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=1.476e^-11)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT 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
wolba	0.0102365

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	2.9724	0.0847

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2833 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
2L	5968820	2L_5968820_SNP [dm3] 2L_5968820_SNP [dm6]	A	G	1.040e^-7	0.083	SYNONYMOUS_CODING Ucp4C	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	6381735	2R_6381735_SNP [dm3] 2R_10494230_SNP [dm6]	T	C	2.154e^-7	0.083	INTRON lola
X	6772781	X_6772781_SNP [dm3] X_6878748_SNP [dm6]	G	A	2.264e^-7	0.083	NON_SYNONYMOUS_CODING CG43736 UTR_3_PRIME CG43736	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	3348146	X_3348146_SNP [dm3] X_3454113_SNP [dm6]	A	T	2.380e^-7	0.083	INTRON CR44999	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	3348142	X_3348142_SNP [dm3] X_3454109_SNP [dm6]	A	T	3.488e^-7	0.083	INTRON CR44999	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	3348153	X_3348153_SNP [dm3] X_3454120_SNP [dm6]	T	C	3.488e^-7	0.083	INTRON CR44999	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	3348200	X_3348200_SNP [dm3] X_3454167_SNP [dm6]	A	C	3.488e^-7	0.083	INTRON CR44999	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	3348130	X_3348130_SNP [dm3] X_3454097_SNP [dm6]	A	G	3.574e^-7	0.083	INTRON CR44999	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	3348184	X_3348184_SNP [dm3] X_3454151_SNP [dm6]	C	T	4.770e^-7	0.09	INTRON CR44999	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	3348168	X_3348168_SNP [dm3] X_3454135_SNP [dm6]	A	G	5.159e^-7	0.09	INTRON CR44999	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	5112616	2L_5112616_SNP [dm3] 2L_5112616_SNP [dm6]	G	A	5.312e^-7	0.09	INTRON Msp300
2L	916727	2L_916727_SNP [dm3] 2L_916727_SNP [dm6]	G	C	7.507e^-7	0.116	SYNONYMOUS_CODING GluRIIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3R	14520367	3R_14520367_SNP [dm3] 3R_18694645_SNP [dm6]	A	G	9.761e^-7	0.14	UPSTREAM CG14300 & 1 other INTERGENIC
3R	20577159	3R_20577159_SNP [dm3] 3R_24751437_SNP [dm6]	A	C	1.100e^-6	0.146	SYNONYMOUS_CODING tld	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	18388834	3L_18388834_SNP [dm3] 3L_18395734_SNP [dm6]	G	A	1.577e^-6	0.196	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	20422830	3L_20422830_SNP [dm3] 3L_20429730_SNP [dm6]	G	C	2.277e^-6	0.256	NON_SYNONYMOUS_CODING CG5262 DOWNSTREAM Las	TF binding site BDTNP1_TFBS_sna mE1_TFBS_sens
3R	17935564	3R_17935564_SNP [dm3] 3R_22109842_SNP [dm6]	G	A	2.336e^-6	0.256	INTRON CG5778	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	6550305	3L_6550305_SNP [dm3] 3L_6557205_SNP [dm6]	G	A	2.803e^-6	0.271	INTRON CG18769
3L	18388564	3L_18388564_SNP [dm3] 3L_18395464_SNP [dm6]	G	A	2.882e^-6	0.271	INTERGENIC
