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=1.653e^-14)
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_2R_NS	0.005523
In_3R_K	0.005510
In_3R_Mo	0.011828

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1954 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
3R	16292687	3R_16292687_SNP [dm3] 3R_20466965_SNP [dm6]	G	A	4.742e^-8	0.089	INTRON Gfrl
3L	6532070	3L_6532070_SNP [dm3] 3L_6538970_SNP [dm6]	T	C	1.125e^-6	0.598	INTRON sfl
2R	12807373	2R_12807373_SNP [dm3] 2R_16919868_SNP [dm6]	A	T	2.380e^-6	0.598	INTERGENIC
2L	4388973	2L_4388973_SNP [dm3] 2L_4388973_SNP [dm6]	A	G	2.694e^-6	0.598	INTRON Tps1
2R	12273989	2R_12273989_SNP [dm3] 2R_16386484_SNP [dm6]	A	G	2.718e^-6	0.598	UPSTREAM Sema-2b DOWNSTREAM CG43187 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2R	12807372	2R_12807372_SNP [dm3] 2R_16919867_SNP [dm6]	T	A	2.723e^-6	0.598	INTERGENIC
2R	12274090	2R_12274090_SNP [dm3] 2R_16386585_SNP [dm6]	G	A	2.875e^-6	0.598	UTR_5_PRIME Sema-2b DOWNSTREAM CG43187	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
X	3661188	X_3661188_SNP [dm3] X_3767155_SNP [dm6]	C	T	2.961e^-6	0.598	INTRON tlk
2L	16500604	2L_16500604_SNP [dm3] 2L_16500604_SNP [dm6]	T	C	3.508e^-6	0.598	INTRON Tpr2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	12274022	2R_12274022_SNP [dm3] 2R_16386517_SNP [dm6]	A	T	3.653e^-6	0.598	UPSTREAM Sema-2b DOWNSTREAM CG43187 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2L	4389054	2L_4389054_SNP [dm3] 2L_4389054_SNP [dm6]	T	C	3.811e^-6	0.598	INTRON Tps1
3L	22779791	3L_22779791_INS [dm3] 3L_22786691_INS [dm6]	T	TAT	4.290e^-6	0.598	UTR_3_PRIME SPoCk
X	3818560	X_3818560_SNP [dm3] X_3924527_SNP [dm6]	A	G	4.698e^-6	0.598	INTRON CG42541
2R	18552034	2R_18552034_INS [dm3] 2R_22664529_INS [dm6]	G	AGACTTGGTTTGTATCACAA...	4.705e^-6	0.598	DOWNSTREAM CG4250 INTERGENIC
X	2670126	X_2670126_SNP [dm3] X_2776093_SNP [dm6]	T	G	4.779e^-6	0.598	INTRON kirre
2R	12273672	2R_12273672_SNP [dm3] 2R_16386167_SNP [dm6]	T	A	6.002e^-6	0.704	UPSTREAM Sema-2b DOWNSTREAM CG43187 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
X	2670124	X_2670124_SNP [dm3] X_2776091_SNP [dm6]	A	T	7.947e^-6	0.8	INTRON kirre
2R	12274094	2R_12274094_SNP [dm3] 2R_16386589_SNP [dm6]	T	G	7.955e^-6	0.8	UTR_5_PRIME Sema-2b DOWNSTREAM CG43187	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2R	12274076	2R_12274076_SNP [dm3] 2R_16386571_SNP [dm6]	A	G	8.106e^-6	0.8	START_GAINED Sema-2b UTR_5_PRIME Sema-2b DOWNSTREAM CG43187	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
X	11117636	X_11117636_SNP [dm3] X_11223603_SNP [dm6]	T	C	9.471e^-6	0.883	UTR_3_PRIME CG44422 DOWNSTREAM CG44422 INTRON CG44422
3L	4891616	3L_4891616_SNP [dm3] 3L_4891616_SNP [dm6]	A	G	1.117e^-5	0.883	INTRON CG17150	TF binding site mE1_TFBS_chinmo
3R	16292858	3R_16292858_DEL [dm3] 3R_20467136_DEL [dm6]	CGTAAGGTTGAGTAGTTTGT...	C	1.124e^-5	0.883	INTRON Gfrl
X	14945539	X_14945539_SNP [dm3] X_15051506_SNP [dm6]	G	C	1.147e^-5	0.883	UTR_3_PRIME CG5541 INTRON hiw
2R	18552038	2R_18552038_INS [dm3] 2R_22664533_INS [dm6]	A	ACGT	1.159e^-5	0.883	DOWNSTREAM CG4250 INTERGENIC
2R	12273658	2R_12273658_SNP [dm3] 2R_16386153_SNP [dm6]	A	C	1.238e^-5	0.883	UPSTREAM Sema-2b DOWNSTREAM CG43187 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Trl
