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=1.876e^-8)
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	0.088677

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	7.9722	0.0048
In_3R_Mo	7.0477	0.0295

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2179 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

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	4388500	3L_4388500_SNP [dm3] 3L_4388500_SNP [dm6]	G	A	8.950e^-7	0.503	INTRON slow
4	806036	4_806036_SNP [dm3] 4_785410_SNP [dm6]	T	A	1.456e^-6	0.503	INTRON MED26	transposable element FlyBase
3R	16033532	3R_16033532_SNP [dm3] 3R_20207810_SNP [dm6]	C	A	1.590e^-6	0.503	DOWNSTREAM CG17199 INTRON Nlg4
3L	4743440	3L_4743440_SNP [dm3] 3L_4743440_SNP [dm6]	C	T	2.929e^-6	0.503	INTRON RhoGEF64C
X	4444006	X_4444006_SNP [dm3] X_4549973_SNP [dm6]	G	C	3.074e^-6	0.503	UTR_3_PRIME CG11436 DOWNSTREAM CG15912 INTRON CR32773
3L	10712124	3L_10712124_INS [dm3] 3L_10719024_INS [dm6]	C	CC	3.123e^-6	0.503	INTERGENIC
4	911281	4_911281_SNP [dm3] 4_890655_SNP [dm6]	G	A	3.400e^-6	0.503	SYNONYMOUS_CODING unc-13 INTRON unc-13
4	1205061	4_1205061_SNP [dm3] 4_1184435_SNP [dm6]	A	T	3.975e^-6	0.503	INTERGENIC	transposable element FlyBase
3L	11925530	3L_11925530_SNP [dm3] 3L_11932430_SNP [dm6]	T	C	3.999e^-6	0.503	INTRON CG44837 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	9877610	3R_9877610_SNP [dm3] 3R_14051888_SNP [dm6]	C	T	4.254e^-6	0.503	INTERGENIC	TF binding site mE1_TFBS_HSA
2R	20045017	2R_20045017_SNP [dm3] 2R_24157494_SNP [dm6]	A	C	4.824e^-6	0.503	SYNONYMOUS_CODING Dat DOWNSTREAM DnaJ-60 & 1 other	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
4	869395	4_869395_SNP [dm3] 4_848769_SNP [dm6]	A	G	4.829e^-6	0.503	INTERGENIC	transposable element FlyBase
4	1072823	4_1072823_SNP [dm3] 4_1052197_SNP [dm6]	G	A	4.846e^-6	0.503	UPSTREAM CaMKII INTRON CaMKII	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb
3L	15252720	3L_15252720_SNP [dm3] 3L_15259620_SNP [dm6]	A	T	4.859e^-6	0.503	INTERGENIC	TF binding site mE1_TFBS_inv
3R	3028276	3R_3028276_SNP [dm3] 3R_7202554_SNP [dm6]	T	A	5.212e^-6	0.503	INTRON CG14609
3L	18199310	3L_18199310_SNP [dm3] 3L_18206210_SNP [dm6]	C	T	6.220e^-6	0.503	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
X	17345871	X_17345871_SNP [dm3] X_17451838_SNP [dm6]	A	T	7.019e^-6	0.503	INTRON CG8568
X	17345933	X_17345933_SNP [dm3] X_17451900_SNP [dm6]	T	C	7.120e^-6	0.503	INTRON CG8568
X	17345945	X_17345945_DEL [dm3] X_17451912_DEL [dm6]	TAA	G	7.120e^-6	0.503	INTRON CG8568
X	17345986	X_17345986_SNP [dm3] X_17451953_SNP [dm6]	C	A	7.120e^-6	0.503	INTRON CG8568
3R	15992223	3R_15992223_SNP [dm3] 3R_20166501_SNP [dm6]	A	G	7.237e^-6	0.503	INTERGENIC
3R	3028275	3R_3028275_SNP [dm3] 3R_7202553_SNP [dm6]	A	G	7.347e^-6	0.503	INTRON CG14609
2L	9083033	2L_9083033_SNP [dm3] 2L_9083033_SNP [dm6]	T	A	8.450e^-6	0.503	INTERGENIC
