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=6.867e^-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	0.06186

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	3.4684	0.0626

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2148 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	3.768e^-7	0.693	DOWNSTREAM tRNA:E4:62Ad & 2 others INTRON Ptp61F	TF binding site mE1_TFBS_HSA
3L	1402125	3L_1402125_SNP [dm3] 3L_1402125_SNP [dm6]	C	A	1.563e^-6	0.693	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	1.586e^-6	0.693	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
3L	1402123	3L_1402123_SNP [dm3] 3L_1402123_SNP [dm6]	C	T	1.734e^-6	0.693	DOWNSTREAM tRNA:E4:62Ad & 2 others INTRON Ptp61F	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	16020028	3R_16020028_SNP [dm3] 3R_20194306_SNP [dm6]	C	G	2.084e^-6	0.693	INTERGENIC
2L	13708418	2L_13708418_SNP [dm3] 2L_13708418_SNP [dm6]	T	C	2.262e^-6	0.693	UTR_5_PRIME CG7311 INTRON CG31814	TF binding site mE1_TFBS_inv
3L	13929147	3L_13929147_SNP [dm3] 3L_13936047_SNP [dm6]	T	C	3.290e^-6	0.693	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	18914456	3L_18914456_SNP [dm3] 3L_18921356_SNP [dm6]	G	C	3.599e^-6	0.693	SYNONYMOUS_CODING CG3819	TF binding site mE1_TFBS_cad
2L	11198371	2L_11198371_SNP [dm3] 2L_11198371_SNP [dm6]	T	A	3.801e^-6	0.693	INTRON Ca-beta
2R	17452381	2R_17452381_DEL [dm3] 2R_21564876_DEL [dm6]	AGA	A	4.029e^-6	0.693	INTRON CG10440
3R	6930497	3R_6930497_SNP [dm3] 3R_11104775_SNP [dm6]	A	T	4.066e^-6	0.693	INTERGENIC
3R	6926659	3R_6926659_SNP [dm3] 3R_11100937_SNP [dm6]	A	C	5.662e^-6	0.852	UPSTREAM CR45579 INTERGENIC
2L	13708932	2L_13708932_SNP [dm3] 2L_13708932_SNP [dm6]	G	T	6.349e^-6	0.852	INTRON CG31814 & 1 other	TF binding site mE1_TFBS_inv
3R	6926668	3R_6926668_SNP [dm3] 3R_11100946_SNP [dm6]	A	C	6.431e^-6	0.852	UPSTREAM CR45579 INTERGENIC
3R	4820643	3R_4820643_SNP [dm3] 3R_8994921_SNP [dm6]	C	A	7.196e^-6	0.852	UTR_3_PRIME CG11975 DOWNSTREAM CG31100 & 1 other
X	13867070	X_13867070_SNP [dm3] X_13973037_SNP [dm6]	C	T	7.782e^-6	0.852	INTRON mamo
3R	16020029	3R_16020029_DEL [dm3] 3R_20194307_DEL [dm6]	GCCATCA	G	8.165e^-6	0.852	INTERGENIC
2R	17452514	2R_17452514_SNP [dm3] 2R_21565009_SNP [dm6]	A	G	8.429e^-6	0.852	INTRON CG10440
X	13867075	X_13867075_INS [dm3] X_13973042_INS [dm6]	A	AT	8.735e^-6	0.852	INTRON mamo
3R	6926647	3R_6926647_DEL [dm3] 3R_11100925_DEL [dm6]	TTAGAAA	G	9.125e^-6	0.852	UPSTREAM CR45579 INTERGENIC
3L	1402051	3L_1402051_DEL [dm3] 3L_1402051_DEL [dm6]	ATAATCTCTA	A	9.660e^-6	0.852	DOWNSTREAM tRNA:E4:62Ad & 2 others INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	11528870	2L_11528870_DEL [dm3] 2L_11528870_DEL [dm6]	TTT	T	1.121e^-5	0.852	UPSTREAM CG31705 DOWNSTREAM CG31706 INTERGENIC
2L	7582875	2L_7582875_SNP [dm3] 2L_7582875_SNP [dm6]	C	T	1.125e^-5	0.852	INTRON Spn28B