3R	25481418	3R_25481418_SNP [dm3] 3R_29655696_SNP [dm6]	A	G	1.272e^-5	0.883	INTRON Dop1R2
3L	7101366	3L_7101366_SNP [dm3] 3L_7108266_SNP [dm6]	T	A	1.336e^-5	0.883	INTRON form3	TF binding site mE1_TFBS_inv
2L	21342305	2L_21342305_SNP [dm3] 2L_21342305_SNP [dm6]	A	C	1.377e^-5	0.883	DOWNSTREAM dimm INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	16168952	2L_16168952_SNP [dm3] 2L_16168952_SNP [dm6]	T	A	1.479e^-5	0.883	INTRON Ca-alpha1D
3R	12566846	3R_12566846_SNP [dm3] 3R_16741124_SNP [dm6]	T	C	1.484e^-5	0.883	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	1405874	2R_1405874_SNP [dm3] 2R_5518369_SNP [dm6]	T	C	1.563e^-5	0.883	UPSTREAM CG30438 INTRON CG30438	transposable element FlyBase
2R	18901109	2R_18901109_SNP [dm3] 2R_23013586_SNP [dm6]	G	A	1.603e^-5	0.883	INTRON twi & 1 other	TF binding site mE1_TFBS_chinmo
3L	16232541	3L_16232541_SNP [dm3] 3L_16239441_SNP [dm6]	A	T	1.610e^-5	0.883	UTR_3_PRIME l_3_72Dr	TF binding site mE1_TFBS_cad
2L	16500603	2L_16500603_SNP [dm3] 2L_16500603_SNP [dm6]	A	G	1.676e^-5	0.883	INTRON Tpr2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	21057413	2L_21057413_SNP [dm3] 2L_21057413_SNP [dm6]	C	A	1.705e^-5	0.883	UTR_3_PRIME Itgbetanu DOWNSTREAM CG9265	transposable element FlyBase
2R	18552045	2R_18552045_SNP [dm3] 2R_22664540_SNP [dm6]	A	C	1.769e^-5	0.883	DOWNSTREAM CG4250 INTERGENIC
3L	22115469	3L_22115469_SNP [dm3] 3L_22122369_SNP [dm6]	G	A	1.879e^-5	0.883	UPSTREAM CR45235 DOWNSTREAM CR45236 INTERGENIC
2R	17575477	2R_17575477_SNP [dm3] 2R_21687972_SNP [dm6]	A	T	1.930e^-5	0.883	UTR_3_PRIME CG30285 UPSTREAM Tbp & 1 other	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA
2R	15120025	2R_15120025_SNP [dm3] 2R_19232520_SNP [dm6]	A	G	1.964e^-5	0.883	INTRON cora	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	14939005	X_14939005_SNP [dm3] X_15044972_SNP [dm6]	G	A	2.076e^-5	0.883	INTRON hiw & 1 other
3R	17841583	3R_17841583_SNP [dm3] 3R_22015861_SNP [dm6]	T	G	2.112e^-5	0.883	SYNONYMOUS_CODING CG6332 DOWNSTREAM CG6439	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad
3L	7699605	3L_7699605_SNP [dm3] 3L_7706505_SNP [dm6]	C	A	2.131e^-5	0.883	SYNONYMOUS_CODING Ank2 INTRON CG32373
2L	3852158	2L_3852158_SNP [dm3] 2L_3852158_SNP [dm6]	G	A	2.131e^-5	0.883	EXON CR45451	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_sens
2R	18552051	2R_18552051_SNP [dm3] 2R_22664546_SNP [dm6]	T	G	2.152e^-5	0.883	DOWNSTREAM CG4250 INTERGENIC
X	9168518	X_9168518_SNP [dm3] X_9274485_SNP [dm6]	T	C	2.261e^-5	0.883	SYNONYMOUS_CODING CG16892 UPSTREAM snoRNA:CG16892-a DOWNSTREAM c11.1	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	16665093	3L_16665093_SNP [dm3] 3L_16671993_SNP [dm6]	G	A	2.285e^-5	0.883	UTR_3_PRIME zetaCOP INTRON zetaCOP
2R	12274015	2R_12274015_SNP [dm3] 2R_16386510_SNP [dm6]	A	G	2.312e^-5	0.883	UPSTREAM Sema-2b DOWNSTREAM CG43187 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
2R	20191495	2R_20191495_SNP [dm3] 2R_24303972_SNP [dm6]	T	C	2.407e^-5	0.883	INTERGENIC	regulatory region REDfly_CRMs
2L	19450243	2L_19450243_SNP [dm3] 2L_19450243_SNP [dm6]	C	T	2.464e^-5	0.883	SYNONYMOUS_CODING Top2
X	19786660	X_19786660_INS [dm3] X_19892627_INS [dm6]	T	TCTG	2.468e^-5	0.883	INTRON Hers
