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=3.229e^-5)
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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3016 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
3R	13477474	3R_13477474_SNP [dm3] 3R_17651752_SNP [dm6]	G	C	1.905e^-7	0.221	DOWNSTREAM CR45223 INTRON CG14322
2L	6191575	2L_6191575_DEL [dm3] 2L_6191575_DEL [dm6]	CCCGAAATGAA...	TGTTCATTT	2.375e^-7	0.221	INTRON CG34380	TF binding site mE1_TFBS_inv
2L	5006057	2L_5006057_SNP [dm3] 2L_5006057_SNP [dm6]	T	A	5.331e^-7	0.331	INTRON Rtnl1
3R	13477448	3R_13477448_DEL [dm3] 3R_17651726_DEL [dm6]	TTTTAAGAACTGTGAACTTG...	T	1.265e^-6	0.381	DOWNSTREAM CR45223 INTRON CG14322
3R	13477517	3R_13477517_SNP [dm3] 3R_17651795_SNP [dm6]	T	A	1.539e^-6	0.381	DOWNSTREAM CR45223 INTRON CG14322
3R	13477561	3R_13477561_SNP [dm3] 3R_17651839_SNP [dm6]	A	T	1.539e^-6	0.381	DOWNSTREAM CR45223 INTRON CG14322
2R	8527807	2R_8527807_SNP [dm3] 2R_12640302_SNP [dm6]	G	A	1.640e^-6	0.381	NON_SYNONYMOUS_CODING Iswi DOWNSTREAM CG8785	TF binding site mE1_TFBS_cad
2R	8533998	2R_8533998_SNP [dm3] 2R_12646493_SNP [dm6]	C	G	1.640e^-6	0.381	INTRON CG8785
3R	13478903	3R_13478903_SNP [dm3] 3R_17653181_SNP [dm6]	C	T	1.954e^-6	0.404	INTRON CG14322 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	20370005	X_20370005_SNP [dm3] X_20498978_SNP [dm6]	G	A	2.792e^-6	0.455	INTRON RhoGAP19D
3L	9610560	3L_9610560_SNP [dm3] 3L_9617460_SNP [dm6]	G	A	3.447e^-6	0.455	INTRON LanB2	TF binding site mE1_TFBS_inv
3R	22071117	3R_22071117_SNP [dm3] 3R_26245395_SNP [dm6]	G	A	3.503e^-6	0.455	INTRON CR42745
3R	1806427	3R_1806427_SNP [dm3] 3R_5980705_SNP [dm6]	A	T	3.606e^-6	0.455	INTERGENIC
3L	6247404	3L_6247404_SNP [dm3] 3L_6254304_SNP [dm6]	A	C	3.766e^-6	0.455	INTRON Best2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	20488836	2L_20488836_SNP [dm3] 2L_20488836_SNP [dm6]	G	T	4.407e^-6	0.455	UPSTREAM CR45359 DOWNSTREAM CR45360 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	9610803	3L_9610803_SNP [dm3] 3L_9617703_SNP [dm6]	G	A	4.484e^-6	0.455	INTRON LanB2
3R	13478789	3R_13478789_SNP [dm3] 3R_17653067_SNP [dm6]	T	C	4.760e^-6	0.455	INTRON CG14322 & 1 other	TF binding site BDTNP1_TFBS_dl
3R	4713655	3R_4713655_SNP [dm3] 3R_8887933_SNP [dm6]	A	C	5.022e^-6	0.455	INTRON pyd
3R	20714808	3R_20714808_SNP [dm3] 3R_24889086_SNP [dm6]	G	T	5.378e^-6	0.455	INTRON CG31121
3L	2603760	3L_2603760_SNP [dm3] 3L_2603760_SNP [dm6]	G	A	5.433e^-6	0.455	SYNONYMOUS_CODING Pxn	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	20862947	2L_20862947_SNP [dm3] 2L_20862947_SNP [dm6]	A	C	5.467e^-6	0.455	INTRON CR9337
2R	11510317	2R_11510317_SNP [dm3] 2R_15622812_SNP [dm6]	T	A	5.982e^-6	0.455	INTRON CG42524	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_chinmo
