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=3.347e^-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	0.0715855

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	2.881	0.0896
In_3R_P	2.7143	0.0995

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

632 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	7883981	2R_7883981_DEL [dm3] 2R_11996476_DEL [dm6]	CCTGACAAGATAA...	T	2.215e^-5	0.952	UPSTREAM CR45319 DOWNSTREAM CR45318 INTERGENIC
2R	1708743	2R_1708743_SNP [dm3] 2R_5821238_SNP [dm6]	A	G	3.311e^-5	0.952	INTRON dpr12	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	2071035	X_2071035_SNP [dm3] X_2177002_SNP [dm6]	G	A	4.809e^-5	0.952	SYNONYMOUS_CODING Cyp4d2 EXON CR44690
3L	18419998	3L_18419998_SNP [dm3] 3L_18426898_SNP [dm6]	A	G	5.075e^-5	0.952	INTERGENIC
3L	18420044	3L_18420044_SNP [dm3] 3L_18426944_SNP [dm6]	A	G	5.075e^-5	0.952	INTERGENIC
3L	18420164	3L_18420164_SNP [dm3] 3L_18427064_SNP [dm6]	A	C	5.075e^-5	0.952	INTERGENIC
3L	14209041	3L_14209041_SNP [dm3] 3L_14215941_SNP [dm6]	C	A	6.073e^-5	0.952	INTRON nuf
3L	10715464	3L_10715464_SNP [dm3] 3L_10722364_SNP [dm6]	C	T	6.362e^-5	0.952	INTERGENIC
2R	8508752	2R_8508752_INS [dm3] 2R_12621247_INS [dm6]	A	AA	7.141e^-5	0.952	UTR_3_PRIME Galphaq DOWNSTREAM Galphaq
3L	1613273	3L_1613273_SNP [dm3] 3L_1613273_SNP [dm6]	A	T	7.980e^-5	0.952	NON_SYNONYMOUS_CODING CG12105 INTRON CG33791 & 1 other	TF binding site mE1_TFBS_cad
3L	16801950	3L_16801950_SNP [dm3] 3L_16808850_SNP [dm6]	T	G	9.016e^-5	0.952	SYNONYMOUS_CODING nudC DOWNSTREAM CG13024	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz mE1_TFBS_HSA
2R	10029833	2R_10029833_SNP [dm3] 2R_14142328_SNP [dm6]	C	G	9.160e^-5	0.952	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_ttk
X	5409592	X_5409592_SNP [dm3] X_5515559_SNP [dm6]	T	C	9.461e^-5	0.952	INTERGENIC
3L	1701602	3L_1701602_SNP [dm3] 3L_1701602_SNP [dm6]	A	T	1.031e^-4	0.952	SYNONYMOUS_CODING CG13931 INTRON CG7991	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	5484356	X_5484356_SNP [dm3] X_5590323_SNP [dm6]	G	A	1.031e^-4	0.952	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	9456384	X_9456384_SNP [dm3] X_9562351_SNP [dm6]	C	G	1.141e^-4	0.952	NON_SYNONYMOUS_CODING Cubn	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2L	1381957	2L_1381957_SNP [dm3] 2L_1381957_SNP [dm6]	A	G	1.158e^-4	0.952	SYNONYMOUS_CODING lea UPSTREAM CR44898 EXON CR44897	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	14268914	2R_14268914_SNP [dm3] 2R_18381409_SNP [dm6]	C	G	1.403e^-4	0.952	UTR_3_PRIME CG43202	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	10029195	2R_10029195_SNP [dm3] 2R_14141690_SNP [dm6]	A	G	1.435e^-4	0.952	UPSTREAM Prosap INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	27204728	3R_27204728_SNP [dm3] 3R_31379006_SNP [dm6]	T	A	1.465e^-4	0.952	INTERGENIC	TF binding site mE1_TFBS_inv
2L	13354858	2L_13354858_SNP [dm3] 2L_13354858_SNP [dm6]	A	T	1.578e^-4	0.952	UTR_5_PRIME CG9395 INTRON CG9395	TF binding site mE1_TFBS_Trl
X	13576722	X_13576722_DEL [dm3] X_13682689_DEL [dm6]	TGA	T	1.579e^-4	0.952	UPSTREAM CG11158 INTERGENIC
