e^-5	0.976	INTRON CG13188
3R	12216024	3R_12216024_SNP [dm3] 3R_16390302_SNP [dm6]	C	G	3.585e^-5	0.976	INTRON ss	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	13580403	3R_13580403_INS [dm3] 3R_17754681_INS [dm6]	G	GAG	3.688e^-5	0.976	INTRON TyrR
3R	17116277	3R_17116277_SNP [dm3] 3R_21290555_SNP [dm6]	T	C	3.726e^-5	0.976	INTRON SIFaR
X	908567	X_908567_SNP [dm3] X_1014534_SNP [dm6]	C	G	3.769e^-5	0.976	UTR_3_PRIME CG11638 INTRON su_w[a]_
2L	20474163	2L_20474163_SNP [dm3] 2L_20474163_SNP [dm6]	C	T	3.892e^-5	0.976	UPSTREAM CG43233 INTRON CR44980
2L	7490336	2L_7490336_SNP [dm3] 2L_7490336_SNP [dm6]	C	T	3.895e^-5	0.976	INTRON Ziz
3L	15877109	3L_15877109_SNP [dm3] 3L_15884009_SNP [dm6]	T	C	3.949e^-5	0.976	DOWNSTREAM CR44050 INTRON pHCl
3L	4630672	3L_4630672_SNP [dm3] 3L_4630672_SNP [dm6]	C	G	4.001e^-5	0.976	INTRON axo
2L	1324939	2L_1324939_SNP [dm3] 2L_1324939_SNP [dm6]	A	G	4.143e^-5	0.976	INTERGENIC
3R	20017195	3R_20017195_SNP [dm3] 3R_24191473_SNP [dm6]	T	C	4.147e^-5	0.976	NON_SYNONYMOUS_CODING jnj
2L	3373880	2L_3373880_SNP [dm3] 2L_3373880_SNP [dm6]	G	A	4.160e^-5	0.976	SYNONYMOUS_CODING CG15412 UPSTREAM CG34394	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	20606786	3R_20606786_SNP [dm3] 3R_24781064_SNP [dm6]	G	A	4.325e^-5	0.976	INTRON CG42331	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_inv
2R	20435834	2R_20435834_SNP [dm3] 2R_24548311_SNP [dm6]	C	A	4.336e^-5	0.976	INTRON CG4622 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	18390972	3R_18390972_SNP [dm3] 3R_22565250_SNP [dm6]	G	A	4.371e^-5	0.976	INTERGENIC
3R	23480876	3R_23480876_SNP [dm3] 3R_27655154_SNP [dm6]	T	A	4.427e^-5	0.976	INTRON tau
3R	23480880	3R_23480880_SNP [dm3] 3R_27655158_SNP [dm6]	T	A	4.427e^-5	0.976	INTRON tau
2L	1284258	2L_1284258_SNP [dm3] 2L_1284258_SNP [dm6]	G	A	4.547e^-5	0.976	INTRON robo3
3R	22018130	3R_22018130_DEL [dm3] 3R_26192408_DEL [dm6]	CAGCTACAACA...	TTTT	4.669e^-5	0.976	INTERGENIC
2L	7548113	2L_7548113_DEL [dm3] 2L_7548113_DEL [dm6]	CAAGA	C	4.712e^-5	0.976	INTRON RapGAP1
X	18719403	X_18719403_SNP [dm3] X_18825370_SNP [dm6]	C	T	4.751e^-5	0.976	SYNONYMOUS_CODING CG42450	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	21927458	2L_21927458_SNP [dm3] 2L_21927458_SNP [dm6]	T	C	4.752e^-5	0.976	INTERGENIC	transposable element FlyBase
3R	7295555	3R_7295555_SNP [dm3] 3R_11469833_SNP [dm6]	A	G	4.814e^-5	0.976	INTERGENIC
3R	25908931	3R_25908931_SNP [dm3] 3R_30083209_SNP [dm6]	C	A	4.912e^-5	0.976	INTRON sima
2L	8348730	2L_8348730_INS [dm3] 2L_8348730_INS [dm6]	T	TTTATCGCAAT...	4.970e^-5	0.976	INTRON CG7778
X	18718629	X_18718629_SNP [dm3] X_18824596_SNP [dm6]	C	T	5.019e^-5	0.976	INTRON CG42450	TF binding site mE1_TFBS_cad
X	18466521	X_18466521_SNP [dm3] X_18572488_SNP [dm6]	C	T	5.091e^-5	0.976	UTR_3_PRIME Bx DOWNSTREAM Bx
3L	5689685	3L_5689685_SNP [dm3] 3L_5696585_SNP [dm6]	G	C	5.097e^-5	0.976	UTR_5_PRIME sif INTRON sif	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	6205832	2L_6205832_SNP [dm3] 2L_6205832_SNP [dm6]	G	C	5.113e^-5	0.976	INTRON CG34380
2L	2591954	2L_2591954_SNP [dm3] 2L_2591954_SNP [dm6]	C	T	5.140e^-5	0.976	START_GAINED CG15394 UTR_5_PRIME CG15394 UPSTREAM CG15394
X	5056165	X_5056165_DEL [dm3] X_5162132_DEL [dm6]	AA	A	5.151e^-5	0.976	INTRON rg & 1 other
2R	19482135	2R_19482135_SNP [dm3] 2R_23594612_SNP [dm6]	G	C	5.170e^-5	0.976	INTRON apt	TF binding site mE1_TFBS_sens
X	5208428	X_5208428_SNP [dm3] X_5314395_SNP [dm6]	T	C	5.264e^-5	0.976	SYNONYMOUS_CODING CG4198 DOWNSTREAM CG15930	TF binding site BDTNP1_TFBS_ftz BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
X	18717955	X_18717955_INS [dm3] X_18823922_INS [dm6]	T	TAAAATATT	5.267e^-5	0.976	INTRON CG42450
3R	25908915	3R_25908915_DEL [dm3] 3R_30083193_DEL [dm6]	CC	C	5.271e^-5	0.976	INTRON sima
3L	15834527	3L_15834527_SNP [dm3] 3L_15841427_SNP [dm6]	G	A	5.343e^-5	0.976	INTRON CG32150
X	16844980	X_16844980_SNP [dm3] X_16950947_SNP [dm6]	T	C	5.385e^-5	0.976	INTRON RhoGAP15B	TF binding site mE1_TFBS_HSA
2L	10814349	2L_10814349_SNP [dm3] 2L_10814349_SNP [dm6]	A	G	5.457e^-5	0.976	INTRON Nos
3R	20017063	3R_20017063_SNP [dm3] 3R_24191341_SNP [dm6]	A	G	5.460e^-5	0.976	INTRON jnj
3R	1910418	3R_1910418_INS [dm3] 3R_6084696_INS [dm6]	A	ATTATATAATTTTATT...	5.526e^-5	0.976	INTERGENIC
3R	20017058	3R_20017058_SNP [dm3] 3R_24191336_SNP [dm6]	C	T	5.560e^-5	0.976	INTRON jnj
2L	9390004	2L_9390004_SNP [dm3] 2L_9390004_SNP [dm6]	G	C	5.578e^-5	0.976	INTRON Shawl & 1 other
2L	20474175	2L_20474175_SNP [dm3] 2L_20474175_SNP [dm6]	C	T	5.707e^-5	0.976	UPSTREAM CG43233 INTRON CR44980
3R	25907670	3R_25907670_DEL [dm3] 3R_30081948_DEL [dm6]	CAA	C	5.778e^-5	0.976	INTRON sima

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Missing results

By genomic position
Variant impact
Gene name

Novel_TEs phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results