3R	20410696	3R_20410696_SNP [dm3] 3R_24584974_SNP [dm6]	T	C	7.086e^-6	0.455	NON_SYNONYMOUS_CODING CG13625 UPSTREAM mld	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2R	16121101	2R_16121101_SNP [dm3] 2R_20233596_SNP [dm6]	G	A	7.347e^-6	0.455	SYNONYMOUS_CODING CG11044 DOWNSTREAM tRNA:G3:56EFb
3R	13488585	3R_13488585_SNP [dm3] 3R_17662863_SNP [dm6]	T	C	7.431e^-6	0.455	SYNONYMOUS_CODING CG14322
3R	13472285	3R_13472285_SNP [dm3] 3R_17646563_SNP [dm6]	A	G	7.669e^-6	0.455	DOWNSTREAM tRNA:CR31578 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
2R	3508450	2R_3508450_SNP [dm3] 2R_7620945_SNP [dm6]	A	T	7.925e^-6	0.455	UPSTREAM CG1358 DOWNSTREAM CR44444 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
2R	3508452	2R_3508452_SNP [dm3] 2R_7620947_SNP [dm6]	C	A	7.925e^-6	0.455	UPSTREAM CG1358 DOWNSTREAM CR44444 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
2R	11512353	2R_11512353_SNP [dm3] 2R_15624848_SNP [dm6]	A	C	8.220e^-6	0.455	INTRON CG42524
3R	22071127	3R_22071127_SNP [dm3] 3R_26245405_SNP [dm6]	A	G	8.261e^-6	0.455	INTRON CR42745
2R	6266409	2R_6266409_SNP [dm3] 2R_10378904_SNP [dm6]	T	C	8.276e^-6	0.455	NON_SYNONYMOUS_CODING Ir47a INTRON CG42732	TF binding site mE1_TFBS_sens
2L	9592110	2L_9592110_SNP [dm3] 2L_9592110_SNP [dm6]	T	C	8.654e^-6	0.455	DOWNSTREAM CG3841 INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_inv
3R	21929381	3R_21929381_SNP [dm3] 3R_26103659_SNP [dm6]	A	C	9.612e^-6	0.455	INTERGENIC
2L	13073026	2L_13073026_DEL [dm3] 2L_13073026_DEL [dm6]	TTATTATGATGT...	T	1.001e^-5	0.455	INTERGENIC
3R	21926232	3R_21926232_SNP [dm3] 3R_26100510_SNP [dm6]	T	C	1.082e^-5	0.455	INTERGENIC	regulatory region REDfly_CRMs
3R	13478989	3R_13478989_SNP [dm3] 3R_17653267_SNP [dm6]	T	C	1.089e^-5	0.455	INTRON CG14322 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	13476708	3R_13476708_SNP [dm3] 3R_17650986_SNP [dm6]	G	A	1.098e^-5	0.455	INTRON CG14322
3L	10198592	3L_10198592_SNP [dm3] 3L_10205492_SNP [dm6]	C	T	1.215e^-5	0.455	UPSTREAM CR44538 INTERGENIC
3R	13477879	3R_13477879_SNP [dm3] 3R_17652157_SNP [dm6]	T	A	1.246e^-5	0.455	DOWNSTREAM CR45223 INTRON CG14322
3R	13477913	3R_13477913_SNP [dm3] 3R_17652191_SNP [dm6]	G	A	1.246e^-5	0.455	INTRON CG14322 EXON CR45223
3R	13478025	3R_13478025_SNP [dm3] 3R_17652303_SNP [dm6]	T	C	1.246e^-5	0.455	INTRON CG14322 EXON CR45223
3R	13478072	3R_13478072_SNP [dm3] 3R_17652350_SNP [dm6]	T	C	1.246e^-5	0.455	INTRON CG14322 EXON CR45223
3R	13478776	3R_13478776_SNP [dm3] 3R_17653054_SNP [dm6]	T	C	1.246e^-5	0.455	INTRON CG14322 & 1 other	TF binding site BDTNP1_TFBS_dl
3R	13478845	3R_13478845_SNP [dm3] 3R_17653123_SNP [dm6]	C	A	1.246e^-5	0.455	INTRON CG14322 & 1 other	TF binding site BDTNP1_TFBS_dl
