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=5.645e^-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_2L_t	0.073476
In_3R_P	0.001191

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	5.0118	0.0816
In_3R_P	11.4023	0.0033

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3038 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	17107284	2R_17107284_SNP [dm3] 2R_21219779_SNP [dm6]	G	A	4.299e^-7	0.342	SYNONYMOUS_CODING ASPP	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3R	8533689	3R_8533689_SNP [dm3] 3R_12707967_SNP [dm6]	T	A	1.180e^-6	0.342	NON_SYNONYMOUS_CODING mus308	TF binding site mE1_TFBS_sens
2R	16487275	2R_16487275_SNP [dm3] 2R_20599770_SNP [dm6]	C	G	1.520e^-6	0.342	INTRON bl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	8204019	3R_8204019_SNP [dm3] 3R_12378297_SNP [dm6]	A	C	1.802e^-6	0.342	UPSTREAM GstD7 DOWNSTREAM GstD6 INTERGENIC
3R	13854142	3R_13854142_SNP [dm3] 3R_18028420_SNP [dm6]	C	T	1.835e^-6	0.342	INTERGENIC
2L	9766020	2L_9766020_SNP [dm3] 2L_9766020_SNP [dm6]	T	C	1.969e^-6	0.342	NON_SYNONYMOUS_CODING ppk18 DOWNSTREAM und
X	2105839	X_2105839_SNP [dm3] X_2211806_SNP [dm6]	G	T	2.242e^-6	0.342	INTRON msta
3R	8279247	3R_8279247_SNP [dm3] 3R_12453525_SNP [dm6]	G	A	2.620e^-6	0.342	DOWNSTREAM CG5509 INTRON CG18549	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
2L	9766707	2L_9766707_SNP [dm3] 2L_9766707_SNP [dm6]	A	G	3.490e^-6	0.342	NON_SYNONYMOUS_CODING ppk18 UPSTREAM CG4017
3R	6884979	3R_6884979_INS [dm3] 3R_11059257_INS [dm6]	T	TGACCTT	3.757e^-6	0.342	INTERGENIC
3R	4040573	3R_4040573_SNP [dm3] 3R_8214851_SNP [dm6]	A	T	4.977e^-6	0.342	INTERGENIC
3R	8278748	3R_8278748_SNP [dm3] 3R_12453026_SNP [dm6]	G	A	5.641e^-6	0.342	UTR_3_PRIME CG5509 INTRON CG18549	TF binding site BDTNP1_TFBS_prd
X	8433755	X_8433755_SNP [dm3] X_8539722_SNP [dm6]	A	G	6.048e^-6	0.342	INTRON Nrg
3L	1851422	3L_1851422_SNP [dm3] 3L_1851422_SNP [dm6]	G	C	6.274e^-6	0.342	INTRON CG13936
X	8433696	X_8433696_SNP [dm3] X_8539663_SNP [dm6]	C	T	6.562e^-6	0.342	INTRON Nrg
3R	9217965	3R_9217965_SNP [dm3] 3R_13392243_SNP [dm6]	T	G	6.565e^-6	0.342	INTRON CCHa2
2R	16487249	2R_16487249_SNP [dm3] 2R_20599744_SNP [dm6]	C	A	6.769e^-6	0.342	INTRON bl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	10453957	3L_10453957_SNP [dm3] 3L_10460857_SNP [dm6]	G	A	6.869e^-6	0.342	SYNONYMOUS_CODING Gem3	TF binding site mE1_TFBS_sens
2R	11024532	2R_11024532_SNP [dm3] 2R_15137027_SNP [dm6]	C	G	7.043e^-6	0.342	INTRON chn	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	5742621	X_5742621_SNP [dm3] X_5848588_SNP [dm6]	C	T	7.084e^-6	0.342	INTERGENIC
3L	3883534	3L_3883534_SNP [dm3] 3L_3883534_SNP [dm6]	A	G	7.547e^-6	0.342	DOWNSTREAM CR43917 INTERGENIC
3L	12876117	3L_12876117_SNP [dm3] 3L_12883017_SNP [dm6]	C	A	7.762e^-6	0.342	INTERGENIC
3R	8381991	3R_8381991_SNP [dm3] 3R_12556269_SNP [dm6]	C	T	7.817e^-6	0.342	INTRON Octbeta2R
