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=8.353e^-2)
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
In_2R_NS	0.0279869
In_3R_P	0.0417529

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1119 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
2R	6058193	2R_6058193_SNP [dm3] 2R_10170688_SNP [dm6]	A	G	3.411e^-6	0.446	INTRON KCNQ
3L	10482061	3L_10482061_SNP [dm3] 3L_10488961_SNP [dm6]	A	C	3.411e^-6	0.446	INTRON A2bp1
3L	17345094	3L_17345094_SNP [dm3] 3L_17351994_SNP [dm6]	C	A	3.411e^-6	0.446	UPSTREAM CG7692 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	8282962	3L_8282962_SNP [dm3] 3L_8289862_SNP [dm6]	A	C	3.411e^-6	0.446	UTR_5_PRIME cert UPSTREAM cert DOWNSTREAM CG7201	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_sens mE1_TFBS_Ubx
X	5485369	X_5485369_SNP [dm3] X_5591336_SNP [dm6]	C	A	3.411e^-6	0.446	INTERGENIC
X	7727681	X_7727681_DEL [dm3] X_7833648_DEL [dm6]	ATCTA	A	3.411e^-6	0.446	INTRON CG1402
X	7727689	X_7727689_SNP [dm3] X_7833656_SNP [dm6]	T	C	3.411e^-6	0.446	INTRON CG1402
2R	13252522	2R_13252522_SNP [dm3] 2R_17365017_SNP [dm6]	C	G	8.544e^-6	0.446	UTR_3_PRIME mbl INTRON mbl	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	5484962	X_5484962_SNP [dm3] X_5590929_SNP [dm6]	T	C	8.544e^-6	0.446	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	10480415	3L_10480415_SNP [dm3] 3L_10487315_SNP [dm6]	G	A	1.053e^-5	0.446	INTRON A2bp1
3L	10480525	3L_10480525_SNP [dm3] 3L_10487425_SNP [dm6]	A	C	1.053e^-5	0.446	INTRON A2bp1
3L	10577011	3L_10577011_SNP [dm3] 3L_10583911_SNP [dm6]	A	T	1.053e^-5	0.446	INTRON A2bp1
3L	10773056	3L_10773056_SNP [dm3] 3L_10779956_SNP [dm6]	T	A	1.053e^-5	0.446	INTERGENIC
3L	10773058	3L_10773058_SNP [dm3] 3L_10779958_SNP [dm6]	G	A	1.053e^-5	0.446	INTERGENIC
3L	10773066	3L_10773066_SNP [dm3] 3L_10779966_SNP [dm6]	G	A	1.053e^-5	0.446	INTERGENIC
3L	11075280	3L_11075280_SNP [dm3] 3L_11082180_SNP [dm6]	A	G	1.053e^-5	0.446	SYNONYMOUS_CODING JIL-1	TF binding site mE1_TFBS_cad
3L	11077228	3L_11077228_SNP [dm3] 3L_11084128_SNP [dm6]	G	T	1.053e^-5	0.446	INTRON JIL-1	TF binding site BDTNP1_TFBS_dl
3L	1127638	3L_1127638_SNP [dm3] 3L_1127638_SNP [dm6]	T	C	1.053e^-5	0.446	INTERGENIC	regulatory region REDfly_CRMs
3L	1127646	3L_1127646_SNP [dm3] 3L_1127646_SNP [dm6]	C	A	1.053e^-5	0.446	INTERGENIC	regulatory region REDfly_CRMs
3L	12333662	3L_12333662_SNP [dm3] 3L_12340562_SNP [dm6]	G	A	1.053e^-5	0.446	INTRON CrzR	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	13330208	3L_13330208_SNP [dm3] 3L_13337108_SNP [dm6]	A	T	1.053e^-5	0.446	INTERGENIC
3L	19266784	3L_19266784_SNP [dm3] 3L_19273684_SNP [dm6]	C	T	1.053e^-5	0.446	NON_SYNONYMOUS_CODING CG14085	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	19272904	3L_19272904_SNP [dm3] 3L_19279804_SNP [dm6]	C	A	1.053e^-5	0.446	NON_SYNONYMOUS_CODING CG14086 DOWNSTREAM CG14089
3L	3266935	3L_3266935_SNP [dm3] 3L_3266935_SNP [dm6]	T	C	1.053e^-5	0.446	INTRON ckd	TF binding site BDTNP1_TFBS_dl
