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=1.305e^-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	0.01135
In_2R_NS	0.07139

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	8.5685	0.0138
In_2R_NS	5.6513	0.0593

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1812 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	13875645	2R_13875645_SNP [dm3] 2R_17988140_SNP [dm6]	T	C	1.133e^-6	0.965	INTRON dpr13
2L	533659	2L_533659_SNP [dm3] 2L_533659_SNP [dm6]	T	C	2.798e^-6	0.965	INTRON ush	TF binding site mE1_TFBS_inv
3L	1363184	3L_1363184_SNP [dm3] 3L_1363184_SNP [dm6]	A	G	4.159e^-6	0.965	INTRON Ptp61F
2R	10178671	2R_10178671_SNP [dm3] 2R_14291166_SNP [dm6]	T	C	5.163e^-6	0.965	NON_SYNONYMOUS_CODING Ih UTR_5_PRIME Ih UPSTREAM Ih	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA mE1_TFBS_inv
2R	1016477	2R_1016477_SNP [dm3] 2R_5128972_SNP [dm6]	G	T	5.418e^-6	0.965	SPLICE_SITE_ACCEPTOR CR43256 UPSTREAM gus INTRON CR43256
2L	16628444	2L_16628444_SNP [dm3] 2L_16628444_SNP [dm6]	G	A	6.074e^-6	0.965	DOWNSTREAM CR44151 INTRON CG42389	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2L	16376542	2L_16376542_INS [dm3] 2L_16376542_INS [dm6]	A	AA	6.841e^-6	0.965	INTERGENIC
3R	21066407	3R_21066407_SNP [dm3] 3R_25240685_SNP [dm6]	G	A	7.091e^-6	0.965	NON_SYNONYMOUS_CODING to	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	7960518	2L_7960518_SNP [dm3] 2L_7960518_SNP [dm6]	T	C	9.387e^-6	0.965	INTRON Snoo
2L	8895957	2L_8895957_SNP [dm3] 2L_8895957_SNP [dm6]	A	G	9.485e^-6	0.965	INTERGENIC
2R	11396075	2R_11396075_SNP [dm3] 2R_15508570_SNP [dm6]	G	T	9.960e^-6	0.965	DOWNSTREAM Ir52d INTERGENIC	TF binding site mE1_TFBS_inv
2R	6340801	2R_6340801_SNP [dm3] 2R_10453296_SNP [dm6]	C	T	1.080e^-5	0.965	UPSTREAM Cyp49a1 INTRON Galphao & 1 other
X	11662833	X_11662833_SNP [dm3] X_11768800_SNP [dm6]	A	G	1.125e^-5	0.965	UTR_3_PRIME m DOWNSTREAM dy
3L	9315202	3L_9315202_SNP [dm3] 3L_9322102_SNP [dm6]	C	T	1.209e^-5	0.965	INTERGENIC
2R	1014099	2R_1014099_SNP [dm3] 2R_5126594_SNP [dm6]	C	T	1.308e^-5	0.965	UPSTREAM CR43256 INTRON gus	transposable element FlyBase
2L	8895939	2L_8895939_SNP [dm3] 2L_8895939_SNP [dm6]	C	T	1.319e^-5	0.965	INTERGENIC
2L	580962	2L_580962_SNP [dm3] 2L_580962_SNP [dm6]	A	G	1.446e^-5	0.965	INTERGENIC
2L	8896128	2L_8896128_SNP [dm3] 2L_8896128_SNP [dm6]	T	A	1.494e^-5	0.965	INTERGENIC
2L	20070325	2L_20070325_SNP [dm3] 2L_20070325_SNP [dm6]	T	C	1.555e^-5	0.965	SYNONYMOUS_CODING CG10730 INTRON bwa	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	16628423	2L_16628423_SNP [dm3] 2L_16628423_SNP [dm6]	T	C	1.653e^-5	0.965	DOWNSTREAM CR44151 INTRON CG42389	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
X	21452450	X_21452450_SNP [dm3] X_21581423_SNP [dm6]	A	T	1.727e^-5	0.965	INTERGENIC