3R	13478913	3R_13478913_SNP [dm3] 3R_17653191_SNP [dm6]	T	A	1.246e^-5	0.455	INTRON CG14322 & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	13481117	3R_13481117_SNP [dm3] 3R_17655395_SNP [dm6]	G	A	1.246e^-5	0.455	INTRON CG14322	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	13481221	3R_13481221_SNP [dm3] 3R_17655499_SNP [dm6]	A	G	1.246e^-5	0.455	INTRON CG14322	TF binding site BDTNP1_TFBS_dl
3R	13488252	3R_13488252_SNP [dm3] 3R_17662530_SNP [dm6]	T	G	1.246e^-5	0.455	SYNONYMOUS_CODING CG14322
3R	13488387	3R_13488387_SNP [dm3] 3R_17662665_SNP [dm6]	C	G	1.246e^-5	0.455	SYNONYMOUS_CODING CG14322
3R	13489628	3R_13489628_SNP [dm3] 3R_17663906_SNP [dm6]	C	A	1.246e^-5	0.455	NON_SYNONYMOUS_CODING CG14322
2L	1922748	2L_1922748_INS [dm3] 2L_1922748_INS [dm6]	C	CCGCACCAC	1.253e^-5	0.455	INTRON CG7337
3R	13478748	3R_13478748_SNP [dm3] 3R_17653026_SNP [dm6]	C	T	1.273e^-5	0.455	INTRON CG14322 & 1 other	TF binding site BDTNP1_TFBS_dl
2R	14193013	2R_14193013_SNP [dm3] 2R_18305508_SNP [dm6]	T	G	1.316e^-5	0.462	INTRON sbb	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
2L	7005610	2L_7005610_SNP [dm3] 2L_7005610_SNP [dm6]	C	A	1.408e^-5	0.462	INTRON uif
3R	13487388	3R_13487388_SNP [dm3] 3R_17661666_SNP [dm6]	G	A	1.421e^-5	0.462	SYNONYMOUS_CODING CG14322	TF binding site mE1_TFBS_sens
2L	20866621	2L_20866621_SNP [dm3] 2L_20866621_SNP [dm6]	G	A	1.422e^-5	0.462	INTRON CG9338
3L	18755854	3L_18755854_SNP [dm3] 3L_18762754_SNP [dm6]	T	C	1.442e^-5	0.462	INTRON ftz-f1
3R	13479029	3R_13479029_SNP [dm3] 3R_17653307_SNP [dm6]	G	C	1.502e^-5	0.462	INTRON CG14322 EXON CR45223	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	7005429	2L_7005429_SNP [dm3] 2L_7005429_SNP [dm6]	A	T	1.516e^-5	0.462	INTRON uif
3R	22071126	3R_22071126_SNP [dm3] 3R_26245404_SNP [dm6]	G	T	1.557e^-5	0.462	INTRON CR42745
2L	20486011	2L_20486011_SNP [dm3] 2L_20486011_SNP [dm6]	G	T	1.559e^-5	0.462	UPSTREAM CR45361 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	2022099	2L_2022099_SNP [dm3] 2L_2022099_SNP [dm6]	T	G	1.565e^-5	0.462	INTRON CG4238
2R	11511131	2R_11511131_SNP [dm3] 2R_15623626_SNP [dm6]	C	A	1.570e^-5	0.462	INTRON CG42524	TF binding site mE1_TFBS_chinmo
2R	11510937	2R_11510937_SNP [dm3] 2R_15623432_SNP [dm6]	A	C	1.607e^-5	0.462	INTRON CG42524	TF binding site mE1_TFBS_chinmo
3R	13469550	3R_13469550_INS [dm3] 3R_17643828_INS [dm6]	A	AAAACCTACTGA...	1.614e^-5	0.462	UPSTREAM CG43175 INTRON CG43175
2R	13906501	2R_13906501_SNP [dm3] 2R_18018996_SNP [dm6]	A	C	1.688e^-5	0.476	INTRON CG5084
3R	26572922	3R_26572922_SNP [dm3] 3R_30747200_SNP [dm6]	C	G	1.771e^-5	0.485	UPSTREAM Npc2h & 1 other INTERGENIC
X	12582410	X_12582410_SNP [dm3] X_12688377_SNP [dm6]	A	T	1.774e^-5	0.485	SYNONYMOUS_CODING Smr	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	9734030	2R_9734030_SNP [dm3] 2R_13846525_SNP [dm6]	A	C	1.908e^-5	0.486	UTR_5_PRIME CG30484 UPSTREAM Syngr	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9169358	2L_9169358_SNP [dm3] 2L_9169358_SNP [dm6]	C	T	1.942e^-5	0.486	INTRON tai