2R	18762021	2R_18762021_SNP [dm3] 2R_22874498_SNP [dm6]	A	G	1.127e^-5	0.852	UPSTREAM PIP5K59B DOWNSTREAM CR45469 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	2419105	2L_2419105_SNP [dm3] 2L_2419105_SNP [dm6]	T	C	1.161e^-5	0.852	SYNONYMOUS_CODING CG34447	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	11702544	3L_11702544_SNP [dm3] 3L_11709444_SNP [dm6]	A	G	1.288e^-5	0.852	UPSTREAM CG11658 INTRON Ccdc56 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	2419042	2L_2419042_SNP [dm3] 2L_2419042_SNP [dm6]	G	T	1.302e^-5	0.852	SYNONYMOUS_CODING CG34447	TF binding site mE1_TFBS_sens
2R	12286796	2R_12286796_SNP [dm3] 2R_16399291_SNP [dm6]	C	T	1.380e^-5	0.852	SYNONYMOUS_CODING Sema-2b	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2L	13708423	2L_13708423_SNP [dm3] 2L_13708423_SNP [dm6]	G	A	1.401e^-5	0.852	UTR_5_PRIME CG7311 INTRON CG31814	TF binding site mE1_TFBS_inv
3R	23207486	3R_23207486_SNP [dm3] 3R_27381764_SNP [dm6]	C	T	1.521e^-5	0.852	UTR_3_PRIME side INTRON side
3R	18703549	3R_18703549_SNP [dm3] 3R_22877827_SNP [dm6]	A	G	1.546e^-5	0.852	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
2R	17452459	2R_17452459_SNP [dm3] 2R_21564954_SNP [dm6]	C	T	1.558e^-5	0.852	INTRON CG10440
X	7882885	X_7882885_SNP [dm3] X_7988852_SNP [dm6]	T	C	1.663e^-5	0.852	INTERGENIC
2L	7582857	2L_7582857_SNP [dm3] 2L_7582857_SNP [dm6]	T	C	1.679e^-5	0.852	INTRON Spn28B
3L	13980020	3L_13980020_SNP [dm3] 3L_13986920_SNP [dm6]	C	T	1.718e^-5	0.852	NON_SYNONYMOUS_CODING CG17362 UPSTREAM CG9040 INTRON CG17364
3R	9340479	3R_9340479_DEL [dm3] 3R_13514757_DEL [dm6]	TG	C	1.727e^-5	0.852	INTERGENIC
3R	16031873	3R_16031873_SNP [dm3] 3R_20206151_SNP [dm6]	G	A	1.727e^-5	0.852	INTRON Nlg4
3L	18913471	3L_18913471_SNP [dm3] 3L_18920371_SNP [dm6]	A	G	1.805e^-5	0.852	UPSTREAM CG18223 DOWNSTREAM CG3819 INTERGENIC
X	10446569	X_10446569_SNP [dm3] X_10552536_SNP [dm6]	G	C	1.808e^-5	0.852	INTRON spri
3R	4822941	3R_4822941_SNP [dm3] 3R_8997219_SNP [dm6]	T	A	1.819e^-5	0.852	UPSTREAM CG11977 INTRON CG31100
3R	23207459	3R_23207459_SNP [dm3] 3R_27381737_SNP [dm6]	T	C	1.933e^-5	0.863	UTR_3_PRIME side INTRON side
3R	4820292	3R_4820292_SNP [dm3] 3R_8994570_SNP [dm6]	T	C	2.018e^-5	0.863	SYNONYMOUS_CODING CG11975 DOWNSTREAM CG31100
X	15281151	X_15281151_SNP [dm3] X_15387118_SNP [dm6]	T	C	2.196e^-5	0.863	UTR_3_PRIME Cngl
2L	3235361	2L_3235361_SNP [dm3] 2L_3235361_SNP [dm6]	T	C	2.283e^-5	0.863	INTERGENIC
3R	6926656	3R_6926656_SNP [dm3] 3R_11100934_SNP [dm6]	C	G	2.411e^-5	0.863	UPSTREAM CR45579 INTERGENIC
2R	17452414	2R_17452414_SNP [dm3] 2R_21564909_SNP [dm6]	T	A	2.460e^-5	0.863	INTRON CG10440
3L	14202312	3L_14202312_SNP [dm3] 3L_14209212_SNP [dm6]	C	T	2.476e^-5	0.863	INTRON nuf
X	4793963	X_4793963_SNP [dm3] X_4899930_SNP [dm6]	A	G	2.477e^-5	0.863	INTRON CG42594
2R	18801389	2R_18801389_SNP [dm3] 2R_22913866_SNP [dm6]	A	T	2.649e^-5	0.863	INTRON nahoda