3L	18388454	3L_18388454_SNP [dm3] 3L_18395354_SNP [dm6]	G	C	3.000e^-6	0.271	INTERGENIC
3R	4383179	3R_4383179_SNP [dm3] 3R_8557457_SNP [dm6]	G	A	3.058e^-6	0.271	INTERGENIC
3R	26070275	3R_26070275_SNP [dm3] 3R_30244553_SNP [dm6]	C	T	3.239e^-6	0.274	SYNONYMOUS_CODING CG9733	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	21891525	2L_21891525_SNP [dm3] 2L_21891525_SNP [dm6]	A	G	3.697e^-6	0.294	UPSTREAM CR45362 INTERGENIC
2L	2867117	2L_2867117_SNP [dm3] 2L_2867117_SNP [dm6]	T	C	4.205e^-6	0.294	SYNONYMOUS_CODING CG2991
3L	10338434	3L_10338434_SNP [dm3] 3L_10345334_SNP [dm6]	G	C	4.522e^-6	0.294	INTERGENIC
3L	10338436	3L_10338436_SNP [dm3] 3L_10345336_SNP [dm6]	G	C	4.522e^-6	0.294	INTERGENIC
2R	9817658	2R_9817658_SNP [dm3] 2R_13930153_SNP [dm6]	C	T	4.653e^-6	0.294	INTRON shot
3L	24224288	3L_24224288_SNP [dm3] 3L_24231188_SNP [dm6]	G	A	4.775e^-6	0.294	INTRON Snap25
3R	26009893	3R_26009893_SNP [dm3] 3R_30184171_SNP [dm6]	A	G	4.956e^-6	0.294	EXON CR44262
3R	14524534	3R_14524534_SNP [dm3] 3R_18698812_SNP [dm6]	A	T	5.071e^-6	0.294	INTERGENIC
3R	20576948	3R_20576948_SNP [dm3] 3R_24751226_SNP [dm6]	C	T	5.392e^-6	0.294	SYNONYMOUS_CODING tld	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3L	10338440	3L_10338440_DEL [dm3] 3L_10345340_DEL [dm6]	AT	A	5.523e^-6	0.294	INTERGENIC
3L	10283261	3L_10283261_SNP [dm3] 3L_10290161_SNP [dm6]	C	A	5.958e^-6	0.294	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad
3R	20577104	3R_20577104_SNP [dm3] 3R_24751382_SNP [dm6]	C	T	6.089e^-6	0.294	SYNONYMOUS_CODING tld	TF binding site mE1_TFBS_cad
2R	18665573	2R_18665573_MNP [dm3] 2R_22778068_MNP [dm6]	AGCA	GAGG	6.175e^-6	0.294	INTRON CG42260
2R	18665544	2R_18665544_DEL [dm3] 2R_22778039_DEL [dm6]	CGCCAGAGG	C	6.527e^-6	0.294	INTRON CG42260
2R	18665570	2R_18665570_SNP [dm3] 2R_22778065_SNP [dm6]	G	A	6.550e^-6	0.294	INTRON CG42260
X	11671740	X_11671740_SNP [dm3] X_11777707_SNP [dm6]	A	G	6.604e^-6	0.294	INTRON dy
X	8367955	X_8367955_SNP [dm3] X_8473922_SNP [dm6]	G	A	6.717e^-6	0.294	NON_SYNONYMOUS_CODING Cp7Fb DOWNSTREAM Cp7Fa INTRON CG33223
3R	13417750	3R_13417750_SNP [dm3] 3R_17592028_SNP [dm6]	T	C	6.800e^-6	0.294	INTERGENIC
3L	18388589	3L_18388589_SNP [dm3] 3L_18395489_SNP [dm6]	A	T	6.822e^-6	0.294	INTERGENIC
3L	420225	3L_420225_SNP [dm3] 3L_420225_SNP [dm6]	T	C	6.845e^-6	0.294	INTERGENIC
3L	420375	3L_420375_SNP [dm3] 3L_420375_SNP [dm6]	G	A	6.845e^-6	0.294	INTERGENIC
3R	11788236	3R_11788236_SNP [dm3] 3R_15962514_SNP [dm6]	C	T	7.156e^-6	0.294	UTR_3_PRIME CG4287 DOWNSTREAM Sap47
2L	9572272	2L_9572272_SNP [dm3] 2L_9572272_SNP [dm6]	T	C	7.196e^-6	0.294	SYNONYMOUS_CODING CG3838
X	11671017	X_11671017_SNP [dm3] X_11776984_SNP [dm6]	A	G	7.510e^-6	0.294	INTRON dy	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2R	18665528	2R_18665528_DEL [dm3] 2R_22778023_DEL [dm6]	TGAATCC	T	7.604e^-6	0.294	INTRON CG42260