2R	12141869	2R_12141869_SNP [dm3] 2R_16254364_SNP [dm6]	C	G	1.760e^-5	0.965	INTRON CngA
2R	1012451	2R_1012451_SNP [dm3] 2R_5124946_SNP [dm6]	A	T	1.785e^-5	0.965	INTRON gus	transposable element FlyBase
3R	24797988	3R_24797988_SNP [dm3] 3R_28972266_SNP [dm6]	G	A	1.810e^-5	0.965	EXON CR45669
2R	16114803	2R_16114803_SNP [dm3] 2R_20227298_SNP [dm6]	A	G	1.837e^-5	0.965	INTERGENIC
2L	8896082	2L_8896082_SNP [dm3] 2L_8896082_SNP [dm6]	T	C	1.975e^-5	0.965	INTERGENIC
2L	6757041	2L_6757041_SNP [dm3] 2L_6757041_SNP [dm6]	T	A	2.036e^-5	0.965	DOWNSTREAM CG11221 & 1 other INTERGENIC
2R	11849206	2R_11849206_SNP [dm3] 2R_15961701_SNP [dm6]	G	A	2.046e^-5	0.965	SYNONYMOUS_CODING Strn-Mlck INTRON Strn-Mlck	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	12141857	2R_12141857_SNP [dm3] 2R_16254352_SNP [dm6]	A	G	2.095e^-5	0.965	INTRON CngA
2L	20773285	2L_20773285_DEL [dm3] 2L_20773285_DEL [dm6]	TTATAT	T	2.097e^-5	0.965	INTRON cad	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2L	8896103	2L_8896103_SNP [dm3] 2L_8896103_SNP [dm6]	C	T	2.120e^-5	0.965	INTERGENIC
3L	12472001	3L_12472001_SNP [dm3] 3L_12478901_SNP [dm6]	T	G	2.172e^-5	0.965	INTRON CG10663
X	13032390	X_13032390_SNP [dm3] X_13138357_SNP [dm6]	A	T	2.177e^-5	0.965	UPSTREAM CG32645 INTERGENIC	TF binding site mE1_TFBS_Trl
2R	1016407	2R_1016407_SNP [dm3] 2R_5128902_SNP [dm6]	A	T	2.179e^-5	0.965	UPSTREAM gus INTRON CR43256
2R	10536054	2R_10536054_SNP [dm3] 2R_14648549_SNP [dm6]	C	G	2.303e^-5	0.965	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	18439482	2R_18439482_SNP [dm3] 2R_22551977_SNP [dm6]	A	G	2.370e^-5	0.965	UTR_3_PRIME CG6018 INTRON px	TF binding site mE1_TFBS_cad
3L	18594907	3L_18594907_SNP [dm3] 3L_18601807_SNP [dm6]	T	C	2.484e^-5	0.965	SPLICE_SITE_REGION CG13380 & 1 other INTRON CG13380 & 1 other
2R	12133569	2R_12133569_DEL [dm3] 2R_16246064_DEL [dm6]	GG	G	2.508e^-5	0.965	INTRON CngA	TF binding site mE1_TFBS_chinmo
3L	2537937	3L_2537937_SNP [dm3] 3L_2537937_SNP [dm6]	A	T	2.521e^-5	0.965	INTRON Spn
3L	9150045	3L_9150045_SNP [dm3] 3L_9156945_SNP [dm6]	G	T	2.544e^-5	0.965	INTRON Rdl
2R	18551006	2R_18551006_SNP [dm3] 2R_22663501_SNP [dm6]	C	G	2.655e^-5	0.965	UPSTREAM CG4250 DOWNSTREAM CG42566 INTERGENIC
X	16455802	X_16455802_SNP [dm3] X_16561769_SNP [dm6]	C	A	2.686e^-5	0.965	UTR_3_PRIME CanA-14F	TF binding site BDTNP1_TFBS_dl
2L	17642886	2L_17642886_SNP [dm3] 2L_17642886_SNP [dm6]	G	A	2.776e^-5	0.965	INTERGENIC
3L	4367121	3L_4367121_SNP [dm3] 3L_4367121_SNP [dm6]	C	T	2.923e^-5	0.965	SYNONYMOUS_CODING CG11342 DOWNSTREAM DopEcR & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	8896144	2L_8896144_SNP [dm3] 2L_8896144_SNP [dm6]	A	T	2.972e^-5	0.965	INTERGENIC
2R	18550983	2R_18550983_SNP [dm3] 2R_22663478_SNP [dm6]	A	G	2.986e^-5	0.965	UPSTREAM CG4250 DOWNSTREAM CG42566 INTERGENIC