2L	11528876	2L_11528876_SNP [dm3] 2L_11528876_SNP [dm6]	A	G	2.669e^-5	0.863	UPSTREAM CG31705 DOWNSTREAM CG31706 INTERGENIC
X	12344474	X_12344474_SNP [dm3] X_12450441_SNP [dm6]	A	G	2.710e^-5	0.863	INTRON Pkcdelta
X	17250044	X_17250044_SNP [dm3] X_17356011_SNP [dm6]	C	T	2.758e^-5	0.863	INTERGENIC
3L	4251343	3L_4251343_SNP [dm3] 3L_4251343_SNP [dm6]	C	T	2.766e^-5	0.863	SYNONYMOUS_CODING ago	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_sens
3R	6930710	3R_6930710_SNP [dm3] 3R_11104988_SNP [dm6]	C	T	2.910e^-5	0.863	INTERGENIC
3L	10829147	3L_10829147_SNP [dm3] 3L_10836047_SNP [dm6]	A	G	2.941e^-5	0.863	INTERGENIC
2L	2424463	2L_2424463_INS [dm3] 2L_2424463_INS [dm6]	A	AA	3.160e^-5	0.863	UTR_3_PRIME CG9886 UPSTREAM CG44139
2L	16852742	2L_16852742_SNP [dm3] 2L_16852742_SNP [dm6]	T	C	3.198e^-5	0.863	UPSTREAM CG31810 DOWNSTREAM CG31809 INTERGENIC
2R	11833661	2R_11833661_SNP [dm3] 2R_15946156_SNP [dm6]	A	C	3.202e^-5	0.863	SYNONYMOUS_CODING Cyp4aa1 DOWNSTREAM mir-4919 & 1 other	TF binding site mE1_TFBS_sens
X	9586639	X_9586639_SNP [dm3] X_9692606_SNP [dm6]	A	T	3.257e^-5	0.863	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	15172277	3R_15172277_SNP [dm3] 3R_19346555_SNP [dm6]	C	A	3.261e^-5	0.863	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
3L	11702080	3L_11702080_SNP [dm3] 3L_11708980_SNP [dm6]	T	C	3.284e^-5	0.863	UTR_5_PRIME Ccdc56 & 1 other UPSTREAM CG11658	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	1748623	2L_1748623_SNP [dm3] 2L_1748623_SNP [dm6]	G	C	3.303e^-5	0.863	INTRON CG17646
3L	9940430	3L_9940430_SNP [dm3] 3L_9947330_SNP [dm6]	G	C	3.308e^-5	0.863	INTRON CG34356
3L	2591249	3L_2591249_SNP [dm3] 3L_2591249_SNP [dm6]	T	C	3.359e^-5	0.863	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
3R	5376033	3R_5376033_SNP [dm3] 3R_9550311_SNP [dm6]	A	G	3.410e^-5	0.863	INTRON mura & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2L	14372505	2L_14372505_SNP [dm3] 2L_14372505_SNP [dm6]	A	T	3.452e^-5	0.863	INTERGENIC
2R	4438449	2R_4438449_SNP [dm3] 2R_8550944_SNP [dm6]	C	A	3.501e^-5	0.863	DOWNSTREAM CG12780 INTERGENIC
3R	10855776	3R_10855776_SNP [dm3] 3R_15030054_SNP [dm6]	C	A	3.506e^-5	0.863	INTERGENIC	TF binding site mE1_TFBS_inv
2L	7582818	2L_7582818_SNP [dm3] 2L_7582818_SNP [dm6]	A	G	3.535e^-5	0.863	NON_SYNONYMOUS_CODING Spn28B
3R	23166521	3R_23166521_SNP [dm3] 3R_27340799_SNP [dm6]	C	G	3.564e^-5	0.863	NON_SYNONYMOUS_CODING CG42534	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	9586373	X_9586373_DEL [dm3] X_9692340_DEL [dm6]	CAAAC	C	3.607e^-5	0.863	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	17566265	2L_17566265_SNP [dm3] 2L_17566265_SNP [dm6]	G	C	3.687e^-5	0.863	UPSTREAM mir-124 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
X	13867079	X_13867079_DEL [dm3] X_13973046_DEL [dm6]	GGTGATCTCATA...	G	3.702e^-5	0.863	INTRON mamo
2L	2522431	2L_2522431_SNP [dm3] 2L_2522431_SNP [dm6]	G	A	3.732e^-5	0.863	INTERGENIC