2R	6382789	2R_6382789_SNP [dm3] 2R_10495284_SNP [dm6]	T	A	7.634e^-6	0.294	INTRON lola
2R	19164414	2R_19164414_SNP [dm3] 2R_23276891_SNP [dm6]	T	C	7.733e^-6	0.294	INTERGENIC
2R	18665556	2R_18665556_DEL [dm3] 2R_22778051_DEL [dm6]	AGTGTCGACCGAC...	A	8.129e^-6	0.302	INTRON CG42260
3L	3122822	3L_3122822_DEL [dm3] 3L_3122822_DEL [dm6]	CC	C	8.583e^-6	0.303	UPSTREAM tRNA:CR32273 INTRON prominin-like
3L	18388585	3L_18388585_SNP [dm3] 3L_18395485_SNP [dm6]	G	A	8.717e^-6	0.303	INTERGENIC
2R	19297599	2R_19297599_SNP [dm3] 2R_23410076_SNP [dm6]	C	T	8.844e^-6	0.303	INTERGENIC
2L	21913412	2L_21913412_SNP [dm3] 2L_21913412_SNP [dm6]	C	T	8.869e^-6	0.303	DOWNSTREAM CG31600 INTERGENIC	transposable element FlyBase
2L	21913750	2L_21913750_SNP [dm3] 2L_21913750_SNP [dm6]	A	T	9.408e^-6	0.303	DOWNSTREAM CG31600 INTERGENIC
3L	7152231	3L_7152231_SNP [dm3] 3L_7159131_SNP [dm6]	C	T	9.534e^-6	0.303	DOWNSTREAM Dscam2 & 1 other INTERGENIC
2L	14183367	2L_14183367_SNP [dm3] 2L_14183367_SNP [dm6]	G	T	9.575e^-6	0.303	INTERGENIC
3L	10989699	3L_10989699_SNP [dm3] 3L_10996599_SNP [dm6]	T	A	9.599e^-6	0.303	INTRON klu	TF binding site BDTNP1_TFBS_da
2L	16707318	2L_16707318_SNP [dm3] 2L_16707318_SNP [dm6]	C	A	9.610e^-6	0.303	INTRON CG31808
X	13187524	X_13187524_SNP [dm3] X_13293491_SNP [dm6]	C	T	9.791e^-6	0.304	SYNONYMOUS_CODING CG15744 DOWNSTREAM CG1764
2R	14116338	2R_14116338_SNP [dm3] 2R_18228833_SNP [dm6]	C	T	1.055e^-5	0.317	DOWNSTREAM CR45310 EXON CR45311
2R	10323995	2R_10323995_SNP [dm3] 2R_14436490_SNP [dm6]	C	T	1.092e^-5	0.317	INTRON Oaz	TF binding site mE1_TFBS_cad
3L	10338574	3L_10338574_SNP [dm3] 3L_10345474_SNP [dm6]	T	A	1.105e^-5	0.317	INTERGENIC
2L	14024259	2L_14024259_DEL [dm3] 2L_14024259_DEL [dm6]	TAT	T	1.111e^-5	0.317	UPSTREAM CR31840 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	9817619	2R_9817619_SNP [dm3] 2R_13930114_SNP [dm6]	A	G	1.120e^-5	0.317	INTRON shot
X	11671741	X_11671741_SNP [dm3] X_11777708_SNP [dm6]	A	T	1.125e^-5	0.317	INTRON dy
X	3349115	X_3349115_SNP [dm3] X_3455082_SNP [dm6]	C	T	1.145e^-5	0.318	INTRON CR44999
3L	18915833	3L_18915833_SNP [dm3] 3L_18922733_SNP [dm6]	T	C	1.175e^-5	0.318	UTR_3_PRIME CG32204 UPSTREAM CG3819
2R	7818433	2R_7818433_SNP [dm3] 2R_11930928_SNP [dm6]	C	G	1.180e^-5	0.318	INTERGENIC	TF binding site BDTNP1_TFBS_Med
X	3350178	X_3350178_DEL [dm3] X_3456145_DEL [dm6]	TTTT	T	1.227e^-5	0.322	INTRON CR44999
X	13187637	X_13187637_SNP [dm3] X_13293604_SNP [dm6]	C	A	1.231e^-5	0.322	NON_SYNONYMOUS_CODING CG15744 DOWNSTREAM CG1764
X	11671627	X_11671627_SNP [dm3] X_11777594_SNP [dm6]	A	C	1.247e^-5	0.322	INTRON dy
2R	18665521	2R_18665521_DEL [dm3] 2R_22778016_DEL [dm6]	TA	G	1.297e^-5	0.322	INTRON CG42260
2R	18665526	2R_18665526_SNP [dm3] 2R_22778021_SNP [dm6]	A	T	1.297e^-5	0.322	INTRON CG42260