3L	3547740	3L_3547740_SNP [dm3] 3L_3547740_SNP [dm6]	A	C	1.053e^-5	0.446	INTRON Eip63E
3R	14705310	3R_14705310_SNP [dm3] 3R_18879588_SNP [dm6]	C	T	1.053e^-5	0.446	INTERGENIC
3R	18693950	3R_18693950_SNP [dm3] 3R_22868228_SNP [dm6]	T	C	1.053e^-5	0.446	INTERGENIC
3R	3811152	3R_3811152_SNP [dm3] 3R_7985430_SNP [dm6]	T	C	1.053e^-5	0.446	INTRON CG2781
3R	9750604	3R_9750604_SNP [dm3] 3R_13924882_SNP [dm6]	C	T	1.053e^-5	0.446	INTERGENIC
3R	9750641	3R_9750641_SNP [dm3] 3R_13924919_SNP [dm6]	T	C	1.053e^-5	0.446	INTERGENIC
3R	9750708	3R_9750708_SNP [dm3] 3R_13924986_SNP [dm6]	A	T	1.053e^-5	0.446	INTERGENIC
3R	9750714	3R_9750714_SNP [dm3] 3R_13924992_SNP [dm6]	A	C	1.053e^-5	0.446	INTERGENIC
X	10028165	X_10028165_DEL [dm3] X_10134132_DEL [dm6]	AA	A	1.053e^-5	0.446	INTRON CR44894 & 1 other
2R	7612908	2R_7612908_SNP [dm3] 2R_11725403_SNP [dm6]	G	A	1.578e^-5	0.446	SYNONYMOUS_CODING pyr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	16674683	3L_16674683_SNP [dm3] 3L_16681583_SNP [dm6]	A	G	1.952e^-5	0.446	INTRON Lasp & 1 other	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	15868393	2R_15868393_SNP [dm3] 2R_19980888_SNP [dm6]	G	T	2.038e^-5	0.446	UTR_5_PRIME CG8654 UPSTREAM CG8654 INTRON CG8654
2R	6058423	2R_6058423_SNP [dm3] 2R_10170918_SNP [dm6]	C	T	2.038e^-5	0.446	INTRON KCNQ
3L	10691025	3L_10691025_SNP [dm3] 3L_10697925_SNP [dm6]	A	C	2.526e^-5	0.446	INTERGENIC
3R	27500827	3R_27500827_SNP [dm3] 3R_31675105_SNP [dm6]	G	A	2.526e^-5	0.446	SYNONYMOUS_CODING CG1815
3R	7188310	3R_7188310_DEL [dm3] 3R_11362588_DEL [dm6]	GGGCGAAGTAT...	G	2.526e^-5	0.446	INTRON pros	regulatory region REDfly_CRMs TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	19377411	2R_19377411_SNP [dm3] 2R_23489888_SNP [dm6]	T	G	3.685e^-5	0.446	SYNONYMOUS_CODING CG43795	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo
3L	17157707	3L_17157707_SNP [dm3] 3L_17164607_SNP [dm6]	A	G	3.685e^-5	0.446	INTRON Rbp6
3L	17157749	3L_17157749_SNP [dm3] 3L_17164649_SNP [dm6]	T	A	3.685e^-5	0.446	INTRON Rbp6
3L	5367044	3L_5367044_SNP [dm3] 3L_5373944_SNP [dm6]	C	T	3.685e^-5	0.446	INTERGENIC
3R	25506690	3R_25506690_SNP [dm3] 3R_29680968_SNP [dm6]	G	C	3.685e^-5	0.446	SYNONYMOUS_CODING CG7582 DOWNSTREAM Cap-D2	TF binding site mE1_TFBS_cad
2R	12171636	2R_12171636_SNP [dm3] 2R_16284131_SNP [dm6]	G	A	3.715e^-5	0.446	SYNONYMOUS_CODING CG9068	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	13834316	2R_13834316_SNP [dm3] 2R_17946811_SNP [dm6]	G	T	3.715e^-5	0.446	INTERGENIC
2R	13834360	2R_13834360_SNP [dm3] 2R_17946855_SNP [dm6]	A	T	3.715e^-5	0.446	INTERGENIC
2R	13834364	2R_13834364_SNP [dm3] 2R_17946859_SNP [dm6]	T	A	3.715e^-5	0.446	INTERGENIC
2R	13834381	2R_13834381_SNP [dm3] 2R_17946876_SNP [dm6]	T	C	3.715e^-5	0.446	INTERGENIC
2R	14093736	2R_14093736_SNP [dm3] 2R_18206231_SNP [dm6]	G	A	3.715e^-5	0.446	INTERGENIC
