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=9.209e^-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
In_3R_P	0.04288

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	5.006	0.0253
In_3R_P	2.7143	0.0995

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

788 significant hits at p-value < 0.001.

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	20627703	2R_20627703_SNP [dm3] 2R_24740180_SNP [dm6]	T	G	6.585e^-5	0.943	UPSTREAM CR44828 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	6989556	2R_6989556_SNP [dm3] 2R_11102051_SNP [dm6]	G	A	6.585e^-5	0.943	INTRON luna	TF binding site mE1_TFBS_cad
X	17540649	X_17540649_SNP [dm3] X_17646616_SNP [dm6]	G	A	6.585e^-5	0.943	INTRON RhoGAPp190
X	17540674	X_17540674_SNP [dm3] X_17646641_SNP [dm6]	A	G	6.585e^-5	0.943	INTRON RhoGAPp190
2R	1803877	2R_1803877_SNP [dm3] 2R_5916372_SNP [dm6]	A	G	1.142e^-4	0.943	INTRON CG43366
2R	10417001	2R_10417001_SNP [dm3] 2R_14529496_SNP [dm6]	A	T	1.147e^-4	0.943	INTRON ttv
2R	17441747	2R_17441747_SNP [dm3] 2R_21554242_SNP [dm6]	G	T	1.186e^-4	0.943	INTRON Egfr	TF binding site mE1_TFBS_HSA
X	17078271	X_17078271_SNP [dm3] X_17184238_SNP [dm6]	T	C	1.186e^-4	0.943	UPSTREAM CR44026 INTRON baz
2R	10028999	2R_10028999_SNP [dm3] 2R_14141494_SNP [dm6]	A	G	1.417e^-4	0.943	UPSTREAM Prosap INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_ttk mE1_TFBS_Ubx
2R	20373901	2R_20373901_SNP [dm3] 2R_24486378_SNP [dm6]	A	G	1.417e^-4	0.943	INTRON CG13579	TF binding site mE1_TFBS_cad
2R	20474931	2R_20474931_SNP [dm3] 2R_24587408_SNP [dm6]	C	A	1.417e^-4	0.943	UPSTREAM pio INTRON pio
2L	5601013	2L_5601013_SNP [dm3] 2L_5601013_SNP [dm6]	T	C	1.425e^-4	0.943	DOWNSTREAM CG14010 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
2L	7601208	2L_7601208_SNP [dm3] 2L_7601208_SNP [dm6]	A	G	1.480e^-4	0.943	INTERGENIC
3L	3949872	3L_3949872_SNP [dm3] 3L_3949872_SNP [dm6]	T	C	1.480e^-4	0.943	UPSTREAM CG14983 INTERGENIC
X	9084014	X_9084014_SNP [dm3] X_9189981_SNP [dm6]	G	C	1.494e^-4	0.943	NON_SYNONYMOUS_CODING CG12115 DOWNSTREAM mei-P26
3L	10861129	3L_10861129_SNP [dm3] 3L_10868029_SNP [dm6]	A	G	1.515e^-4	0.943	INTRON tna	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	11943091	3L_11943091_SNP [dm3] 3L_11949991_SNP [dm6]	A	G	1.515e^-4	0.943	NON_SYNONYMOUS_CODING CG17826 DOWNSTREAM CG7252
3L	11943153	3L_11943153_SNP [dm3] 3L_11950053_SNP [dm6]	T	C	1.515e^-4	0.943	SYNONYMOUS_CODING CG17826 DOWNSTREAM CG7252
3L	11943294	3L_11943294_SNP [dm3] 3L_11950194_SNP [dm6]	A	G	1.515e^-4	0.943	SYNONYMOUS_CODING CG17826 DOWNSTREAM CG7252
3L	11943303	3L_11943303_SNP [dm3] 3L_11950203_SNP [dm6]	A	G	1.515e^-4	0.943	SYNONYMOUS_CODING CG17826 DOWNSTREAM CG7252
3L	17687735	3L_17687735_SNP [dm3] 3L_17694635_SNP [dm6]	T	C	1.515e^-4	0.943	INTRON Ccn
3L	4971834	3L_4971834_SNP [dm3] 3L_4971834_SNP [dm6]	A	C	1.515e^-4	0.943	INTRON Con
