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=6.252e^-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
wolba	0.06011

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	3.8982	0.0483

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2062 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	1402237	3L_1402237_SNP [dm3] 3L_1402237_SNP [dm6]	G	A	4.197e^-7	0.588	DOWNSTREAM tRNA:E4:62Ad & 2 others INTRON Ptp61F	TF binding site mE1_TFBS_HSA
3R	16020028	3R_16020028_SNP [dm3] 3R_20194306_SNP [dm6]	C	G	1.295e^-6	0.588	INTERGENIC
3L	1402125	3L_1402125_SNP [dm3] 3L_1402125_SNP [dm6]	C	A	1.402e^-6	0.588	DOWNSTREAM tRNA:E4:62Ad & 2 others INTRON Ptp61F	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	18914456	3L_18914456_SNP [dm3] 3L_18921356_SNP [dm6]	G	C	1.527e^-6	0.588	SYNONYMOUS_CODING CG3819	TF binding site mE1_TFBS_cad
3L	1402123	3L_1402123_SNP [dm3] 3L_1402123_SNP [dm6]	C	T	1.569e^-6	0.588	DOWNSTREAM tRNA:E4:62Ad & 2 others INTRON Ptp61F	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	15137983	3R_15137983_SNP [dm3] 3R_19312261_SNP [dm6]	G	A	2.241e^-6	0.607	INTRON Dl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	13708418	2L_13708418_SNP [dm3] 2L_13708418_SNP [dm6]	T	C	2.315e^-6	0.607	UTR_5_PRIME CG7311 INTRON CG31814	TF binding site mE1_TFBS_inv
3L	13929147	3L_13929147_SNP [dm3] 3L_13936047_SNP [dm6]	T	C	2.591e^-6	0.607	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	13867070	X_13867070_SNP [dm3] X_13973037_SNP [dm6]	C	T	3.841e^-6	0.696	INTRON mamo
3R	6930497	3R_6930497_SNP [dm3] 3R_11104775_SNP [dm6]	A	T	3.925e^-6	0.696	INTERGENIC
X	13867075	X_13867075_INS [dm3] X_13973042_INS [dm6]	A	AT	4.085e^-6	0.696	INTRON mamo
2L	2419105	2L_2419105_SNP [dm3] 2L_2419105_SNP [dm6]	T	C	5.046e^-6	0.788	SYNONYMOUS_CODING CG34447	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	16020029	3R_16020029_DEL [dm3] 3R_20194307_DEL [dm6]	GCCATCA	G	5.958e^-6	0.815	INTERGENIC
3R	4820643	3R_4820643_SNP [dm3] 3R_8994921_SNP [dm6]	C	A	7.264e^-6	0.815	UTR_3_PRIME CG11975 DOWNSTREAM CG31100 & 1 other
3R	9340479	3R_9340479_DEL [dm3] 3R_13514757_DEL [dm6]	TG	C	7.281e^-6	0.815	INTERGENIC
3R	6926668	3R_6926668_SNP [dm3] 3R_11100946_SNP [dm6]	A	C	7.639e^-6	0.815	UPSTREAM CR45579 INTERGENIC
2R	18801389	2R_18801389_SNP [dm3] 2R_22913866_SNP [dm6]	A	T	8.470e^-6	0.815	INTRON nahoda
2L	7582875	2L_7582875_SNP [dm3] 2L_7582875_SNP [dm6]	C	T	8.582e^-6	0.815	INTRON Spn28B
2R	17452381	2R_17452381_DEL [dm3] 2R_21564876_DEL [dm6]	AGA	A	8.878e^-6	0.815	INTRON CG10440
2R	17452514	2R_17452514_SNP [dm3] 2R_21565009_SNP [dm6]	A	G	8.994e^-6	0.815	INTRON CG10440
2L	13708932	2L_13708932_SNP [dm3] 2L_13708932_SNP [dm6]	G	T	9.617e^-6	0.815	INTRON CG31814 & 1 other	TF binding site mE1_TFBS_inv
3R	6926659	3R_6926659_SNP [dm3] 3R_11100937_SNP [dm6]	A	C	9.772e^-6	0.815	UPSTREAM CR45579 INTERGENIC
3L	1402051	3L_1402051_DEL [dm3] 3L_1402051_DEL [dm6]	ATAATCTCTA	A	1.118e^-5	0.815	DOWNSTREAM tRNA:E4:62Ad & 2 others INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	13708423	2L_13708423_SNP [dm3] 2L_13708423_SNP [dm6]	G	A	1.133e^-5	0.815	UTR_5_PRIME CG7311 INTRON CG31814	TF binding site mE1_TFBS_inv