X	3819659	X_3819659_SNP [dm3] X_3925626_SNP [dm6]	A	G	2.601e^-5	0.883	INTRON CG42541
2L	21674895	2L_21674895_SNP [dm3] 2L_21674895_SNP [dm6]	C	T	2.640e^-5	0.883	INTRON CG2225	transposable element FlyBase
X	13918407	X_13918407_SNP [dm3] X_14024374_SNP [dm6]	A	G	2.684e^-5	0.883	DOWNSTREAM tRNA:S774:12Ec INTERGENIC
2R	4475942	2R_4475942_SNP [dm3] 2R_8588437_SNP [dm6]	C	T	2.693e^-5	0.883	INTERGENIC
2L	18359189	2L_18359189_SNP [dm3] 2L_18359189_SNP [dm6]	C	T	2.702e^-5	0.883	UPSTREAM Acp36DE INTRON Fas3	TF binding site BDTNP1_TFBS_da
2L	4388947	2L_4388947_SNP [dm3] 2L_4388947_SNP [dm6]	G	A	2.704e^-5	0.883	INTRON Tps1
2L	21677150	2L_21677150_SNP [dm3] 2L_21677150_SNP [dm6]	G	T	2.741e^-5	0.883	UTR_5_PRIME CG2225 UPSTREAM CG2225 DOWNSTREAM EF2 INTRON CG2225	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
X	14939048	X_14939048_SNP [dm3] X_15045015_SNP [dm6]	A	G	2.867e^-5	0.883	INTRON hiw & 1 other
2R	6634600	2R_6634600_SNP [dm3] 2R_10747095_SNP [dm6]	C	T	2.942e^-5	0.883	INTRON CG33144
3L	16230885	3L_16230885_SNP [dm3] 3L_16237785_SNP [dm6]	C	T	2.994e^-5	0.883	NON_SYNONYMOUS_CODING l_3_72Dr DOWNSTREAM l_3_72Dp
2R	14532977	2R_14532977_SNP [dm3] 2R_18645472_SNP [dm6]	A	C	3.024e^-5	0.883	INTRON SP2637	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	4636932	3L_4636932_INS [dm3] 3L_4636932_INS [dm6]	T	TTT	3.038e^-5	0.883	UTR_3_PRIME axo INTRON axo
2L	2791977	2L_2791977_SNP [dm3] 2L_2791977_SNP [dm6]	A	T	3.091e^-5	0.883	INTRON Syt1
3L	18601521	3L_18601521_SNP [dm3] 3L_18608421_SNP [dm6]	T	C	3.093e^-5	0.883	INTRON CG4174 & 2 others
2R	14423807	2R_14423807_SNP [dm3] 2R_18536302_SNP [dm6]	T	A	3.112e^-5	0.883	UPSTREAM Pepck & 1 other DOWNSTREAM CG10924 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2L	2742587	2L_2742587_SNP [dm3] 2L_2742587_SNP [dm6]	G	A	3.140e^-5	0.883	SYNONYMOUS_CODING Hrs DOWNSTREAM CG9961	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	1028334	3R_1028334_SNP [dm3] 3R_5202612_SNP [dm6]	A	C	3.155e^-5	0.883	INTRON cno
X	14945772	X_14945772_SNP [dm3] X_15051739_SNP [dm6]	A	G	3.224e^-5	0.889	UTR_3_PRIME CG5541 INTRON hiw
2R	20347054	2R_20347054_SNP [dm3] 2R_24459531_SNP [dm6]	A	T	3.293e^-5	0.889	INTRON CG13579
3L	6291176	3L_6291176_SNP [dm3] 3L_6298076_SNP [dm6]	G	A	3.342e^-5	0.889	INTERGENIC	TF binding site mE1_TFBS_cad
2R	19153963	2R_19153963_SNP [dm3] 2R_23266440_SNP [dm6]	G	C	3.395e^-5	0.889	UPSTREAM CG12782 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	19117890	3L_19117890_SNP [dm3] 3L_19124790_SNP [dm6]	G	T	3.417e^-5	0.889	INTRON CG14082
X	2670119	X_2670119_DEL [dm3] X_2776086_DEL [dm6]	AGCC	A	3.461e^-5	0.889	INTRON kirre
2R	10709878	2R_10709878_SNP [dm3] 2R_14822373_SNP [dm6]	G	A	3.554e^-5	0.901	INTERGENIC
3L	22749097	3L_22749097_SNP [dm3] 3L_22755997_SNP [dm6]	T	A	3.612e^-5	0.903	INTRON SPoCk
X	15865050	X_15865050_INS [dm3] X_15971017_INS [dm6]	C	CC	3.871e^-5	0.92	INTRON mmd	TF binding site mE1_TFBS_HSA
2L	19394909	2L_19394909_SNP [dm3] 2L_19394909_SNP [dm6]	C	T	3.882e^-5	0.92	SYNONYMOUS_CODING CG31798 INTRON CG17544	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	24748946	3R_24748946_SNP [dm3] 3R_28923224_SNP [dm6]	T	C	3.886e^-5	0.92	DOWNSTREAM Doa INTRON CG11828