2L	2424473	2L_2424473_SNP [dm3] 2L_2424473_SNP [dm6]	C	T	3.752e^-5	0.863	UTR_3_PRIME CG9886 UPSTREAM CG44139
2R	16730343	2R_16730343_SNP [dm3] 2R_20842838_SNP [dm6]	A	G	3.752e^-5	0.863	INTERGENIC
3R	9726547	3R_9726547_SNP [dm3] 3R_13900825_SNP [dm6]	A	T	3.767e^-5	0.863	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad
3L	16553942	3L_16553942_SNP [dm3] 3L_16560842_SNP [dm6]	C	A	3.876e^-5	0.863	INTERGENIC
2L	13082829	2L_13082829_SNP [dm3] 2L_13082829_SNP [dm6]	G	A	3.904e^-5	0.863	INTERGENIC
X	2662880	X_2662880_SNP [dm3] X_2768847_SNP [dm6]	T	A	3.928e^-5	0.863	INTRON kirre
3R	13442278	3R_13442278_SNP [dm3] 3R_17616556_SNP [dm6]	C	T	3.954e^-5	0.863	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_zfh1
X	9589543	X_9589543_SNP [dm3] X_9695510_SNP [dm6]	C	T	4.031e^-5	0.863	INTRON btd	TF binding site BDTNP1_TFBS_dl
X	4793688	X_4793688_SNP [dm3] X_4899655_SNP [dm6]	G	C	4.069e^-5	0.863	INTRON CG42594	TF binding site mE1_TFBS_HSA
3R	13442613	3R_13442613_SNP [dm3] 3R_17616891_SNP [dm6]	C	G	4.143e^-5	0.863	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
2L	2256587	2L_2256587_SNP [dm3] 2L_2256587_SNP [dm6]	C	T	4.150e^-5	0.863	INTERGENIC
2L	11198388	2L_11198388_SNP [dm3] 2L_11198388_SNP [dm6]	C	T	4.277e^-5	0.863	INTRON Ca-beta
X	9584618	X_9584618_SNP [dm3] X_9690585_SNP [dm6]	C	T	4.304e^-5	0.863	DOWNSTREAM CR44016 INTERGENIC	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
2L	8492891	2L_8492891_SNP [dm3] 2L_8492891_SNP [dm6]	G	A	4.360e^-5	0.863	INTRON Dh31
2L	17534394	2L_17534394_SNP [dm3] 2L_17534394_SNP [dm6]	G	C	4.405e^-5	0.863	INTERGENIC
2L	11882120	2L_11882120_SNP [dm3] 2L_11882120_SNP [dm6]	G	T	4.430e^-5	0.863	INTRON Pde1c
2R	4178767	2R_4178767_SNP [dm3] 2R_8291262_SNP [dm6]	A	T	4.590e^-5	0.863	INTERGENIC
X	2662858	X_2662858_SNP [dm3] X_2768825_SNP [dm6]	G	A	4.660e^-5	0.863	INTRON kirre
3R	26219628	3R_26219628_SNP [dm3] 3R_30393906_SNP [dm6]	A	T	4.669e^-5	0.863	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	17252673	X_17252673_SNP [dm3] X_17358640_SNP [dm6]	C	A	4.697e^-5	0.863	INTERGENIC
2L	10288766	2L_10288766_SNP [dm3] 2L_10288766_SNP [dm6]	A	C	4.746e^-5	0.863	NON_SYNONYMOUS_CODING CG5604	TF binding site mE1_TFBS_cad
2L	2757738	2L_2757738_DEL [dm3] 2L_2757738_DEL [dm6]	AT	A	4.767e^-5	0.863	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
X	13867065	X_13867065_SNP [dm3] X_13973032_SNP [dm6]	C	T	4.788e^-5	0.863	INTRON mamo
2L	9855206	2L_9855206_SNP [dm3] 2L_9855206_SNP [dm6]	C	T	4.891e^-5	0.863	INTRON nAChRalpha6
2R	18157692	2R_18157692_SNP [dm3] 2R_22270187_SNP [dm6]	A	C	4.953e^-5	0.863	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	6930453	3R_6930453_DEL [dm3] 3R_11104731_DEL [dm6]	CC	C	5.010e^-5	0.863	INTERGENIC

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FC phenotype

Phenotype distribution and association to known covariates

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GWAS results