2L	2419042	2L_2419042_SNP [dm3] 2L_2419042_SNP [dm6]	G	T	1.154e^-5	0.815	SYNONYMOUS_CODING CG34447	TF binding site mE1_TFBS_sens
2L	11198371	2L_11198371_SNP [dm3] 2L_11198371_SNP [dm6]	T	A	1.208e^-5	0.815	INTRON Ca-beta
2L	1748623	2L_1748623_SNP [dm3] 2L_1748623_SNP [dm6]	G	C	1.214e^-5	0.815	INTRON CG17646
X	7882885	X_7882885_SNP [dm3] X_7988852_SNP [dm6]	T	C	1.218e^-5	0.815	INTERGENIC
2L	13082829	2L_13082829_SNP [dm3] 2L_13082829_SNP [dm6]	G	A	1.329e^-5	0.839	INTERGENIC
3L	11702544	3L_11702544_SNP [dm3] 3L_11709444_SNP [dm6]	A	G	1.536e^-5	0.839	UPSTREAM CG11658 INTRON Ccdc56 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	4822941	3R_4822941_SNP [dm3] 3R_8997219_SNP [dm6]	T	A	1.553e^-5	0.839	UPSTREAM CG11977 INTRON CG31100
3R	6926647	3R_6926647_DEL [dm3] 3R_11100925_DEL [dm6]	TTAGAAA	G	1.605e^-5	0.839	UPSTREAM CR45579 INTERGENIC
2L	7582857	2L_7582857_SNP [dm3] 2L_7582857_SNP [dm6]	T	C	1.607e^-5	0.839	INTRON Spn28B
3R	23207486	3R_23207486_SNP [dm3] 3R_27381764_SNP [dm6]	C	T	1.610e^-5	0.839	UTR_3_PRIME side INTRON side
X	13867065	X_13867065_SNP [dm3] X_13973032_SNP [dm6]	C	T	1.656e^-5	0.839	INTRON mamo
2R	10034388	2R_10034388_SNP [dm3] 2R_14146883_SNP [dm6]	A	C	1.665e^-5	0.839	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2R	12148290	2R_12148290_SNP [dm3] 2R_16260785_SNP [dm6]	A	T	1.783e^-5	0.839	UPSTREAM CngA INTERGENIC
3R	4820292	3R_4820292_SNP [dm3] 3R_8994570_SNP [dm6]	T	C	1.794e^-5	0.839	SYNONYMOUS_CODING CG11975 DOWNSTREAM CG31100
X	13867079	X_13867079_DEL [dm3] X_13973046_DEL [dm6]	GGTGATCTCATA...	G	1.826e^-5	0.839	INTRON mamo
3L	18913471	3L_18913471_SNP [dm3] 3L_18920371_SNP [dm6]	A	G	1.832e^-5	0.839	UPSTREAM CG18223 DOWNSTREAM CG3819 INTERGENIC
2L	2424463	2L_2424463_INS [dm3] 2L_2424463_INS [dm6]	A	AA	1.835e^-5	0.839	UTR_3_PRIME CG9886 UPSTREAM CG44139
2R	17452459	2R_17452459_SNP [dm3] 2R_21564954_SNP [dm6]	C	T	1.907e^-5	0.839	INTRON CG10440
3R	10855776	3R_10855776_SNP [dm3] 3R_15030054_SNP [dm6]	C	A	1.925e^-5	0.839	INTERGENIC	TF binding site mE1_TFBS_inv
2L	2256587	2L_2256587_SNP [dm3] 2L_2256587_SNP [dm6]	C	T	2.067e^-5	0.848	INTERGENIC
3R	25946408	3R_25946408_SNP [dm3] 3R_30120686_SNP [dm6]	C	T	2.100e^-5	0.848	SYNONYMOUS_CODING sima UTR_3_PRIME sima	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	18762021	2R_18762021_SNP [dm3] 2R_22874498_SNP [dm6]	A	G	2.130e^-5	0.848	UPSTREAM PIP5K59B DOWNSTREAM CR45469 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	2424473	2L_2424473_SNP [dm3] 2L_2424473_SNP [dm6]	C	T	2.298e^-5	0.848	UTR_3_PRIME CG9886 UPSTREAM CG44139
2R	11833661	2R_11833661_SNP [dm3] 2R_15946156_SNP [dm6]	A	C	2.315e^-5	0.848	SYNONYMOUS_CODING Cyp4aa1 DOWNSTREAM mir-4919 & 1 other	TF binding site mE1_TFBS_sens
2R	18157692	2R_18157692_SNP [dm3] 2R_22270187_SNP [dm6]	A	C	2.334e^-5	0.848	UPSTREAM dve INTRON dve	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3R	25930610	3R_25930610_SNP [dm3] 3R_30104888_SNP [dm6]	A	G	2.335e^-5	0.848	INTRON sima
X	4793688	X_4793688_SNP [dm3] X_4899655_SNP [dm6]	G	C	2.335e^-5	0.848	INTRON CG42594	TF binding site mE1_TFBS_HSA
