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=3.609e^-21)
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_3R_K	6.003e-07

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	12.6572	0.0018

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3341 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	15348697	2L_15348697_SNP [dm3] 2L_15348697_SNP [dm6]	C	T	2.239e^-8	0.028	INTERGENIC
2L	15348712	2L_15348712_INS [dm3] 2L_15348712_INS [dm6]	G	AA	3.030e^-8	0.028	INTERGENIC
2L	15348728	2L_15348728_SNP [dm3] 2L_15348728_SNP [dm6]	T	A	2.026e^-7	0.127	INTERGENIC
3R	14626457	3R_14626457_SNP [dm3] 3R_18800735_SNP [dm6]	T	G	3.247e^-7	0.147	UTR_3_PRIME CG18208
2L	9469433	2L_9469433_SNP [dm3] 2L_9469433_SNP [dm6]	C	T	4.481e^-7	0.147	UPSTREAM CR43769 INTERGENIC
2L	15348643	2L_15348643_SNP [dm3] 2L_15348643_SNP [dm6]	G	T	4.717e^-7	0.147	INTERGENIC
2L	8884999	2L_8884999_SNP [dm3] 2L_8884999_SNP [dm6]	C	T	1.227e^-6	0.303	INTERGENIC
3R	14626385	3R_14626385_SNP [dm3] 3R_18800663_SNP [dm6]	T	C	1.293e^-6	0.303	UTR_3_PRIME CG18208
X	11237150	X_11237150_INS [dm3] X_11343117_INS [dm6]	T	TT	1.542e^-6	0.315	INTRON CG34348
2L	15337740	2L_15337740_SNP [dm3] 2L_15337740_SNP [dm6]	C	T	1.890e^-6	0.315	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	6976287	2R_6976287_INS [dm3] 2R_11088782_INS [dm6]	A	ATACACA	2.164e^-6	0.315	DOWNSTREAM CG43188 INTRON luna
3R	14626440	3R_14626440_SNP [dm3] 3R_18800718_SNP [dm6]	G	C	2.245e^-6	0.315	UTR_3_PRIME CG18208
2L	8892181	2L_8892181_SNP [dm3] 2L_8892181_SNP [dm6]	C	T	2.925e^-6	0.315	DOWNSTREAM CG42713 INTERGENIC
2L	12226680	2L_12226680_SNP [dm3] 2L_12226680_SNP [dm6]	G	T	3.210e^-6	0.315	INTRON aret
2L	12226681	2L_12226681_SNP [dm3] 2L_12226681_SNP [dm6]	G	T	3.210e^-6	0.315	INTRON aret
2L	8891353	2L_8891353_SNP [dm3] 2L_8891353_SNP [dm6]	T	G	3.282e^-6	0.315	UPSTREAM CG42713 INTERGENIC
3L	16334434	3L_16334434_SNP [dm3] 3L_16341334_SNP [dm6]	A	C	3.341e^-6	0.315	SYNONYMOUS_CODING CG4998	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	8890918	2L_8890918_SNP [dm3] 2L_8890918_SNP [dm6]	G	A	3.450e^-6	0.315	UPSTREAM CG42713 INTERGENIC
2L	12147885	2L_12147885_SNP [dm3] 2L_12147885_SNP [dm6]	C	T	3.506e^-6	0.315	INTRON CG31760
3L	16334602	3L_16334602_SNP [dm3] 3L_16341502_SNP [dm6]	T	C	3.664e^-6	0.315	SYNONYMOUS_CODING CG4998	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	18436654	2R_18436654_SNP [dm3] 2R_22549149_SNP [dm6]	C	A	3.761e^-6	0.315	UPSTREAM CG6018 INTRON px
2L	10426736	2L_10426736_INS [dm3] 2L_10426736_INS [dm6]	T	TGTT	3.883e^-6	0.315	UPSTREAM KdelR & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_Ubx
X	19297289	X_19297289_SNP [dm3] X_19403256_SNP [dm6]	G	A	3.945e^-6	0.315	INTRON kek5
3R	13271279	3R_13271279_SNP [dm3] 3R_17445557_SNP [dm6]	A	T	4.165e^-6	0.315	INTRON CG5873
X	10381386	X_10381386_SNP [dm3] X_10487353_SNP [dm6]	C	A	4.194e^-6	0.315	UPSTREAM CG32687 INTERGENIC
3L	9646361	3L_9646361_SNP [dm3] 3L_9653261_SNP [dm6]	G	T	4.491e^-6	0.324	INTRON fry & 1 other