X	15446998	X_15446998_SNP [dm3] X_15552965_SNP [dm6]	C	T	3.892e^-5	0.92	INTRON Ac13E	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	2748413	2L_2748413_SNP [dm3] 2L_2748413_SNP [dm6]	C	G	4.037e^-5	0.92	UTR_5_PRIME Pgk	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_sens
X	14944423	X_14944423_SNP [dm3] X_15050390_SNP [dm6]	A	G	4.210e^-5	0.92	INTRON hiw & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	18588006	3R_18588006_SNP [dm3] 3R_22762284_SNP [dm6]	A	C	4.217e^-5	0.92	NON_SYNONYMOUS_CODING CG4723 INTRON Usp12-46 & 1 other
2R	18902506	2R_18902506_SNP [dm3] 2R_23014983_SNP [dm6]	C	T	4.248e^-5	0.92	INTRON twi & 1 other	TF binding site BDTNP1_TFBS_twi
X	14944443	X_14944443_SNP [dm3] X_15050410_SNP [dm6]	C	A	4.266e^-5	0.92	INTRON hiw & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	12561389	3R_12561389_SNP [dm3] 3R_16735667_SNP [dm6]	G	A	4.291e^-5	0.92	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_z
2L	16502284	2L_16502284_SNP [dm3] 2L_16502284_SNP [dm6]	A	G	4.313e^-5	0.92	INTRON Tpr2
3L	8467604	3L_8467604_SNP [dm3] 3L_8474504_SNP [dm6]	C	A	4.399e^-5	0.92	SYNONYMOUS_CODING CG43163	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	17998445	3L_17998445_SNP [dm3] 3L_18005345_SNP [dm6]	T	A	4.526e^-5	0.92	INTRON Eip75B	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens mE1_TFBS_Trl
X	14937567	X_14937567_SNP [dm3] X_15043534_SNP [dm6]	C	G	4.714e^-5	0.92	UPSTREAM CG5541 INTRON hiw	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	2749206	2L_2749206_SNP [dm3] 2L_2749206_SNP [dm6]	C	A	4.723e^-5	0.92	UPSTREAM Pgk INTRON Pgk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	14425225	2R_14425225_SNP [dm3] 2R_18537720_SNP [dm6]	T	A	4.842e^-5	0.92	SYNONYMOUS_CODING Pepck UTR_3_PRIME CG45087	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	17873037	2R_17873037_SNP [dm3] 2R_21985532_SNP [dm6]	C	A	4.878e^-5	0.92	DOWNSTREAM CG30401 INTERGENIC
2R	17873059	2R_17873059_SNP [dm3] 2R_21985554_SNP [dm6]	T	C	4.956e^-5	0.92	DOWNSTREAM CG30401 INTERGENIC
2L	6142260	2L_6142260_SNP [dm3] 2L_6142260_SNP [dm6]	G	A	4.977e^-5	0.92	SYNONYMOUS_CODING CG13991	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	6634598	2R_6634598_SNP [dm3] 2R_10747093_SNP [dm6]	T	C	5.060e^-5	0.92	INTRON CG33144
X	21511037	X_21511037_SNP [dm3] X_21640010_SNP [dm6]	C	T	5.100e^-5	0.92	INTERGENIC
2R	19104986	2R_19104986_SNP [dm3] 2R_23217463_SNP [dm6]	C	T	5.109e^-5	0.92	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9743884	3R_9743884_SNP [dm3] 3R_13918162_SNP [dm6]	T	C	5.122e^-5	0.92	INTERGENIC
X	15446898	X_15446898_SNP [dm3] X_15552865_SNP [dm6]	T	G	5.143e^-5	0.92	INTRON Ac13E	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	11902993	2R_11902993_SNP [dm3] 2R_16015488_SNP [dm6]	C	T	5.288e^-5	0.92	SYNONYMOUS_CODING Rrp42 UPSTREAM Prosbeta1 DOWNSTREAM CG8397	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_chinmo mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_sens

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By genomic position
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Mitochon_Consens_Dif phenotype

Phenotype distribution and association to known covariates

QQplot

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GWAS results