3R	22662469	3R_22662469_SNP [dm3] 3R_26836747_SNP [dm6]	A	G	8.763e^-6	0.503	INTRON Tl
3R	16033563	3R_16033563_SNP [dm3] 3R_20207841_SNP [dm6]	G	A	9.075e^-6	0.503	DOWNSTREAM CG17199 INTRON Nlg4
3L	10712198	3L_10712198_SNP [dm3] 3L_10719098_SNP [dm6]	G	A	9.529e^-6	0.503	INTERGENIC
X	17345922	X_17345922_SNP [dm3] X_17451889_SNP [dm6]	A	C	9.891e^-6	0.503	INTRON CG8568
4	912580	4_912580_SNP [dm3] 4_891954_SNP [dm6]	G	C	9.980e^-6	0.503	NON_SYNONYMOUS_CODING unc-13 INTRON unc-13
3L	10712195	3L_10712195_SNP [dm3] 3L_10719095_SNP [dm6]	C	A	1.053e^-5	0.503	INTERGENIC
3R	14854506	3R_14854506_SNP [dm3] 3R_19028784_SNP [dm6]	T	G	1.067e^-5	0.503	UTR_5_PRIME gatA UPSTREAM P5cr DOWNSTREAM NP15.6	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	14218680	2R_14218680_DEL [dm3] 2R_18331175_DEL [dm6]	CC	C	1.092e^-5	0.503	INTRON sbb
3L	2171477	3L_2171477_SNP [dm3] 3L_2171477_SNP [dm6]	A	C	1.286e^-5	0.503	UPSTREAM CG5704 DOWNSTREAM CR15821 INTERGENIC
4	569787	4_569787_DEL [dm3] 4_549161_DEL [dm6]	TCT	T	1.293e^-5	0.503	INTRON Thd1	transposable element FlyBase
4	1028630	4_1028630_SNP [dm3] 4_1008004_SNP [dm6]	A	C	1.457e^-5	0.503	DOWNSTREAM toy INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb
2L	19399204	2L_19399204_SNP [dm3] 2L_19399204_SNP [dm6]	C	A	1.462e^-5	0.503	UPSTREAM CG17544 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
4	967150	4_967150_SNP [dm3] 4_946524_SNP [dm6]	A	T	1.477e^-5	0.503	SYNONYMOUS_CODING mGluR UTR_3_PRIME mGluR	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
4	809073	4_809073_SNP [dm3] 4_788447_SNP [dm6]	C	T	1.477e^-5	0.503	UPSTREAM MED26 INTRON MED26	TF binding site BDTNP1_TFBS_dl
4	982386	4_982386_SNP [dm3] 4_961760_SNP [dm6]	G	C	1.477e^-5	0.503	DOWNSTREAM fuss INTRON CR44030	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
4	917516	4_917516_DEL [dm3] 4_896890_DEL [dm6]	TT	T	1.496e^-5	0.503	INTRON unc-13
4	1024906	4_1024906_SNP [dm3] 4_1004280_SNP [dm6]	A	G	1.499e^-5	0.503	SYNONYMOUS_CODING toy
4	1028952	4_1028952_SNP [dm3] 4_1008326_SNP [dm6]	G	A	1.499e^-5	0.503	DOWNSTREAM toy INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA mE1_TFBS_Trl
4	1045415	4_1045415_SNP [dm3] 4_1024789_SNP [dm6]	A	C	1.499e^-5	0.503	INTRON PlexA	transposable element FlyBase
4	1268508	4_1268508_SNP [dm3] 4_1264782_SNP [dm6]	G	A	1.499e^-5	0.503	SYNONYMOUS_CODING Caps
4	849672	4_849672_SNP [dm3] 4_829046_SNP [dm6]	A	T	1.499e^-5	0.503	INTRON Sox102F	TF binding site BDTNP1_TFBS_twi
4	849677	4_849677_INS [dm3] 4_829051_INS [dm6]	A	AGTATTTTTATTCTTGATCA...	1.499e^-5	0.503	INTRON Sox102F	TF binding site BDTNP1_TFBS_twi
4	917974	4_917974_SNP [dm3] 4_897348_SNP [dm6]	C	G	1.499e^-5	0.503	INTRON unc-13
4	927054	4_927054_SNP [dm3] 4_906428_SNP [dm6]	A	G	1.499e^-5	0.503	UTR_5_PRIME unc-13 UPSTREAM CR43361 INTRON CR43361	transposable element FlyBase
4	941570	4_941570_SNP [dm3] 4_920944_SNP [dm6]	A	G	1.499e^-5	0.503	NON_SYNONYMOUS_CODING eIF4G