X	9497046	X_9497046_SNP [dm3] X_9603013_SNP [dm6]	T	A	4.682e^-6	0.324	SYNONYMOUS_CODING Gga	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	11594068	3R_11594068_SNP [dm3] 3R_15768346_SNP [dm6]	A	G	4.902e^-6	0.324	UPSTREAM CG5623 INTERGENIC
3R	6478421	3R_6478421_SNP [dm3] 3R_10652699_SNP [dm6]	G	A	5.705e^-6	0.324	INTERGENIC	TF binding site BDTNP1_TFBS_prd
3R	6478427	3R_6478427_SNP [dm3] 3R_10652705_SNP [dm6]	T	C	5.705e^-6	0.324	INTERGENIC	TF binding site BDTNP1_TFBS_prd
X	7407114	X_7407114_SNP [dm3] X_7513081_SNP [dm6]	T	G	6.157e^-6	0.324	INTRON CG32719
3L	16333699	3L_16333699_SNP [dm3] 3L_16340599_SNP [dm6]	G	A	6.315e^-6	0.324	SYNONYMOUS_CODING CG4998	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	16553942	3L_16553942_SNP [dm3] 3L_16560842_SNP [dm6]	C	A	6.345e^-6	0.324	INTERGENIC
2L	12202139	2L_12202139_SNP [dm3] 2L_12202139_SNP [dm6]	C	T	6.638e^-6	0.324	INTRON aret
2R	14626277	2R_14626277_SNP [dm3] 2R_18738772_SNP [dm6]	C	G	6.682e^-6	0.324	NON_SYNONYMOUS_CODING CG33998 DOWNSTREAM CR30121 INTRON Hs3st-A
3L	3491918	3L_3491918_SNP [dm3] 3L_3491918_SNP [dm6]	G	A	7.069e^-6	0.324	INTRON CG42324
2R	12342361	2R_12342361_SNP [dm3] 2R_16454856_SNP [dm6]	C	G	7.312e^-6	0.324	INTERGENIC
X	9622010	X_9622010_SNP [dm3] X_9727977_SNP [dm6]	T	G	7.426e^-6	0.324	EXON CR43498	TF binding site BDTNP1_TFBS_dl
3R	5013334	3R_5013334_SNP [dm3] 3R_9187612_SNP [dm6]	G	A	7.734e^-6	0.324	INTRON pum	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	4313712	3L_4313712_SNP [dm3] 3L_4313712_SNP [dm6]	C	T	7.804e^-6	0.324	SYNONYMOUS_CODING Claspin	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	1266966	3R_1266966_SNP [dm3] 3R_5441244_SNP [dm6]	C	T	7.836e^-6	0.324	INTRON CG14669
3L	9484303	3L_9484303_SNP [dm3] 3L_9491203_SNP [dm6]	T	G	8.069e^-6	0.324	INTRON CG32037	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	6469464	3R_6469464_SNP [dm3] 3R_10643742_SNP [dm6]	G	C	8.088e^-6	0.324	EXON CR44018	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
X	5251757	X_5251757_SNP [dm3] X_5357724_SNP [dm6]	C	T	8.094e^-6	0.324	UPSTREAM SK INTRON SK
2R	15654591	2R_15654591_SNP [dm3] 2R_19767086_SNP [dm6]	G	C	8.121e^-6	0.324	UPSTREAM 5SrRNA:CR33353 INTERGENIC
3R	6094576	3R_6094576_SNP [dm3] 3R_10268854_SNP [dm6]	G	T	8.202e^-6	0.324	INTRON CG43143	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
X	9497043	X_9497043_SNP [dm3] X_9603010_SNP [dm6]	G	A	8.359e^-6	0.324	SYNONYMOUS_CODING Gga	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	7462458	3R_7462458_SNP [dm3] 3R_11636736_SNP [dm6]	G	A	8.839e^-6	0.324	SYNONYMOUS_CODING Csk UPSTREAM CR44137	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	6012950	3R_6012950_SNP [dm3] 3R_10187228_SNP [dm6]	C	T	8.943e^-6	0.324	INTRON CG12814
3R	6478481	3R_6478481_SNP [dm3] 3R_10652759_SNP [dm6]	T	C	8.956e^-6	0.324	INTERGENIC	TF binding site BDTNP1_TFBS_prd
3R	6478485	3R_6478485_INS [dm3] 3R_10652763_INS [dm6]	A	GC	8.956e^-6	0.324	INTERGENIC	TF binding site BDTNP1_TFBS_prd