3L	5899543	3L_5899543_SNP [dm3] 3L_5906443_SNP [dm6]	A	G	1.515e^-4	0.943	NON_SYNONYMOUS_CODING CG10486 UPSTREAM CG13288	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	5900313	3L_5900313_SNP [dm3] 3L_5907213_SNP [dm6]	C	G	1.515e^-4	0.943	UPSTREAM CG13288 & 1 other INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	6027432	3L_6027432_SNP [dm3] 3L_6034332_SNP [dm6]	A	G	1.515e^-4	0.943	UPSTREAM yip7 INTRON CG10477
3L	6027451	3L_6027451_SNP [dm3] 3L_6034351_SNP [dm6]	G	A	1.515e^-4	0.943	SYNONYMOUS_CODING CG10477 UPSTREAM yip7
3L	6027472	3L_6027472_SNP [dm3] 3L_6034372_SNP [dm6]	T	A	1.515e^-4	0.943	SYNONYMOUS_CODING CG10477 UPSTREAM yip7
3L	9692038	3L_9692038_SNP [dm3] 3L_9698938_SNP [dm6]	G	C	1.515e^-4	0.943	INTRON UbcD4	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	9692060	3L_9692060_SNP [dm3] 3L_9698960_SNP [dm6]	G	A	1.515e^-4	0.943	SPLICE_SITE_REGION UbcD4 INTRON UbcD4	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3L	9948018	3L_9948018_SNP [dm3] 3L_9954918_SNP [dm6]	C	T	1.515e^-4	0.943	INTRON CG34356
3R	21356972	3R_21356972_SNP [dm3] 3R_25531250_SNP [dm6]	T	A	1.515e^-4	0.943	INTRON msi
3R	21357127	3R_21357127_SNP [dm3] 3R_25531405_SNP [dm6]	A	C	1.515e^-4	0.943	INTRON msi
X	8719259	X_8719259_INS [dm3] X_8825226_INS [dm6]	A	GC	1.515e^-4	0.943	INTERGENIC
X	8719261	X_8719261_SNP [dm3] X_8825228_SNP [dm6]	C	A	1.515e^-4	0.943	INTERGENIC
X	8719265	X_8719265_SNP [dm3] X_8825232_SNP [dm6]	G	T	1.515e^-4	0.943	INTERGENIC
3L	17687731	3L_17687731_SNP [dm3] 3L_17694631_SNP [dm6]	T	A	1.605e^-4	0.943	INTRON Ccn
2R	20329772	2R_20329772_SNP [dm3] 2R_24442249_SNP [dm6]	T	A	1.689e^-4	0.943	INTERGENIC	TF binding site BDTNP1_TFBS_hb
3R	26599230	3R_26599230_SNP [dm3] 3R_30773508_SNP [dm6]	C	T	1.689e^-4	0.943	INTRON zfh1	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_Trl
2R	10417036	2R_10417036_SNP [dm3] 2R_14529531_SNP [dm6]	G	A	1.741e^-4	0.943	INTRON ttv
2L	6379900	2L_6379900_SNP [dm3] 2L_6379900_SNP [dm6]	T	C	1.788e^-4	0.943	INTRON CG42368
2R	9962745	2R_9962745_DEL [dm3] 2R_14075240_DEL [dm6]	AA	A	1.788e^-4	0.943	INTRON Prosap
2R	13367827	2R_13367827_SNP [dm3] 2R_17480322_SNP [dm6]	C	A	1.950e^-4	0.943	UTR_3_PRIME CG43110 INTRON veil	TF binding site mE1_TFBS_cad
2R	17112331	2R_17112331_SNP [dm3] 2R_21224826_SNP [dm6]	G	C	1.950e^-4	0.943	UPSTREAM ASPP INTRON ASPP
2R	19052996	2R_19052996_SNP [dm3] 2R_23165473_SNP [dm6]	C	A	1.950e^-4	0.943	INTRON CG34371	TF binding site BDTNP1_TFBS_twi
3L	11819188	3L_11819188_SNP [dm3] 3L_11826088_SNP [dm6]	G	A	1.950e^-4	0.943	UPSTREAM CG32095 DOWNSTREAM CycA INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11819210	3L_11819210_INS [dm3] 3L_11826110_INS [dm6]	C	CTATGTC	1.950e^-4	0.943	UPSTREAM CG32095 DOWNSTREAM CycA INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	11819215	3L_11819215_SNP [dm3] 3L_11826115_SNP [dm6]	G	A	1.950e^-4	0.943	UPSTREAM CG32095 DOWNSTREAM CycA INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	11819226	3L_11819226_DEL [dm3] 3L_11826126_DEL [dm6]	CGAGTC	C	1.950e^-4	0.943	UPSTREAM CG32095 DOWNSTREAM CycA INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	11819237	3L_11819237_SNP [dm3] 3L_11826137_SNP [dm6]	G	C	1.950e^-4	0.943	UPSTREAM CG32095 DOWNSTREAM CycA INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	11819383	3L_11819383_SNP [dm3] 3L_11826283_SNP [dm6]	A	C	1.950e^-4	0.943	UPSTREAM CG32095 DOWNSTREAM CycA INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	11819548	3L_11819548_SNP [dm3] 3L_11826448_SNP [dm6]	C	A	1.950e^-4	0.943	UPSTREAM CG32095 DOWNSTREAM CycA INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	12611856	3L_12611856_SNP [dm3] 3L_12618756_SNP [dm6]	C	T	1.950e^-4	0.943	INTRON caup
3L	13732427	3L_13732427_SNP [dm3] 3L_13739327_SNP [dm6]	C	T	1.950e^-4	0.943	INTRON bru-3
3L	1689748	3L_1689748_SNP [dm3] 3L_1689748_SNP [dm6]	A	T	1.950e^-4	0.943	INTRON CG7991
3L	1700239	3L_1700239_SNP [dm3] 3L_1700239_SNP [dm6]	C	T	1.950e^-4	0.943	DOWNSTREAM CG13931 INTRON CG7991	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_sna mE1_TFBS_HSA
3L	3629245	3L_3629245_SNP [dm3] 3L_3629245_SNP [dm6]	A	T	1.950e^-4	0.943	INTRON dar1
3L	6673515	3L_6673515_SNP [dm3] 3L_6680415_SNP [dm6]	G	T	1.950e^-4	0.943	INTERGENIC
X	16841651	X_16841651_SNP [dm3] X_16947618_SNP [dm6]	A	T	1.950e^-4	0.943	DOWNSTREAM CG13000 INTRON RhoGAP15B
X	16841725	X_16841725_SNP [dm3] X_16947692_SNP [dm6]	T	C	1.950e^-4	0.943	DOWNSTREAM CG13000 INTRON RhoGAP15B
X	16841797	X_16841797_SNP [dm3] X_16947764_SNP [dm6]	T	C	1.950e^-4	0.943	DOWNSTREAM CG13000 INTRON RhoGAP15B
X	4536891	X_4536891_SNP [dm3] X_4642858_SNP [dm6]	G	C	1.950e^-4	0.943	INTRON CG3081 & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	8242576	X_8242576_SNP [dm3] X_8348543_SNP [dm6]	A	G	1.950e^-4	0.943	INTRON nAChRalpha3
3L	13842661	3L_13842661_SNP [dm3] 3L_13849561_SNP [dm6]	C	T	2.235e^-4	0.943	SYNONYMOUS_CODING Hml
3L	13842803	3L_13842803_SNP [dm3] 3L_13849703_SNP [dm6]	G	A	2.235e^-4	0.943	INTRON Hml
3L	13842828	3L_13842828_SNP [dm3] 3L_13849728_SNP [dm6]	C	A	2.235e^-4	0.943	INTRON Hml
3L	9295216	3L_9295216_DEL [dm3] 3L_9302116_DEL [dm6]	TT	T	2.235e^-4	0.943	INTERGENIC
X	10530023	X_10530023_SNP [dm3] X_10635990_SNP [dm6]	T	C	2.288e^-4	0.943	INTRON X11Lbeta
3L	1866710	3L_1866710_SNP [dm3] 3L_1866710_SNP [dm6]	C	A	2.336e^-4	0.943	INTRON CG12025	TF binding site mE1_TFBS_cad
3L	9225005	3L_9225005_SNP [dm3] 3L_9231905_SNP [dm6]	G	A	2.336e^-4	0.943	INTERGENIC	TF binding site mE1_TFBS_inv
2L	20289867	2L_20289867_SNP [dm3] 2L_20289867_SNP [dm6]	A	G	2.401e^-4	0.943	INTERGENIC
2L	4933552	2L_4933552_SNP [dm3] 2L_4933552_SNP [dm6]	C	T	2.506e^-4	0.943	SYNONYMOUS_CODING hoe2
3R	21357066	3R_21357066_SNP [dm3] 3R_25531344_SNP [dm6]	T	A	2.542e^-4	0.943	INTRON msi
3R	21357075	3R_21357075_SNP [dm3] 3R_25531353_SNP [dm6]	A	G	2.542e^-4	0.943	INTRON msi
3R	21357088	3R_21357088_SNP [dm3] 3R_25531366_SNP [dm6]	A	G	2.542e^-4	0.943	INTRON msi
2R	18168406	2R_18168406_SNP [dm3] 2R_22280901_SNP [dm6]	T	C	2.544e^-4	0.943	INTRON dve
2L	7192212	2L_7192212_SNP [dm3] 2L_7192212_SNP [dm6]	T	A	2.549e^-4	0.943	INTRON CG4497	TF binding site mE1_TFBS_inv