2L	11370376	2L_11370376_SNP [dm3] 2L_11370376_SNP [dm6]	G	A	7.889e^-6	0.342	INTRON salr
3L	3883537	3L_3883537_SNP [dm3] 3L_3883537_SNP [dm6]	C	T	8.115e^-6	0.342	DOWNSTREAM CR43917 INTERGENIC
2L	8217978	2L_8217978_SNP [dm3] 2L_8217978_SNP [dm6]	A	G	8.216e^-6	0.342	UTR_5_PRIME CG8292 DOWNSTREAM Snx6	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3R	8423178	3R_8423178_SNP [dm3] 3R_12597456_SNP [dm6]	G	A	8.245e^-6	0.342	INTERGENIC
3R	8416003	3R_8416003_SNP [dm3] 3R_12590281_SNP [dm6]	G	A	8.328e^-6	0.342	INTRON Octbeta2R
3R	8425752	3R_8425752_SNP [dm3] 3R_12600030_SNP [dm6]	C	A	8.328e^-6	0.342	INTERGENIC
3R	8426517	3R_8426517_SNP [dm3] 3R_12600795_SNP [dm6]	C	T	8.328e^-6	0.342	INTERGENIC
3R	8427469	3R_8427469_SNP [dm3] 3R_12601747_SNP [dm6]	A	C	8.328e^-6	0.342	INTERGENIC
2R	12023230	2R_12023230_INS [dm3] 2R_16135725_INS [dm6]	C	CTCGC	8.569e^-6	0.342	INTRON spin	TF binding site mE1_TFBS_hkb
3R	8411355	3R_8411355_SNP [dm3] 3R_12585633_SNP [dm6]	T	A	8.895e^-6	0.342	INTRON Octbeta2R
3R	8470406	3R_8470406_SNP [dm3] 3R_12644684_SNP [dm6]	G	C	9.237e^-6	0.342	INTERGENIC
3R	8421207	3R_8421207_SNP [dm3] 3R_12595485_SNP [dm6]	C	T	9.443e^-6	0.342	UTR_5_PRIME Octbeta2R INTRON Octbeta2R	TF binding site BDTNP1_TFBS_z mE1_TFBS_chinmo mE1_TFBS_HSA
2L	2251336	2L_2251336_SNP [dm3] 2L_2251336_SNP [dm6]	A	G	9.467e^-6	0.342	UPSTREAM Ser12 DOWNSTREAM CG17239 INTERGENIC
3L	12073733	3L_12073733_SNP [dm3] 3L_12080633_SNP [dm6]	T	C	9.577e^-6	0.342	INTRON Sema-5c	TF binding site BDTNP1_TFBS_Med
3R	8156335	3R_8156335_SNP [dm3] 3R_12330613_SNP [dm6]	A	C	9.642e^-6	0.342	DOWNSTREAM CR45583 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	8164115	3R_8164115_SNP [dm3] 3R_12338393_SNP [dm6]	C	T	9.642e^-6	0.342	INTRON CR44941
3R	8352681	3R_8352681_SNP [dm3] 3R_12526959_SNP [dm6]	G	A	9.817e^-6	0.342	INTRON Octbeta3R & 1 other
3R	8451840	3R_8451840_SNP [dm3] 3R_12626118_SNP [dm6]	G	C	9.831e^-6	0.342	SYNONYMOUS_CODING Vha55	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 mE1_TFBS_cad
3L	9113341	3L_9113341_SNP [dm3] 3L_9120241_SNP [dm6]	A	C	9.900e^-6	0.342	INTRON bol
3R	8156176	3R_8156176_SNP [dm3] 3R_12330454_SNP [dm6]	G	A	1.000e^-5	0.342	DOWNSTREAM CR45583 INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	8533318	3R_8533318_SNP [dm3] 3R_12707596_SNP [dm6]	G	T	1.014e^-5	0.342	NON_SYNONYMOUS_CODING mus308
3R	8453924	3R_8453924_SNP [dm3] 3R_12628202_SNP [dm6]	C	A	1.019e^-5	0.342	UTR_5_PRIME Snx3 UPSTREAM Vha55	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_sens
3R	8539332	3R_8539332_SNP [dm3] 3R_12713610_SNP [dm6]	G	A	1.031e^-5	0.342	SYNONYMOUS_CODING Men	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
3R	8442785	3R_8442785_SNP [dm3] 3R_12617063_SNP [dm6]	A	T	1.048e^-5	0.342	INTERGENIC
3R	8383782	3R_8383782_SNP [dm3] 3R_12558060_SNP [dm6]	C	T	1.056e^-5	0.342	INTRON Octbeta2R