3L	1679278	3L_1679278_SNP [dm3] 3L_1679278_SNP [dm6]	A	C	9.138e^-6	0.324	INTRON CG7991
3R	6501185	3R_6501185_SNP [dm3] 3R_10675463_SNP [dm6]	T	A	9.254e^-6	0.324	DOWNSTREAM CG6465 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cnc mE1_TFBS_HSA
2L	8890113	2L_8890113_SNP [dm3] 2L_8890113_SNP [dm6]	T	G	9.499e^-6	0.324	INTERGENIC
3L	3842852	3L_3842852_SNP [dm3] 3L_3842852_SNP [dm6]	T	A	9.634e^-6	0.324	DOWNSTREAM enc INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad
2R	15086854	2R_15086854_SNP [dm3] 2R_19199349_SNP [dm6]	C	G	9.661e^-6	0.324	INTRON hppy
2L	12388049	2L_12388049_SNP [dm3] 2L_12388049_SNP [dm6]	T	C	1.017e^-5	0.335	INTRON bru-2
3L	21472359	3L_21472359_DEL [dm3] 3L_21479259_DEL [dm6]	CC	C	1.036e^-5	0.335	INTERGENIC	regulatory region REDfly_CRMs silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Trl
3R	4815832	3R_4815832_SNP [dm3] 3R_8990110_SNP [dm6]	G	A	1.103e^-5	0.35	SYNONYMOUS_CODING CG11970 DOWNSTREAM E_var_3-9
2R	7017096	2R_7017096_SNP [dm3] 2R_11129591_SNP [dm6]	C	T	1.139e^-5	0.35	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	5995489	3R_5995489_SNP [dm3] 3R_10169767_SNP [dm6]	G	T	1.176e^-5	0.35	INTRON Best1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
2L	8885223	2L_8885223_SNP [dm3] 2L_8885223_SNP [dm6]	G	T	1.179e^-5	0.35	INTERGENIC
3R	4818934	3R_4818934_SNP [dm3] 3R_8993212_SNP [dm6]	G	A	1.203e^-5	0.35	UPSTREAM CG11975 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3R	5162097	3R_5162097_SNP [dm3] 3R_9336375_SNP [dm6]	T	C	1.203e^-5	0.35	INTRON CG8121
3R	6014373	3R_6014373_SNP [dm3] 3R_10188651_SNP [dm6]	T	A	1.212e^-5	0.35	INTRON CG12814
3R	11594134	3R_11594134_SNP [dm3] 3R_15768412_SNP [dm6]	C	T	1.238e^-5	0.352	UPSTREAM CG5623 INTERGENIC
X	9868764	X_9868764_SNP [dm3] X_9974731_SNP [dm6]	G	A	1.357e^-5	0.353	INTRON CG43386
2L	8890163	2L_8890163_INS [dm3] 2L_8890163_INS [dm6]	T	TTCTA	1.367e^-5	0.353	INTERGENIC
2R	18907121	2R_18907121_SNP [dm3] 2R_23019598_SNP [dm6]	A	T	1.382e^-5	0.353	INTRON twi & 1 other
2L	7627931	2L_7627931_DEL [dm3] 2L_7627931_DEL [dm6]	GGC	G	1.424e^-5	0.353	INTERGENIC	TF binding site mE1_TFBS_sens
3R	11594071	3R_11594071_SNP [dm3] 3R_15768349_SNP [dm6]	T	C	1.437e^-5	0.353	UPSTREAM CG5623 INTERGENIC
2L	8889335	2L_8889335_SNP [dm3] 2L_8889335_SNP [dm6]	A	T	1.474e^-5	0.353	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_ttk
2L	12202242	2L_12202242_SNP [dm3] 2L_12202242_SNP [dm6]	T	A	1.500e^-5	0.353	INTRON aret
3R	16175110	3R_16175110_SNP [dm3] 3R_20349388_SNP [dm6]	C	T	1.500e^-5	0.353	INTERGENIC
2L	5064085	2L_5064085_SNP [dm3] 2L_5064085_SNP [dm6]	T	C	1.508e^-5	0.353	UPSTREAM qtc & 1 other INTRON qtc	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	6014393	3R_6014393_SNP [dm3] 3R_10188671_SNP [dm6]	A	C	1.517e^-5	0.353	INTRON CG12814
3L	8798491	3L_8798491_SNP [dm3] 3L_8805391_SNP [dm6]	C	T	1.523e^-5	0.353	SYNONYMOUS_CODING CG34427 DOWNSTREAM CG13312	TF binding site mE1_TFBS_chinmo