3L	9221875	3L_9221875_SNP [dm3] 3L_9228775_SNP [dm6]	G	A	2.554e^-4	0.943	INTERGENIC
3L	4057579	3L_4057579_SNP [dm3] 3L_4057579_SNP [dm6]	C	G	2.568e^-4	0.943	NON_SYNONYMOUS_CODING CG1136	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	10417114	2R_10417114_INS [dm3] 2R_14529609_INS [dm6]	G	GG	2.571e^-4	0.943	INTRON ttv
2L	4078444	2L_4078444_SNP [dm3] 2L_4078444_SNP [dm6]	C	T	2.619e^-4	0.943	INTRON ed
2R	11820792	2R_11820792_SNP [dm3] 2R_15933287_SNP [dm6]	T	G	2.668e^-4	0.943	NON_SYNONYMOUS_CODING Iap2	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3L	10537663	3L_10537663_SNP [dm3] 3L_10544563_SNP [dm6]	T	G	2.678e^-4	0.943	INTRON A2bp1
3L	465564	3L_465564_SNP [dm3] 3L_465564_SNP [dm6]	A	C	2.681e^-4	0.943	INTRON klar
3L	465582	3L_465582_SNP [dm3] 3L_465582_SNP [dm6]	A	G	2.681e^-4	0.943	INTRON klar
3R	15156112	3R_15156112_DEL [dm3] 3R_19330390_DEL [dm6]	GAGTAGC	A	2.684e^-4	0.943	EXON CR43258	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4993282	3L_4993282_SNP [dm3] 3L_4993282_SNP [dm6]	A	G	2.692e^-4	0.943	DOWNSTREAM CG32232 INTRON Con	TF binding site mE1_TFBS_HSA
2R	18173625	2R_18173625_INS [dm3] 2R_22286120_INS [dm6]	C	CC	2.714e^-4	0.943	UTR_3_PRIME dve
2R	10274800	2R_10274800_SNP [dm3] 2R_14387295_SNP [dm6]	T	C	2.738e^-4	0.943	INTERGENIC
2R	10344064	2R_10344064_SNP [dm3] 2R_14456559_SNP [dm6]	A	G	2.738e^-4	0.943	INTRON Oaz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10344066	2R_10344066_SNP [dm3] 2R_14456561_SNP [dm6]	T	A	2.738e^-4	0.943	INTRON Oaz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10344067	2R_10344067_SNP [dm3] 2R_14456562_SNP [dm6]	G	C	2.738e^-4	0.943	INTRON Oaz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10344070	2R_10344070_SNP [dm3] 2R_14456565_SNP [dm6]	G	C	2.738e^-4	0.943	INTRON Oaz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10344071	2R_10344071_INS [dm3] 2R_14456566_INS [dm6]	A	ACT	2.738e^-4	0.943	INTRON Oaz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	10344543	2R_10344543_SNP [dm3] 2R_14457038_SNP [dm6]	T	C	2.738e^-4	0.943	INTRON Oaz	TF binding site BDTNP1_TFBS_dl
2R	10344621	2R_10344621_SNP [dm3] 2R_14457116_SNP [dm6]	C	G	2.738e^-4	0.943	INTRON Oaz	TF binding site BDTNP1_TFBS_dl
2R	10344627	2R_10344627_SNP [dm3] 2R_14457122_SNP [dm6]	T	C	2.738e^-4	0.943	INTRON Oaz	TF binding site BDTNP1_TFBS_dl
2R	10345297	2R_10345297_SNP [dm3] 2R_14457792_SNP [dm6]	G	T	2.738e^-4	0.943	UPSTREAM Oaz INTRON Oaz	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
2R	10345346	2R_10345346_SNP [dm3] 2R_14457841_SNP [dm6]	T	G	2.738e^-4	0.943	UPSTREAM Oaz INTRON Oaz	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
2R	10346210	2R_10346210_SNP [dm3] 2R_14458705_SNP [dm6]	G	T	2.738e^-4	0.943	UTR_5_PRIME Oaz INTRON Oaz	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
2R	20627546	2R_20627546_SNP [dm3] 2R_24740023_SNP [dm6]	A	C	2.738e^-4	0.943	UPSTREAM CR44828 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

Climb_Week3 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results