3R	23207459	3R_23207459_SNP [dm3] 3R_27381737_SNP [dm6]	T	C	2.378e^-5	0.848	UTR_3_PRIME side INTRON side
2L	11528870	2L_11528870_DEL [dm3] 2L_11528870_DEL [dm6]	TTT	T	2.411e^-5	0.848	UPSTREAM CG31705 DOWNSTREAM CG31706 INTERGENIC
3R	10966643	3R_10966643_SNP [dm3] 3R_15140921_SNP [dm6]	C	G	2.456e^-5	0.848	SYNONYMOUS_CODING CG3987 UPSTREAM CR45600 DOWNSTREAM GlyS	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	16852742	2L_16852742_SNP [dm3] 2L_16852742_SNP [dm6]	T	C	2.488e^-5	0.848	UPSTREAM CG31810 DOWNSTREAM CG31809 INTERGENIC
X	7903375	X_7903375_SNP [dm3] X_8009342_SNP [dm6]	T	C	2.607e^-5	0.862	INTRON Tbh
3L	9940430	3L_9940430_SNP [dm3] 3L_9947330_SNP [dm6]	G	C	2.623e^-5	0.862	INTRON CG34356
3R	5376033	3R_5376033_SNP [dm3] 3R_9550311_SNP [dm6]	A	G	2.737e^-5	0.862	INTRON mura & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	10829147	3L_10829147_SNP [dm3] 3L_10836047_SNP [dm6]	A	G	2.803e^-5	0.862	INTERGENIC
2L	3529530	2L_3529530_SNP [dm3] 2L_3529530_SNP [dm6]	T	A	2.882e^-5	0.862	SPLICE_SITE_REGION Spindly INTRON Spindly	TF binding site mE1_TFBS_sens
X	10446569	X_10446569_SNP [dm3] X_10552536_SNP [dm6]	G	C	2.925e^-5	0.862	INTRON spri
3R	18703549	3R_18703549_SNP [dm3] 3R_22877827_SNP [dm6]	A	G	2.928e^-5	0.862	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	2522431	2L_2522431_SNP [dm3] 2L_2522431_SNP [dm6]	G	A	3.028e^-5	0.862	INTERGENIC
X	17250044	X_17250044_SNP [dm3] X_17356011_SNP [dm6]	C	T	3.035e^-5	0.862	INTERGENIC
2R	17452414	2R_17452414_SNP [dm3] 2R_21564909_SNP [dm6]	T	A	3.070e^-5	0.862	INTRON CG10440
2L	14372505	2L_14372505_SNP [dm3] 2L_14372505_SNP [dm6]	A	T	3.076e^-5	0.862	INTERGENIC
3L	14202312	3L_14202312_SNP [dm3] 3L_14209212_SNP [dm6]	C	T	3.081e^-5	0.862	INTRON nuf
2L	9855206	2L_9855206_SNP [dm3] 2L_9855206_SNP [dm6]	C	T	3.203e^-5	0.87	INTRON nAChRalpha6
X	4793963	X_4793963_SNP [dm3] X_4899930_SNP [dm6]	A	G	3.204e^-5	0.87	INTRON CG42594
2R	18157656	2R_18157656_SNP [dm3] 2R_22270151_SNP [dm6]	A	T	3.255e^-5	0.872	UPSTREAM dve INTRON dve	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2R	2354330	2R_2354330_SNP [dm3] 2R_6466825_SNP [dm6]	C	T	3.470e^-5	0.879	INTERGENIC	transposable element FlyBase
2L	17566265	2L_17566265_SNP [dm3] 2L_17566265_SNP [dm6]	G	C	3.549e^-5	0.879	UPSTREAM mir-124 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3L	18913570	3L_18913570_SNP [dm3] 3L_18920470_SNP [dm6]	A	T	3.724e^-5	0.879	UTR_3_PRIME CG3819 UPSTREAM CG18223 DOWNSTREAM CG3819
2L	10288766	2L_10288766_SNP [dm3] 2L_10288766_SNP [dm6]	A	C	3.759e^-5	0.879	NON_SYNONYMOUS_CODING CG5604	TF binding site mE1_TFBS_cad
X	20838659	X_20838659_SNP [dm3] X_20967632_SNP [dm6]	A	G	3.776e^-5	0.879	INTERGENIC
3L	2591792	3L_2591792_SNP [dm3] 3L_2591792_SNP [dm6]	G	T	3.810e^-5	0.879	INTRON dos	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
X	9589543	X_9589543_SNP [dm3] X_9695510_SNP [dm6]	C	T	3.848e^-5	0.879	INTRON btd	TF binding site BDTNP1_TFBS_dl
3R	6926656	3R_6926656_SNP [dm3] 3R_11100934_SNP [dm6]	C	G	3.885e^-5	0.879	UPSTREAM CR45579 INTERGENIC
2R	17836522	2R_17836522_DEL [dm3] 2R_21949017_DEL [dm6]	AGGAAAGGGTTCA...	A	3.986e^-5	0.879	INTERGENIC