2R	14093832	2R_14093832_SNP [dm3] 2R_18206327_SNP [dm6]	G	C	3.715e^-5	0.446	INTERGENIC
2R	15869441	2R_15869441_SNP [dm3] 2R_19981936_SNP [dm6]	G	A	3.715e^-5	0.446	UPSTREAM CG8654 INTRON CG8654	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad
2R	17022463	2R_17022463_SNP [dm3] 2R_21134958_SNP [dm6]	T	C	3.715e^-5	0.446	INTRON Magi	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	17837322	2R_17837322_INS [dm3] 2R_21949817_INS [dm6]	C	CCG	3.715e^-5	0.446	INTERGENIC
2R	18993376	2R_18993376_SNP [dm3] 2R_23105853_SNP [dm6]	C	T	3.715e^-5	0.446	UPSTREAM Gr59d INTERGENIC
2R	18993855	2R_18993855_SNP [dm3] 2R_23106332_SNP [dm6]	A	C	3.715e^-5	0.446	INTERGENIC
2R	19647732	2R_19647732_SNP [dm3] 2R_23760209_SNP [dm6]	A	T	3.715e^-5	0.446	INTRON CG9850	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1
2R	8520177	2R_8520177_SNP [dm3] 2R_12632672_SNP [dm6]	C	T	3.715e^-5	0.446	UPSTREAM CG33792 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Ubx
2R	8520198	2R_8520198_SNP [dm3] 2R_12632693_SNP [dm6]	C	A	3.715e^-5	0.446	NON_SYNONYMOUS_CODING CG33792 UPSTREAM muskelin & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Ubx
2R	8520254	2R_8520254_SNP [dm3] 2R_12632749_SNP [dm6]	A	G	3.715e^-5	0.446	UPSTREAM muskelin & 1 other INTRON CG33792	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Ubx
2R	8520256	2R_8520256_SNP [dm3] 2R_12632751_SNP [dm6]	A	T	3.715e^-5	0.446	UPSTREAM muskelin & 1 other INTRON CG33792	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Ubx
2R	8520263	2R_8520263_SNP [dm3] 2R_12632758_SNP [dm6]	C	T	3.715e^-5	0.446	UPSTREAM muskelin & 1 other INTRON CG33792	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Ubx
2R	8527164	2R_8527164_SNP [dm3] 2R_12639659_SNP [dm6]	T	C	3.715e^-5	0.446	SYNONYMOUS_CODING Iswi	TF binding site mE1_TFBS_cad
2R	9538817	2R_9538817_SNP [dm3] 2R_13651312_SNP [dm6]	T	C	3.715e^-5	0.446	INTRON fas
2R	9937930	2R_9937930_SNP [dm3] 2R_14050425_SNP [dm6]	T	A	3.715e^-5	0.446	INTRON mam
3L	10438667	3L_10438667_SNP [dm3] 3L_10445567_SNP [dm6]	C	G	3.715e^-5	0.446	INTERGENIC
3L	10479306	3L_10479306_SNP [dm3] 3L_10486206_SNP [dm6]	A	G	3.715e^-5	0.446	INTRON A2bp1
3L	10479314	3L_10479314_INS [dm3] 3L_10486214_INS [dm6]	A	ACTAT	3.715e^-5	0.446	INTRON A2bp1
3L	10479340	3L_10479340_SNP [dm3] 3L_10486240_SNP [dm6]	G	C	3.715e^-5	0.446	INTRON A2bp1
3L	10479345	3L_10479345_SNP [dm3] 3L_10486245_SNP [dm6]	G	T	3.715e^-5	0.446	INTRON A2bp1
3L	10479348	3L_10479348_SNP [dm3] 3L_10486248_SNP [dm6]	T	C	3.715e^-5	0.446	INTRON A2bp1
3L	10479556	3L_10479556_SNP [dm3] 3L_10486456_SNP [dm6]	A	G	3.715e^-5	0.446	INTRON A2bp1
3L	10479559	3L_10479559_SNP [dm3] 3L_10486459_SNP [dm6]	A	T	3.715e^-5	0.446	INTRON A2bp1
3L	10479589	3L_10479589_SNP [dm3] 3L_10486489_SNP [dm6]	A	T	3.715e^-5	0.446	INTRON A2bp1
3L	10479590	3L_10479590_SNP [dm3] 3L_10486490_SNP [dm6]	G	T	3.715e^-5	0.446	INTRON A2bp1
3L	10479595	3L_10479595_SNP [dm3] 3L_10486495_SNP [dm6]	G	T	3.715e^-5	0.446	INTRON A2bp1