2R	1015170	2R_1015170_DEL [dm3] 2R_5127665_DEL [dm6]	TA	T	3.014e^-5	0.965	UPSTREAM CR43256 INTRON gus & 1 other	TF binding site BDTNP1_TFBS_dl transposable element FlyBase
3L	1363163	3L_1363163_SNP [dm3] 3L_1363163_SNP [dm6]	G	A	3.065e^-5	0.965	INTRON Ptp61F
3L	1363173	3L_1363173_SNP [dm3] 3L_1363173_SNP [dm6]	G	A	3.189e^-5	0.965	INTRON Ptp61F
2L	8896151	2L_8896151_SNP [dm3] 2L_8896151_SNP [dm6]	T	A	3.231e^-5	0.965	INTERGENIC
3L	2335415	3L_2335415_SNP [dm3] 3L_2335415_SNP [dm6]	T	C	3.237e^-5	0.965	INTRON MsR1
2L	15978655	2L_15978655_SNP [dm3] 2L_15978655_SNP [dm6]	C	A	3.321e^-5	0.965	UPSTREAM CG10839 INTERGENIC
2L	8896148	2L_8896148_SNP [dm3] 2L_8896148_SNP [dm6]	T	A	3.408e^-5	0.965	INTERGENIC
2L	8896052	2L_8896052_SNP [dm3] 2L_8896052_SNP [dm6]	A	G	3.543e^-5	0.965	INTERGENIC
2L	14307501	2L_14307501_SNP [dm3] 2L_14307501_SNP [dm6]	T	G	3.547e^-5	0.965	INTRON wb
2L	19775435	2L_19775435_SNP [dm3] 2L_19775435_SNP [dm6]	C	G	3.572e^-5	0.965	UTR_3_PRIME CdGAPr DOWNSTREAM CdGAPr
3R	9451895	3R_9451895_MNP [dm3] 3R_13626173_MNP [dm6]	TGA	AAT	3.596e^-5	0.965	INTERGENIC
2R	1023664	2R_1023664_SNP [dm3] 2R_5136159_SNP [dm6]	A	T	3.639e^-5	0.965	INTERGENIC	transposable element FlyBase
3L	8764226	3L_8764226_SNP [dm3] 3L_8771126_SNP [dm6]	G	A	3.646e^-5	0.965	INTRON Fhos
3L	4367097	3L_4367097_SNP [dm3] 3L_4367097_SNP [dm6]	C	T	3.654e^-5	0.965	SYNONYMOUS_CODING CG11342 DOWNSTREAM DopEcR & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	4433984	2R_4433984_SNP [dm3] 2R_8546479_SNP [dm6]	C	T	3.834e^-5	0.965	INTERGENIC
2R	4434002	2R_4434002_SNP [dm3] 2R_8546497_SNP [dm6]	G	A	3.834e^-5	0.965	INTERGENIC
2L	581667	2L_581667_SNP [dm3] 2L_581667_SNP [dm6]	A	T	3.840e^-5	0.965	INTERGENIC
3L	5638590	3L_5638590_SNP [dm3] 3L_5645490_SNP [dm6]	A	T	3.993e^-5	0.965	INTRON Blimp-1
2L	8896079	2L_8896079_SNP [dm3] 2L_8896079_SNP [dm6]	C	T	3.995e^-5	0.965	INTERGENIC
2L	21067737	2L_21067737_SNP [dm3] 2L_21067737_SNP [dm6]	A	G	4.061e^-5	0.965	INTRON CG9265
3L	1363178	3L_1363178_INS [dm3] 3L_1363178_INS [dm6]	A	ATGGGCACCTAATTACTTTG...	4.133e^-5	0.965	INTRON Ptp61F
2L	8896157	2L_8896157_SNP [dm3] 2L_8896157_SNP [dm6]	C	A	4.151e^-5	0.965	INTERGENIC
X	10855844	X_10855844_SNP [dm3] X_10961811_SNP [dm6]	G	A	4.152e^-5	0.965	INTRON Myo10A
3L	1363177	3L_1363177_SNP [dm3] 3L_1363177_SNP [dm6]	T	A	4.154e^-5	0.965	INTRON Ptp61F
2R	17696189	2R_17696189_SNP [dm3] 2R_21808684_SNP [dm6]	A	C	4.181e^-5	0.965	INTERGENIC
2R	17278177	2R_17278177_SNP [dm3] 2R_21390672_SNP [dm6]	C	T	4.225e^-5	0.965	SYNONYMOUS_CODING Acox57D-d	TF binding site mE1_TFBS_cad
3L	8760685	3L_8760685_SNP [dm3] 3L_8767585_SNP [dm6]	C	T	4.441e^-5	0.965	INTRON Fhos
2R	14635901	2R_14635901_SNP [dm3] 2R_18748396_SNP [dm6]	C	T	4.563e^-5	0.965	SYNONYMOUS_CODING Hs3st-A
2R	17309989	2R_17309989_SNP [dm3] 2R_21422484_SNP [dm6]	C	A	4.577e^-5	0.965	INTRON Sdc