2R	19145065	2R_19145065_SNP [dm3] 2R_23257542_SNP [dm6]	C	T	1.058e^-5	0.342	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	2249813	2L_2249813_SNP [dm3] 2L_2249813_SNP [dm6]	T	A	1.061e^-5	0.342	DOWNSTREAM Ser12 INTERGENIC
3R	8135405	3R_8135405_SNP [dm3] 3R_12309683_SNP [dm6]	A	C	1.084e^-5	0.342	INTERGENIC
3R	8147005	3R_8147005_SNP [dm3] 3R_12321283_SNP [dm6]	C	T	1.084e^-5	0.342	INTERGENIC	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
3R	8571924	3R_8571924_SNP [dm3] 3R_12746202_SNP [dm6]	T	G	1.088e^-5	0.342	UTR_3_PRIME beat-Vc
X	6678498	X_6678498_SNP [dm3] X_6784465_SNP [dm6]	C	T	1.109e^-5	0.342	NON_SYNONYMOUS_CODING C3G	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	2250009	2L_2250009_DEL [dm3] 2L_2250009_DEL [dm6]	CT	C	1.118e^-5	0.342	DOWNSTREAM Ser12 INTERGENIC
3R	8373139	3R_8373139_SNP [dm3] 3R_12547417_SNP [dm6]	G	C	1.168e^-5	0.342	UTR_5_PRIME Octbeta3R
X	8433732	X_8433732_SNP [dm3] X_8539699_SNP [dm6]	G	T	1.174e^-5	0.342	INTRON Nrg
3R	8369544	3R_8369544_SNP [dm3] 3R_12543822_SNP [dm6]	C	A	1.174e^-5	0.342	INTRON Octbeta3R
3L	9113339	3L_9113339_SNP [dm3] 3L_9120239_SNP [dm6]	C	T	1.190e^-5	0.342	INTRON bol
2R	16486430	2R_16486430_SNP [dm3] 2R_20598925_SNP [dm6]	G	A	1.192e^-5	0.342	INTRON bl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	13858081	3R_13858081_SNP [dm3] 3R_18032359_SNP [dm6]	G	T	1.198e^-5	0.342	INTERGENIC
3R	13867841	3R_13867841_SNP [dm3] 3R_18042119_SNP [dm6]	T	C	1.220e^-5	0.342	INTERGENIC
3R	8382154	3R_8382154_SNP [dm3] 3R_12556432_SNP [dm6]	C	A	1.222e^-5	0.342	INTRON Octbeta2R
2L	18986450	2L_18986450_SNP [dm3] 2L_18986450_SNP [dm6]	T	C	1.224e^-5	0.342	INTRON Swip-1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
3L	17717884	3L_17717884_SNP [dm3] 3L_17724784_SNP [dm6]	A	G	1.251e^-5	0.342	SYNONYMOUS_CODING CG6052 INTRON Ccn
2L	2250387	2L_2250387_SNP [dm3] 2L_2250387_SNP [dm6]	A	G	1.256e^-5	0.342	DOWNSTREAM Ser12 INTERGENIC
3L	1851606	3L_1851606_SNP [dm3] 3L_1851606_SNP [dm6]	T	G	1.265e^-5	0.342	INTRON CG13936	TF binding site mE1_TFBS_cad
3R	13869799	3R_13869799_SNP [dm3] 3R_18044077_SNP [dm6]	A	T	1.269e^-5	0.342	INTERGENIC
2R	16486762	2R_16486762_SNP [dm3] 2R_20599257_SNP [dm6]	A	G	1.316e^-5	0.342	INTRON bl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	5273681	3L_5273681_SNP [dm3] 3L_5280581_SNP [dm6]	G	C	1.344e^-5	0.342	INTERGENIC
2L	10107744	2L_10107744_SNP [dm3] 2L_10107744_SNP [dm6]	C	A	1.355e^-5	0.342	INTRON CG44153 & 1 other
3R	8367190	3R_8367190_SNP [dm3] 3R_12541468_SNP [dm6]	C	G	1.371e^-5	0.342	INTRON Octbeta3R
X	8433736	X_8433736_SNP [dm3] X_8539703_SNP [dm6]	C	G	1.382e^-5	0.342	INTRON Nrg
3R	8422633	3R_8422633_SNP [dm3] 3R_12596911_SNP [dm6]	C	G	1.408e^-5	0.342	INTERGENIC
2L	2249820	2L_2249820_SNP [dm3] 2L_2249820_SNP [dm6]	C	T	1.413e^-5	0.342	DOWNSTREAM Ser12 INTERGENIC