4	942408	4_942408_SNP [dm3] 4_921782_SNP [dm6]	A	G	1.499e^-5	0.503	INTRON eIF4G	transposable element FlyBase
4	943898	4_943898_SNP [dm3] 4_923272_SNP [dm6]	G	C	1.499e^-5	0.503	INTRON eIF4G
4	954021	4_954021_SNP [dm3] 4_933395_SNP [dm6]	A	T	1.499e^-5	0.503	INTERGENIC	transposable element FlyBase
4	954869	4_954869_SNP [dm3] 4_934243_SNP [dm6]	A	G	1.499e^-5	0.503	INTERGENIC	transposable element FlyBase
4	960927	4_960927_SNP [dm3] 4_940301_SNP [dm6]	G	A	1.499e^-5	0.503	SYNONYMOUS_CODING mGluR INTRON mGluR
4	962616	4_962616_SNP [dm3] 4_941990_SNP [dm6]	A	T	1.499e^-5	0.503	INTRON mGluR	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	10388922	3L_10388922_SNP [dm3] 3L_10395822_SNP [dm6]	C	G	1.511e^-5	0.503	INTERGENIC
3R	25837950	3R_25837950_SNP [dm3] 3R_30012228_SNP [dm6]	T	C	1.546e^-5	0.503	INTRON CG7920	TF binding site mE1_TFBS_cad
3L	1444508	3L_1444508_SNP [dm3] 3L_1444508_SNP [dm6]	G	A	1.571e^-5	0.503	INTRON Ptp61F
4	960207	4_960207_SNP [dm3] 4_939581_SNP [dm6]	G	A	1.584e^-5	0.503	INTRON mGluR
4	1163376	4_1163376_SNP [dm3] 4_1142750_SNP [dm6]	T	C	1.596e^-5	0.503	INTRON CG32017
4	947747	4_947747_INS [dm3] 4_927121_INS [dm6]	T	TT	1.637e^-5	0.504	INTRON eIF4G
4	975007	4_975007_SNP [dm3] 4_954381_SNP [dm6]	G	A	1.667e^-5	0.504	INTRON 4E-T
2R	17622164	2R_17622164_SNP [dm3] 2R_21734659_SNP [dm6]	G	A	1.709e^-5	0.504	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	18923691	2R_18923691_SNP [dm3] 2R_23036168_SNP [dm6]	A	G	1.797e^-5	0.504	INTRON twi & 1 other	TF binding site mE1_TFBS_inv
4	1067002	4_1067002_SNP [dm3] 4_1046376_SNP [dm6]	C	T	1.806e^-5	0.504	INTRON CaMKII	transposable element FlyBase
4	1015712	4_1015712_SNP [dm3] 4_995086_SNP [dm6]	G	A	1.824e^-5	0.504	INTRON toy	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	26861958	3R_26861958_INS [dm3] 3R_31036236_INS [dm6]	G	GC	1.877e^-5	0.504	DOWNSTREAM CG33773 INTERGENIC
3R	26861930	3R_26861930_INS [dm3] 3R_31036208_INS [dm6]	G	GATTACCTGATCG...	1.904e^-5	0.504	DOWNSTREAM CG33773 INTERGENIC
3R	26862064	3R_26862064_SNP [dm3] 3R_31036342_SNP [dm6]	C	G	1.904e^-5	0.504	DOWNSTREAM CG33773 INTERGENIC
4	903318	4_903318_SNP [dm3] 4_882692_SNP [dm6]	C	T	1.926e^-5	0.504	NON_SYNONYMOUS_CODING unc-13 INTRON unc-13 EXON CR44029
3L	3031708	3L_3031708_SNP [dm3] 3L_3031708_SNP [dm6]	A	G	1.936e^-5	0.504	INTERGENIC
X	17346209	X_17346209_SNP [dm3] X_17452176_SNP [dm6]	T	A	2.038e^-5	0.504	SYNONYMOUS_CODING CG8568
4	842553	4_842553_INS [dm3] 4_821927_INS [dm6]	T	TTTTAAAAGTGTGGACGTGA...	2.099e^-5	0.504	INTRON Sox102F
4	904179	4_904179_SNP [dm3] 4_883553_SNP [dm6]	G	C	2.113e^-5	0.504	DOWNSTREAM CR44029 INTRON unc-13 EXON CR44029	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
4	904654	4_904654_SNP [dm3] 4_884028_SNP [dm6]	T	C	2.125e^-5	0.504	DOWNSTREAM CR44029 INTRON unc-13 EXON CR44029	TF binding site BDTNP1_TFBS_twi
4	959139	4_959139_SNP [dm3] 4_938513_SNP [dm6]	T	C	2.155e^-5	0.504	SYNONYMOUS_CODING mGluR