2R	12286796	2R_12286796_SNP [dm3] 2R_16399291_SNP [dm6]	C	T	3.997e^-5	0.879	SYNONYMOUS_CODING Sema-2b	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2R	18157671	2R_18157671_SNP [dm3] 2R_22270166_SNP [dm6]	T	A	4.089e^-5	0.879	UPSTREAM dve INTRON dve	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
X	9586639	X_9586639_SNP [dm3] X_9692606_SNP [dm6]	A	T	4.173e^-5	0.879	UPSTREAM CR44016 INTERGENIC	regulatory region FlyBase REDfly_CRMs silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_Trl
3R	23166521	3R_23166521_SNP [dm3] 3R_27340799_SNP [dm6]	C	G	4.189e^-5	0.879	NON_SYNONYMOUS_CODING CG42534	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	4496786	3L_4496786_SNP [dm3] 3L_4496786_SNP [dm6]	T	A	4.373e^-5	0.879	DOWNSTREAM CG13721 INTERGENIC	TF binding site mE1_TFBS_inv
3R	26219628	3R_26219628_SNP [dm3] 3R_30393906_SNP [dm6]	A	T	4.518e^-5	0.879	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	13442278	3R_13442278_SNP [dm3] 3R_17616556_SNP [dm6]	C	T	4.528e^-5	0.879	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_zfh1
3R	15172277	3R_15172277_SNP [dm3] 3R_19346555_SNP [dm6]	C	A	4.540e^-5	0.879	INTERGENIC	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
3R	16031873	3R_16031873_SNP [dm3] 3R_20206151_SNP [dm6]	G	A	4.609e^-5	0.879	INTRON Nlg4
2L	3235361	2L_3235361_SNP [dm3] 2L_3235361_SNP [dm6]	T	C	4.618e^-5	0.879	INTERGENIC
X	9586373	X_9586373_DEL [dm3] X_9692340_DEL [dm6]	CAAAC	C	4.630e^-5	0.879	INTRON CR44016	regulatory region FlyBase REDfly_CRMs silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	2757738	2L_2757738_DEL [dm3] 2L_2757738_DEL [dm6]	AT	A	4.651e^-5	0.879	UTR_3_PRIME Bacc DOWNSTREAM CR44772 & 2 others	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_sens
2L	3233789	2L_3233789_SNP [dm3] 2L_3233789_SNP [dm6]	C	T	4.655e^-5	0.879	INTERGENIC
X	16977067	X_16977067_SNP [dm3] X_17083034_SNP [dm6]	C	T	4.668e^-5	0.879	NON_SYNONYMOUS_CODING CG4955 INTRON CG8945
3L	2591249	3L_2591249_SNP [dm3] 3L_2591249_SNP [dm6]	T	C	4.839e^-5	0.879	UTR_5_PRIME dos INTRON dos	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Stat92E
X	4793808	X_4793808_SNP [dm3] X_4899775_SNP [dm6]	T	C	4.894e^-5	0.879	INTRON CG42594
3R	13442613	3R_13442613_SNP [dm3] 3R_17616891_SNP [dm6]	C	G	4.914e^-5	0.879	UPSTREAM tRNA:V3b:90BC INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_zfh1
3L	11702080	3L_11702080_SNP [dm3] 3L_11708980_SNP [dm6]	T	C	4.943e^-5	0.879	UTR_5_PRIME Ccdc56 & 1 other UPSTREAM CG11658	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	1745855	2L_1745855_SNP [dm3] 2L_1745855_SNP [dm6]	C	T	5.027e^-5	0.879	SYNONYMOUS_CODING CG17646
2L	11881357	2L_11881357_SNP [dm3] 2L_11881357_SNP [dm6]	C	T	5.033e^-5	0.879	INTRON Pde1c	TF binding site mE1_TFBS_inv
3R	13443392	3R_13443392_SNP [dm3] 3R_17617670_SNP [dm6]	C	A	5.046e^-5	0.879	UPSTREAM tRNA:V3b:90BC DOWNSTREAM tRNA:P:90Ca & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_zfh1

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FP phenotype

Phenotype distribution and association to known covariates

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GWAS results