2L	6978291	2L_6978291_SNP [dm3] 2L_6978291_SNP [dm6]	G	A	1.299e^-5	0.322	SYNONYMOUS_CODING uif	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	16306925	3L_16306925_INS [dm3] 3L_16313825_INS [dm6]	A	AGAGGTAAAAACTTGTTTGC...	1.340e^-5	0.328	UPSTREAM CG13062 INTERGENIC
3L	24292019	3L_24292019_SNP [dm3] 3L_24298919_SNP [dm6]	A	C	1.389e^-5	0.33	UTR_3_PRIME Snap25
X	14195840	X_14195840_SNP [dm3] X_14301807_SNP [dm6]	A	T	1.394e^-5	0.33	INTERGENIC
3R	18490175	3R_18490175_SNP [dm3] 3R_22664453_SNP [dm6]	C	A	1.401e^-5	0.33	INTRON CG45058	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	15262577	3R_15262577_SNP [dm3] 3R_19436855_SNP [dm6]	A	G	1.418e^-5	0.33	INTRON CG31221
2R	14140809	2R_14140809_SNP [dm3] 2R_18253304_SNP [dm6]	T	A	1.454e^-5	0.332	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	11671617	X_11671617_SNP [dm3] X_11777584_SNP [dm6]	C	T	1.468e^-5	0.332	INTRON dy
2R	6058508	2R_6058508_SNP [dm3] 2R_10171003_SNP [dm6]	G	A	1.511e^-5	0.332	INTRON KCNQ
X	3349640	X_3349640_SNP [dm3] X_3455607_SNP [dm6]	G	A	1.548e^-5	0.332	INTRON CR44999
3L	10338535	3L_10338535_SNP [dm3] 3L_10345435_SNP [dm6]	T	A	1.558e^-5	0.332	INTERGENIC
X	11671625	X_11671625_SNP [dm3] X_11777592_SNP [dm6]	C	A	1.560e^-5	0.332	INTRON dy
X	11671595	X_11671595_SNP [dm3] X_11777562_SNP [dm6]	G	T	1.565e^-5	0.332	INTRON dy	TF binding site mE1_TFBS_Trl
X	8367912	X_8367912_SNP [dm3] X_8473879_SNP [dm6]	A	G	1.568e^-5	0.332	SYNONYMOUS_CODING Cp7Fb DOWNSTREAM Cp7Fa INTRON CG33223
3L	13980536	3L_13980536_SNP [dm3] 3L_13987436_SNP [dm6]	A	T	1.596e^-5	0.334	UPSTREAM CG9040 DOWNSTREAM CG17362 INTRON CG17364
2L	8585314	2L_8585314_SNP [dm3] 2L_8585314_SNP [dm6]	A	G	1.648e^-5	0.334	INTRON Sema-1a	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	19244391	X_19244391_SNP [dm3] X_19350358_SNP [dm6]	G	A	1.694e^-5	0.334	INTERGENIC
3L	10338706	3L_10338706_SNP [dm3] 3L_10345606_SNP [dm6]	A	G	1.722e^-5	0.334	INTERGENIC
2R	14140936	2R_14140936_SNP [dm3] 2R_18253431_SNP [dm6]	T	G	1.758e^-5	0.334	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	8541526	3L_8541526_SNP [dm3] 3L_8548426_SNP [dm6]	G	A	1.801e^-5	0.334	INTRON rhea	TF binding site mE1_TFBS_inv
2L	16113853	2L_16113853_SNP [dm3] 2L_16113853_SNP [dm6]	T	C	1.840e^-5	0.334	INTERGENIC
X	3349612	X_3349612_SNP [dm3] X_3455579_SNP [dm6]	T	C	1.846e^-5	0.334	INTRON CR44999
X	3349618	X_3349618_DEL [dm3] X_3455585_DEL [dm6]	CTC	C	1.846e^-5	0.334	INTRON CR44999
3R	20576765	3R_20576765_SNP [dm3] 3R_24751043_SNP [dm6]	T	C	1.860e^-5	0.334	SYNONYMOUS_CODING tld	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	7816381	2R_7816381_SNP [dm3] 2R_11928876_SNP [dm6]	T	C	1.861e^-5	0.334	DOWNSTREAM CR44312 INTERGENIC
2R	16795600	2R_16795600_DEL [dm3] 2R_20908095_DEL [dm6]	AAA	A	1.865e^-5	0.334	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA

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By genomic position
Variant impact
Gene name

Microbiota_OTU007 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results