X	13576735	X_13576735_DEL [dm3] X_13682702_DEL [dm6]	TG	T	1.579e^-4	0.952	UPSTREAM CG11158 INTERGENIC
3L	679529	3L_679529_SNP [dm3] 3L_679529_SNP [dm6]	G	A	1.617e^-4	0.952	NON_SYNONYMOUS_CODING CG17129 DOWNSTREAM CG3386	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	679543	3L_679543_SNP [dm3] 3L_679543_SNP [dm6]	A	T	1.617e^-4	0.952	NON_SYNONYMOUS_CODING CG17129 DOWNSTREAM CG3386	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	679564	3L_679564_SNP [dm3] 3L_679564_SNP [dm6]	C	G	1.617e^-4	0.952	NON_SYNONYMOUS_CODING CG17129 DOWNSTREAM CG3386	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	679569	3L_679569_SNP [dm3] 3L_679569_SNP [dm6]	A	G	1.617e^-4	0.952	SYNONYMOUS_CODING CG17129 DOWNSTREAM CG3386	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	8999028	3L_8999028_SNP [dm3] 3L_9005928_SNP [dm6]	G	A	1.617e^-4	0.952	SYNONYMOUS_CODING Doc3	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	12678466	3L_12678466_SNP [dm3] 3L_12685366_SNP [dm6]	G	C	1.655e^-4	0.952	INTERGENIC
2R	12131054	2R_12131054_SNP [dm3] 2R_16243549_SNP [dm6]	A	G	1.674e^-4	0.952	UTR_3_PRIME CngA	TF binding site mE1_TFBS_inv
2R	9853361	2R_9853361_SNP [dm3] 2R_13965856_SNP [dm6]	G	A	1.674e^-4	0.952	DOWNSTREAM CG42806 INTRON Cp1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	9853371	2R_9853371_SNP [dm3] 2R_13965866_SNP [dm6]	G	A	1.674e^-4	0.952	DOWNSTREAM CG42806 INTRON Cp1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	4971178	3L_4971178_SNP [dm3] 3L_4971178_SNP [dm6]	G	A	1.674e^-4	0.952	INTRON Con
X	10559165	X_10559165_SNP [dm3] X_10665132_SNP [dm6]	G	A	1.674e^-4	0.952	INTRON X11Lbeta
X	16840856	X_16840856_SNP [dm3] X_16946823_SNP [dm6]	T	C	1.674e^-4	0.952	INTRON RhoGAP15B	TF binding site mE1_TFBS_zfh1
X	16841640	X_16841640_SNP [dm3] X_16947607_SNP [dm6]	A	G	1.674e^-4	0.952	DOWNSTREAM CG13000 INTRON RhoGAP15B
X	16841666	X_16841666_SNP [dm3] X_16947633_SNP [dm6]	T	G	1.674e^-4	0.952	DOWNSTREAM CG13000 INTRON RhoGAP15B
X	16841682	X_16841682_SNP [dm3] X_16947649_SNP [dm6]	C	A	1.674e^-4	0.952	DOWNSTREAM CG13000 INTRON RhoGAP15B
X	16842407	X_16842407_SNP [dm3] X_16948374_SNP [dm6]	G	C	1.674e^-4	0.952	NON_SYNONYMOUS_CODING CG13000 INTRON RhoGAP15B	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	6924102	2R_6924102_SNP [dm3] 2R_11036597_SNP [dm6]	C	G	1.702e^-4	0.952	INTRON luna
2R	19143044	2R_19143044_SNP [dm3] 2R_23255521_SNP [dm6]	T	C	1.746e^-4	0.952	INTERGENIC
X	13576720	X_13576720_SNP [dm3] X_13682687_SNP [dm6]	G	A	1.751e^-4	0.952	UPSTREAM CG11158 INTERGENIC
X	13576721	X_13576721_SNP [dm3] X_13682688_SNP [dm6]	A	T	1.751e^-4	0.952	UPSTREAM CG11158 INTERGENIC
3R	14346895	3R_14346895_SNP [dm3] 3R_18521173_SNP [dm6]	T	C	1.882e^-4	0.952	INTRON fru
3L	8856179	3L_8856179_SNP [dm3] 3L_8863079_SNP [dm6]	C	T	1.885e^-4	0.952	INTRON dally	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi
2L	16795414	2L_16795414_SNP [dm3] 2L_16795414_SNP [dm6]	C	T	1.915e^-4	0.952	SYNONYMOUS_CODING Ugt36Ba
2L	7004183	2L_7004183_SNP [dm3] 2L_7004183_SNP [dm6]	C	G	1.919e^-4	0.952	INTRON uif	TF binding site BDTNP1_TFBS_dl