3R	14974114	3R_14974114_SNP [dm3] 3R_19148392_SNP [dm6]	A	G	1.418e^-5	0.342	UPSTREAM Ppcs & 1 other DOWNSTREAM CG5835 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Ubx
3L	11453118	3L_11453118_SNP [dm3] 3L_11460018_SNP [dm6]	G	T	1.430e^-5	0.342	DOWNSTREAM CG7551 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	8362287	3R_8362287_SNP [dm3] 3R_12536565_SNP [dm6]	A	G	1.450e^-5	0.342	INTRON Octbeta3R
2R	3776384	2R_3776384_DEL [dm3] 2R_7888879_DEL [dm6]	GAATTTTA	G	1.459e^-5	0.342	INTERGENIC	TF binding site mE1_TFBS_chinmo
3L	4754783	3L_4754783_SNP [dm3] 3L_4754783_SNP [dm6]	T	A	1.482e^-5	0.342	UPSTREAM CR43881 INTRON RhoGEF64C
3R	8200799	3R_8200799_SNP [dm3] 3R_12375077_SNP [dm6]	C	A	1.491e^-5	0.342	UPSTREAM GstD5 DOWNSTREAM GstD4 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	3776945	2R_3776945_SNP [dm3] 2R_7889440_SNP [dm6]	C	A	1.514e^-5	0.342	UPSTREAM CG30377 INTERGENIC
3L	9113362	3L_9113362_SNP [dm3] 3L_9120262_SNP [dm6]	C	T	1.514e^-5	0.342	INTRON bol
3R	25410652	3R_25410652_DEL [dm3] 3R_29584930_DEL [dm6]	AA	A	1.574e^-5	0.351	INTERGENIC
3R	8527509	3R_8527509_SNP [dm3] 3R_12701787_SNP [dm6]	T	A	1.610e^-5	0.354	INTRON Past1
3R	8514953	3R_8514953_SNP [dm3] 3R_12689231_SNP [dm6]	C	T	1.625e^-5	0.354	UTR_5_PRIME kar DOWNSTREAM Su_fu_	TF binding site mE1_TFBS_chinmo
2L	16762818	2L_16762818_SNP [dm3] 2L_16762818_SNP [dm6]	C	A	1.645e^-5	0.355	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	9113360	3L_9113360_SNP [dm3] 3L_9120260_SNP [dm6]	A	T	1.664e^-5	0.355	INTRON bol
2L	10079342	2L_10079342_SNP [dm3] 2L_10079342_SNP [dm6]	A	G	1.699e^-5	0.358	INTRON CG44153
3L	11215510	3L_11215510_SNP [dm3] 3L_11222410_SNP [dm6]	C	T	1.716e^-5	0.358	INTRON CG42671
3L	12875986	3L_12875986_SNP [dm3] 3L_12882886_SNP [dm6]	T	C	1.739e^-5	0.358	INTERGENIC
3L	17717872	3L_17717872_SNP [dm3] 3L_17724772_SNP [dm6]	G	T	1.786e^-5	0.364	SYNONYMOUS_CODING CG6052 INTRON Ccn
2R	9826796	2R_9826796_SNP [dm3] 2R_13939291_SNP [dm6]	C	T	1.840e^-5	0.367	INTRON shot	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3R	13848782	3R_13848782_SNP [dm3] 3R_18023060_SNP [dm6]	A	T	1.863e^-5	0.367	UTR_3_PRIME CG7785 UPSTREAM CG7794
2R	3777601	2R_3777601_SNP [dm3] 2R_7890096_SNP [dm6]	T	C	1.879e^-5	0.367	START_GAINED CG30377 UTR_5_PRIME CG30377
2L	2250128	2L_2250128_SNP [dm3] 2L_2250128_SNP [dm6]	A	C	1.883e^-5	0.367	DOWNSTREAM Ser12 INTERGENIC
2R	8984745	2R_8984745_SNP [dm3] 2R_13097240_SNP [dm6]	G	A	1.901e^-5	0.367	INTERGENIC
X	5042890	X_5042890_SNP [dm3] X_5148857_SNP [dm6]	C	G	2.004e^-5	0.372	INTRON rg & 1 other
3L	11215468	3L_11215468_SNP [dm3] 3L_11222368_SNP [dm6]	A	T	2.011e^-5	0.372	INTRON CG42671
3R	8132514	3R_8132514_SNP [dm3] 3R_12306792_SNP [dm6]	C	T	2.034e^-5	0.372	INTERGENIC

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By genomic position
Variant impact
Gene name

Locomot_Activity_MPH phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results