4	978162	4_978162_SNP [dm3] 4_957536_SNP [dm6]	A	G	2.159e^-5	0.504	NON_SYNONYMOUS_CODING 4E-T	TF binding site mE1_TFBS_sens
2L	12813157	2L_12813157_SNP [dm3] 2L_12813157_SNP [dm6]	C	T	2.201e^-5	0.504	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	3031716	3L_3031716_SNP [dm3] 3L_3031716_SNP [dm6]	C	T	2.207e^-5	0.504	INTERGENIC
3R	16033539	3R_16033539_SNP [dm3] 3R_20207817_SNP [dm6]	C	T	2.247e^-5	0.504	DOWNSTREAM CG17199 INTRON Nlg4
3L	8115095	3L_8115095_SNP [dm3] 3L_8121995_SNP [dm6]	T	A	2.250e^-5	0.504	NON_SYNONYMOUS_CODING ldbr DOWNSTREAM msk	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	1572463	3L_1572463_SNP [dm3] 3L_1572463_SNP [dm6]	G	A	2.261e^-5	0.504	SPLICE_SITE_REGION CG12004 INTRON CG12004	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
4	939355	4_939355_SNP [dm3] 4_918729_SNP [dm6]	T	C	2.269e^-5	0.504	SYNONYMOUS_CODING eIF4G
X	4696353	X_4696353_SNP [dm3] X_4802320_SNP [dm6]	G	C	2.272e^-5	0.504	NON_SYNONYMOUS_CODING CG2861
4	945632	4_945632_SNP [dm3] 4_925006_SNP [dm6]	C	T	2.301e^-5	0.504	INTRON eIF4G
4	960702	4_960702_SNP [dm3] 4_940076_SNP [dm6]	A	C	2.312e^-5	0.504	INTRON mGluR	transposable element FlyBase
4	1214837	4_1214837_SNP [dm3] 4_1194211_SNP [dm6]	T	C	2.371e^-5	0.504	INTRON PIP4K
3L	9969208	3L_9969208_SNP [dm3] 3L_9976108_SNP [dm6]	C	T	2.375e^-5	0.504	INTRON dpr6
3R	17362928	3R_17362928_SNP [dm3] 3R_21537206_SNP [dm6]	T	C	2.398e^-5	0.504	INTERGENIC	TF binding site mE1_TFBS_cad
3L	3351403	3L_3351403_SNP [dm3] 3L_3351403_SNP [dm6]	A	T	2.409e^-5	0.504	INTRON kst	TF binding site mE1_TFBS_cad
4	1190136	4_1190136_SNP [dm3] 4_1169510_SNP [dm6]	C	T	2.479e^-5	0.508	DOWNSTREAM Kif3C INTERGENIC	transposable element FlyBase
4	920474	4_920474_SNP [dm3] 4_899848_SNP [dm6]	T	C	2.483e^-5	0.508	SYNONYMOUS_CODING unc-13
3L	13783484	3L_13783484_SNP [dm3] 3L_13790384_SNP [dm6]	A	G	2.575e^-5	0.521	INTRON bru-3
4	1183560	4_1183560_INS [dm3] 4_1162934_INS [dm6]	A	TCGGGACTTTTCT...	2.652e^-5	0.526	UPSTREAM CG32017 INTRON Kif3C	transposable element FlyBase
3R	14689012	3R_14689012_SNP [dm3] 3R_18863290_SNP [dm6]	T	G	2.658e^-5	0.526	INTERGENIC
3R	26344696	3R_26344696_SNP [dm3] 3R_30518974_SNP [dm6]	T	G	2.705e^-5	0.526	DOWNSTREAM jdp INTRON jdp
4	921497	4_921497_SNP [dm3] 4_900871_SNP [dm6]	C	G	2.715e^-5	0.526	SYNONYMOUS_CODING unc-13
4	798906	4_798906_DEL [dm3] 4_778280_DEL [dm6]	AA	A	2.772e^-5	0.529	DOWNSTREAM MED26 INTERGENIC
4	917004	4_917004_SNP [dm3] 4_896378_SNP [dm6]	A	C	2.797e^-5	0.529	INTRON unc-13
4	1120871	4_1120871_SNP [dm3] 4_1100245_SNP [dm6]	G	A	2.830e^-5	0.529	INTRON sv
4	955133	4_955133_SNP [dm3] 4_934507_SNP [dm6]	C	A	2.874e^-5	0.529	INTERGENIC	transposable element FlyBase

Showing 1 to 100 of 1,000 entries

Previous1 2 3 4 5…10Next

By genomic position
Variant impact
Gene name

Microbiota_OTU121 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results