2R	16891892	2R_16891892_SNP [dm3] 2R_21004387_SNP [dm6]	C	T	1.924e^-4	0.952	NON_SYNONYMOUS_CODING CG10543	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	11558445	X_11558445_SNP [dm3] X_11664412_SNP [dm6]	T	C	1.924e^-4	0.952	INTRON Ptp10D
X	11558448	X_11558448_SNP [dm3] X_11664415_SNP [dm6]	C	T	1.924e^-4	0.952	INTRON Ptp10D
X	11558451	X_11558451_SNP [dm3] X_11664418_SNP [dm6]	C	T	1.924e^-4	0.952	INTRON Ptp10D
2R	9853362	2R_9853362_SNP [dm3] 2R_13965857_SNP [dm6]	T	C	1.966e^-4	0.952	DOWNSTREAM CG42806 INTRON Cp1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2R	11587511	2R_11587511_SNP [dm3] 2R_15700006_SNP [dm6]	T	C	1.970e^-4	0.952	UTR_5_PRIME CG42662 UTR_3_PRIME CG30080 UPSTREAM CG42662	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	18271908	3L_18271908_SNP [dm3] 3L_18278808_SNP [dm6]	A	C	1.981e^-4	0.952	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr
X	13444972	X_13444972_SNP [dm3] X_13550939_SNP [dm6]	A	C	1.981e^-4	0.952	INTERGENIC
X	5409591	X_5409591_SNP [dm3] X_5515558_SNP [dm6]	C	T	1.982e^-4	0.952	INTERGENIC
2R	4496087	2R_4496087_SNP [dm3] 2R_8608582_SNP [dm6]	T	C	2.046e^-4	0.952	INTRON rgr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	6758704	3L_6758704_SNP [dm3] 3L_6765604_SNP [dm6]	G	A	2.131e^-4	0.952	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
X	8127826	X_8127826_SNP [dm3] X_8233793_SNP [dm6]	G	A	2.142e^-4	0.952	INTRON sdt	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
X	8127868	X_8127868_SNP [dm3] X_8233835_SNP [dm6]	C	A	2.142e^-4	0.952	INTRON sdt	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
X	2320148	X_2320148_SNP [dm3] X_2426115_SNP [dm6]	C	T	2.230e^-4	0.952	UPSTREAM CG32797 DOWNSTREAM gt INTERGENIC	transposable element FlyBase
3L	1608120	3L_1608120_SNP [dm3] 3L_1608120_SNP [dm6]	G	C	2.233e^-4	0.952	NON_SYNONYMOUS_CODING CG33791 UTR_3_PRIME CG18170 INTRON CG33791 & 1 other	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo
X	12648515	X_12648515_SNP [dm3] X_12754482_SNP [dm6]	C	T	2.233e^-4	0.952	EXON CR44619	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA
2R	4962248	2R_4962248_SNP [dm3] 2R_9074743_SNP [dm6]	G	A	2.272e^-4	0.952	INTRON ana
3R	10284730	3R_10284730_SNP [dm3] 3R_14459008_SNP [dm6]	T	C	2.300e^-4	0.952	INTRON cv-c
3R	3642548	3R_3642548_SNP [dm3] 3R_7816826_SNP [dm6]	G	A	2.300e^-4	0.952	INTRON CG34384
2R	10269884	2R_10269884_SNP [dm3] 2R_14382379_SNP [dm6]	C	T	2.333e^-4	0.952	SYNONYMOUS_CODING Dh44-R1
2R	10269890	2R_10269890_SNP [dm3] 2R_14382385_SNP [dm6]	C	T	2.333e^-4	0.952	SYNONYMOUS_CODING Dh44-R1
2R	19977451	2R_19977451_SNP [dm3] 2R_24089928_SNP [dm6]	T	C	2.333e^-4	0.952	SYNONYMOUS_CODING snama DOWNSTREAM snama
3R	24419837	3R_24419837_SNP [dm3] 3R_28594115_SNP [dm6]	A	G	2.379e^-4	0.952	EXON CR43440
3R	24419847	3R_24419847_SNP [dm3] 3R_28594125_SNP [dm6]	T	C	2.379e^-4	0.952	EXON CR43440
3R	24787956	3R_24787956_SNP [dm3] 3R_28962234_SNP [dm6]	A	T	2.379e^-4	0.952	INTRON CG14521
3R	24788083	3R_24788083_SNP [dm3] 3R_28962361_SNP [dm6]	G	C	2.379e^-4	0.952	INTRON CG14521
3R	7105516	3R_7105516_SNP [dm3] 3R_11279794_SNP [dm6]	A	T	2.379e^-4	0.952	INTRON CR31386