3L	10479601	3L_10479601_SNP [dm3] 3L_10486501_SNP [dm6]	T	A	3.715e^-5	0.446	INTRON A2bp1
3L	10479615	3L_10479615_SNP [dm3] 3L_10486515_SNP [dm6]	T	C	3.715e^-5	0.446	INTRON A2bp1
3L	10479616	3L_10479616_SNP [dm3] 3L_10486516_SNP [dm6]	G	A	3.715e^-5	0.446	INTRON A2bp1
3L	10479652	3L_10479652_SNP [dm3] 3L_10486552_SNP [dm6]	C	T	3.715e^-5	0.446	INTRON A2bp1
3L	10963779	3L_10963779_SNP [dm3] 3L_10970679_SNP [dm6]	C	T	3.715e^-5	0.446	INTERGENIC
3L	11075076	3L_11075076_SNP [dm3] 3L_11081976_SNP [dm6]	T	A	3.715e^-5	0.446	INTRON JIL-1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3L	11075283	3L_11075283_SNP [dm3] 3L_11082183_SNP [dm6]	G	A	3.715e^-5	0.446	SYNONYMOUS_CODING JIL-1	TF binding site mE1_TFBS_cad
3L	11076442	3L_11076442_SNP [dm3] 3L_11083342_SNP [dm6]	C	A	3.715e^-5	0.446	SPLICE_SITE_REGION JIL-1 INTRON JIL-1	TF binding site mE1_TFBS_cad
3L	11076450	3L_11076450_SNP [dm3] 3L_11083350_SNP [dm6]	C	A	3.715e^-5	0.446	INTRON JIL-1	TF binding site mE1_TFBS_cad
3L	11076494	3L_11076494_SNP [dm3] 3L_11083394_SNP [dm6]	A	G	3.715e^-5	0.446	SPLICE_SITE_REGION JIL-1 INTRON JIL-1	TF binding site mE1_TFBS_cad
3L	11079309	3L_11079309_SNP [dm3] 3L_11086209_SNP [dm6]	C	G	3.715e^-5	0.446	INTRON JIL-1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11079850	3L_11079850_SNP [dm3] 3L_11086750_SNP [dm6]	G	A	3.715e^-5	0.446	INTRON JIL-1	TF binding site BDTNP1_TFBS_twi
3L	11079961	3L_11079961_SNP [dm3] 3L_11086861_SNP [dm6]	A	T	3.715e^-5	0.446	INTRON JIL-1	TF binding site BDTNP1_TFBS_twi
3L	11079994	3L_11079994_SNP [dm3] 3L_11086894_SNP [dm6]	A	C	3.715e^-5	0.446	INTRON JIL-1	TF binding site BDTNP1_TFBS_twi
3L	11080142	3L_11080142_SNP [dm3] 3L_11087042_SNP [dm6]	C	T	3.715e^-5	0.446	INTRON JIL-1	TF binding site BDTNP1_TFBS_twi
3L	11080144	3L_11080144_DEL [dm3] 3L_11087044_DEL [dm6]	AGAGTTGAGCCTGCTCGA...	A	3.715e^-5	0.446	INTRON JIL-1	TF binding site BDTNP1_TFBS_twi
3L	11081969	3L_11081969_SNP [dm3] 3L_11088869_SNP [dm6]	G	C	3.715e^-5	0.446	INTRON JIL-1
3L	13388053	3L_13388053_SNP [dm3] 3L_13394953_SNP [dm6]	A	T	3.715e^-5	0.446	INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA mE1_TFBS_sens
3L	19218565	3L_19218565_SNP [dm3] 3L_19225465_SNP [dm6]	A	C	3.715e^-5	0.446	INTRON fz2
3L	19222164	3L_19222164_SNP [dm3] 3L_19229064_SNP [dm6]	G	T	3.715e^-5	0.446	INTRON fz2 EXON CR43893
3L	19222533	3L_19222533_SNP [dm3] 3L_19229433_SNP [dm6]	T	A	3.715e^-5	0.446	INTRON fz2 EXON CR43893
3L	19222597	3L_19222597_SNP [dm3] 3L_19229497_SNP [dm6]	G	A	3.715e^-5	0.446	INTRON fz2 EXON CR43893
3L	19224104	3L_19224104_SNP [dm3] 3L_19231004_SNP [dm6]	C	T	3.715e^-5	0.446	DOWNSTREAM CR43893 INTRON fz2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl

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By genomic position
Variant impact
Gene name

Climb_Decline phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results