2R	15840265	2R_15840265_SNP [dm3] 2R_19952760_SNP [dm6]	T	C	4.580e^-5	0.965	DOWNSTREAM CG10822 INTERGENIC
3L	8030125	3L_8030125_SNP [dm3] 3L_8037025_SNP [dm6]	C	T	4.620e^-5	0.965	INTRON nmo	TF binding site mE1_TFBS_inv
2L	9214896	2L_9214896_SNP [dm3] 2L_9214896_SNP [dm6]	T	C	4.670e^-5	0.965	INTRON tai
3L	8760691	3L_8760691_SNP [dm3] 3L_8767591_SNP [dm6]	C	T	4.708e^-5	0.965	INTRON Fhos
2R	11792282	2R_11792282_SNP [dm3] 2R_15904777_SNP [dm6]	G	A	4.800e^-5	0.965	INTRON sli	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	8896084	2L_8896084_SNP [dm3] 2L_8896084_SNP [dm6]	A	T	4.835e^-5	0.965	INTERGENIC
3L	1362941	3L_1362941_SNP [dm3] 3L_1362941_SNP [dm6]	A	G	4.843e^-5	0.965	INTRON Ptp61F
3L	12829099	3L_12829099_SNP [dm3] 3L_12835999_SNP [dm6]	G	A	4.849e^-5	0.965	INTRON CG10960	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
2R	6340800	2R_6340800_SNP [dm3] 2R_10453295_SNP [dm6]	C	A	4.886e^-5	0.965	UPSTREAM Cyp49a1 INTRON Galphao & 1 other
2L	8896064	2L_8896064_SNP [dm3] 2L_8896064_SNP [dm6]	G	T	4.947e^-5	0.965	INTERGENIC
3L	11645273	3L_11645273_SNP [dm3] 3L_11652173_SNP [dm6]	G	T	4.996e^-5	0.965	INTRON CG32085
2L	4311371	2L_4311371_SNP [dm3] 2L_4311371_SNP [dm6]	A	C	5.067e^-5	0.965	INTRON tutl
3L	12471948	3L_12471948_SNP [dm3] 3L_12478848_SNP [dm6]	T	C	5.169e^-5	0.965	INTRON CG10663
X	13967118	X_13967118_SNP [dm3] X_14073085_SNP [dm6]	T	C	5.235e^-5	0.965	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_run
2R	17210639	2R_17210639_SNP [dm3] 2R_21323134_SNP [dm6]	G	A	5.250e^-5	0.965	UTR_5_PRIME CG30394 UPSTREAM dom INTRON CG30394	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_sens
3L	19961322	3L_19961322_SNP [dm3] 3L_19968222_SNP [dm6]	A	G	5.298e^-5	0.965	INTRON Ac76E
2R	1016999	2R_1016999_SNP [dm3] 2R_5129494_SNP [dm6]	A	C	5.329e^-5	0.965	DOWNSTREAM CR43256 INTERGENIC
3L	8761259	3L_8761259_SNP [dm3] 3L_8768159_SNP [dm6]	A	G	5.342e^-5	0.965	INTRON Fhos
2R	1013465	2R_1013465_SNP [dm3] 2R_5125960_SNP [dm6]	T	A	5.354e^-5	0.965	INTRON gus	transposable element FlyBase
2L	9783980	2L_9783980_SNP [dm3] 2L_9783980_SNP [dm6]	G	A	5.357e^-5	0.965	INTRON IP3K1
3R	23865322	3R_23865322_SNP [dm3] 3R_28039600_SNP [dm6]	T	A	5.373e^-5	0.965	INTRON CG34362
2R	1020514	2R_1020514_SNP [dm3] 2R_5133009_SNP [dm6]	C	G	5.456e^-5	0.965	INTERGENIC	transposable element FlyBase
2L	17641292	2L_17641292_INS [dm3] 2L_17641292_INS [dm6]	A	ATTCCTAGAACGAGGAATAT...	5.471e^-5	0.965	INTERGENIC
3R	22814530	3R_22814530_SNP [dm3] 3R_26988808_SNP [dm6]	T	A	5.549e^-5	0.965	UPSTREAM CG31075 DOWNSTREAM CG31076 INTERGENIC
3L	8760774	3L_8760774_SNP [dm3] 3L_8767674_SNP [dm6]	G	A	5.564e^-5	0.965	INTRON Fhos

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By genomic position
Variant impact
Gene name

Tolerance_PRettgeri phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results