2R	1700442	2R_1700442_SNP [dm3] 2R_5812937_SNP [dm6]	C	A	2.393e^-4	0.952	INTRON dpr12	TF binding site mE1_TFBS_chinmo
X	16844610	X_16844610_SNP [dm3] X_16950577_SNP [dm6]	G	T	2.442e^-4	0.952	INTRON RhoGAP15B
3R	9978236	3R_9978236_SNP [dm3] 3R_14152514_SNP [dm6]	G	A	2.554e^-4	0.952	SYNONYMOUS_CODING CG42500 UPSTREAM CG14355 DOWNSTREAM CG9722
X	17814402	X_17814402_SNP [dm3] X_17920369_SNP [dm6]	C	G	2.557e^-4	0.952	INTRON CG6847
2L	736882	2L_736882_SNP [dm3] 2L_736882_SNP [dm6]	A	T	2.627e^-4	0.952	DOWNSTREAM Eaat2 INTERGENIC
2L	9424216	2L_9424216_SNP [dm3] 2L_9424216_SNP [dm6]	T	G	2.644e^-4	0.952	SYNONYMOUS_CODING Mco1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	1613197	3L_1613197_SNP [dm3] 3L_1613197_SNP [dm6]	C	T	2.655e^-4	0.952	SYNONYMOUS_CODING CG12105 INTRON CG33791 & 1 other
3L	19461976	3L_19461976_SNP [dm3] 3L_19468876_SNP [dm6]	A	G	2.655e^-4	0.952	DOWNSTREAM CG32214 INTERGENIC
3L	5234005	3L_5234005_SNP [dm3] 3L_5240905_SNP [dm6]	C	T	2.655e^-4	0.952	INTRON shep
3L	8033348	3L_8033348_SNP [dm3] 3L_8040248_SNP [dm6]	A	G	2.655e^-4	0.952	INTRON nmo
3L	8033368	3L_8033368_SNP [dm3] 3L_8040268_SNP [dm6]	C	T	2.655e^-4	0.952	INTRON nmo
3L	9257439	3L_9257439_SNP [dm3] 3L_9264339_SNP [dm6]	G	A	2.655e^-4	0.952	INTRON GluRIB
3L	9282104	3L_9282104_SNP [dm3] 3L_9289004_SNP [dm6]	T	G	2.661e^-4	0.952	DOWNSTREAM GluRIB INTERGENIC
2L	13354916	2L_13354916_SNP [dm3] 2L_13354916_SNP [dm6]	T	G	2.670e^-4	0.952	UTR_5_PRIME CG9395 INTRON CG9395	TF binding site mE1_TFBS_Trl
X	11103607	X_11103607_SNP [dm3] X_11209574_SNP [dm6]	T	C	2.722e^-4	0.952	INTERGENIC
X	11103616	X_11103616_SNP [dm3] X_11209583_SNP [dm6]	A	G	2.722e^-4	0.952	INTERGENIC
2R	10029505	2R_10029505_SNP [dm3] 2R_14142000_SNP [dm6]	A	T	2.756e^-4	0.952	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_ttk
2R	10029374	2R_10029374_DEL [dm3] 2R_14141869_DEL [dm6]	TT	T	2.769e^-4	0.952	UPSTREAM Prosap INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1
2R	11707907	2R_11707907_SNP [dm3] 2R_15820402_SNP [dm6]	C	T	2.769e^-4	0.952	NON_SYNONYMOUS_CODING CG33465 INTRON tun
3L	15621088	3L_15621088_SNP [dm3] 3L_15627988_SNP [dm6]	T	A	2.772e^-4	0.952	INTRON comm3
X	2359121	X_2359121_SNP [dm3] X_2465088_SNP [dm6]	A	G	2.777e^-4	0.952	INTRON boi	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
X	13576797	X_13576797_SNP [dm3] X_13682764_SNP [dm6]	T	A	2.797e^-4	0.952	UPSTREAM CG11158 INTERGENIC
3L	13185079	3L_13185079_SNP [dm3] 3L_13191979_SNP [dm6]	C	T	2.832e^-4	0.952	INTERGENIC
X	14101213	X_14101213_DEL [dm3] X_14207180_DEL [dm6]	TT	T	2.832e^-4	0.952	INTRON l_1_G0007 & 1 other
3L	18152242	3L_18152242_SNP [dm3] 3L_18159142_SNP [dm6]	A	G	2.867e^-4	0.952	NON_SYNONYMOUS_CODING CG13699	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
X	11988121	X_11988121_DEL [dm3] X_12094088_DEL [dm6]	ATGTGAAACGTAACTGCACT...	A	2.867e^-4	0.952	INTRON CR43960 & 1 other

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By genomic position
Variant impact
Gene name

Climb_Week4 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results