2R	15587692	2R_15587692_SNP [dm3] 2R_19700187_SNP [dm6]	C	T	1.539e^-5	0.353	NON_SYNONYMOUS_CODING Obp56c UPSTREAM Obp56b	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
3L	9993334	3L_9993334_SNP [dm3] 3L_10000234_SNP [dm6]	C	A	1.545e^-5	0.353	INTRON dpr6
2L	8893686	2L_8893686_SNP [dm3] 2L_8893686_SNP [dm6]	G	A	1.561e^-5	0.353	INTERGENIC
3L	20540759	3L_20540759_DEL [dm3] 3L_20547659_DEL [dm6]	CG	T	1.622e^-5	0.353	INTERGENIC
3R	6538718	3R_6538718_SNP [dm3] 3R_10712996_SNP [dm6]	A	T	1.651e^-5	0.353	INTERGENIC
X	10443035	X_10443035_SNP [dm3] X_10549002_SNP [dm6]	C	T	1.658e^-5	0.353	INTRON spri
2L	10873518	2L_10873518_SNP [dm3] 2L_10873518_SNP [dm6]	A	G	1.660e^-5	0.353	INTERGENIC
2L	8890162	2L_8890162_SNP [dm3] 2L_8890162_SNP [dm6]	A	G	1.756e^-5	0.353	INTERGENIC
3R	4817263	3R_4817263_SNP [dm3] 3R_8991541_SNP [dm6]	G	T	1.760e^-5	0.353	NON_SYNONYMOUS_CODING E_var_3-9 DOWNSTREAM CG11970
3R	6011219	3R_6011219_SNP [dm3] 3R_10185497_SNP [dm6]	A	G	1.771e^-5	0.353	INTRON CG12814
X	10440823	X_10440823_SNP [dm3] X_10546790_SNP [dm6]	A	G	1.791e^-5	0.353	UPSTREAM spri INTRON spri	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
X	10441001	X_10441001_SNP [dm3] X_10546968_SNP [dm6]	G	A	1.791e^-5	0.353	UPSTREAM spri INTRON spri	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	5238270	3L_5238270_SNP [dm3] 3L_5245170_SNP [dm6]	A	G	1.847e^-5	0.353	INTRON shep
2L	2373193	2L_2373193_SNP [dm3] 2L_2373193_SNP [dm6]	G	A	1.847e^-5	0.353	SYNONYMOUS_CODING CG3609	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	15579895	X_15579895_SNP [dm3] X_15685862_SNP [dm6]	A	T	1.905e^-5	0.353	NON_SYNONYMOUS_CODING CG15599	TF binding site BDTNP1_TFBS_prd mE1_TFBS_sens
2L	8888880	2L_8888880_DEL [dm3] 2L_8888880_DEL [dm6]	CCCTCAAAATCCTTATAAAG...	C	1.913e^-5	0.353	UPSTREAM CR44415 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_ttk
2L	8888986	2L_8888986_SNP [dm3] 2L_8888986_SNP [dm6]	A	T	1.913e^-5	0.353	UPSTREAM CR44415 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_ttk
2L	8889165	2L_8889165_SNP [dm3] 2L_8889165_SNP [dm6]	T	C	1.927e^-5	0.353	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_sens mE1_TFBS_ttk
2L	13283596	2L_13283596_SNP [dm3] 2L_13283596_SNP [dm6]	C	G	1.930e^-5	0.353	UTR_3_PRIME CG44085 DOWNSTREAM Drep-4
2L	8888944	2L_8888944_DEL [dm3] 2L_8888944_DEL [dm6]	CAT	C	1.933e^-5	0.353	UPSTREAM CR44415 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_GATAe mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_kn mE1_TFBS_ttk
3R	6320297	3R_6320297_SNP [dm3] 3R_10494575_SNP [dm6]	G	T	1.941e^-5	0.353	INTERGENIC
3R	6478518	3R_6478518_SNP [dm3] 3R_10652796_SNP [dm6]	A	G	1.961e^-5	0.353	INTERGENIC	TF binding site BDTNP1_TFBS_prd
2L	13230934	2L_13230934_SNP [dm3] 2L_13230934_SNP [dm6]	C	G	1.967e^-5	0.353	DOWNSTREAM CG16815 INTERGENIC	TF binding site BDTNP1_TFBS_hb

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SegregVariants_3L phenotype

Phenotype distribution and association to known covariates

QQplot

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GWAS results