3L	5864630	3L_5864630_SNP [dm3] 3L_5871530_SNP [dm6]	C	G	1.976e^-5	0.486	UTR_5_PRIME CG5568
2L	5238251	2L_5238251_SNP [dm3] 2L_5238251_SNP [dm6]	C	T	1.983e^-5	0.486	UPSTREAM tkv INTRON tkv	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_Trl
3R	13469488	3R_13469488_SNP [dm3] 3R_17643766_SNP [dm6]	A	G	2.083e^-5	0.486	UPSTREAM CG43175 INTRON CG43175
3L	2603766	3L_2603766_SNP [dm3] 3L_2603766_SNP [dm6]	G	A	2.122e^-5	0.486	SYNONYMOUS_CODING Pxn	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	3947252	2L_3947252_SNP [dm3] 2L_3947252_SNP [dm6]	G	T	2.144e^-5	0.486	INTRON fred
3R	25149967	3R_25149967_SNP [dm3] 3R_29324245_SNP [dm6]	C	A	2.166e^-5	0.486	INTERGENIC
2L	20503598	2L_20503598_SNP [dm3] 2L_20503598_SNP [dm6]	G	A	2.188e^-5	0.486	INTERGENIC
3L	12399798	3L_12399798_SNP [dm3] 3L_12406698_SNP [dm6]	G	A	2.193e^-5	0.486	INTRON CG32103
2L	20492294	2L_20492294_DEL [dm3] 2L_20492294_DEL [dm6]	CAACCGAGC	C	2.199e^-5	0.486	INTERGENIC
3R	21535960	3R_21535960_DEL [dm3] 3R_25710238_DEL [dm6]	AG	A	2.228e^-5	0.486	INTRON LpR2
3R	21535964	3R_21535964_SNP [dm3] 3R_25710242_SNP [dm6]	G	A	2.228e^-5	0.486	INTRON LpR2
3R	21535999	3R_21535999_SNP [dm3] 3R_25710277_SNP [dm6]	T	A	2.228e^-5	0.486	INTRON LpR2
3R	13490831	3R_13490831_SNP [dm3] 3R_17665109_SNP [dm6]	C	T	2.243e^-5	0.486	INTRON CG14322	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
3R	22071100	3R_22071100_SNP [dm3] 3R_26245378_SNP [dm6]	T	A	2.276e^-5	0.486	INTRON CR42745
2L	3156268	2L_3156268_SNP [dm3] 2L_3156268_SNP [dm6]	C	T	2.293e^-5	0.486	INTRON Mad	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
3R	13493055	3R_13493055_SNP [dm3] 3R_17667333_SNP [dm6]	C	A	2.342e^-5	0.486	UPSTREAM CR45045 & 1 other INTRON CG14322	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_Trl
3L	9614934	3L_9614934_SNP [dm3] 3L_9621834_SNP [dm6]	C	T	2.343e^-5	0.486	SYNONYMOUS_CODING LanB2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	22741700	3R_22741700_INS [dm3] 3R_26915978_INS [dm6]	G	GG	2.520e^-5	0.486	INTRON sda	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA
2L	12839360	2L_12839360_SNP [dm3] 2L_12839360_SNP [dm6]	A	C	2.542e^-5	0.486	INTERGENIC
3R	26572912	3R_26572912_INS [dm3] 3R_30747190_INS [dm6]	G	GGC	2.589e^-5	0.486	UPSTREAM Npc2h & 1 other INTERGENIC
2R	18696685	2R_18696685_SNP [dm3] 2R_22809180_SNP [dm6]	C	T	2.604e^-5	0.486	INTRON stl
2R	3508473	2R_3508473_SNP [dm3] 2R_7620968_SNP [dm6]	C	G	2.611e^-5	0.486	UPSTREAM CG1358 DOWNSTREAM CR44444 INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3R	13471161	3R_13471161_SNP [dm3] 3R_17645439_SNP [dm6]	A	T	2.619e^-5	0.486	UPSTREAM tRNA:CR31578 & 2 others DOWNSTREAM CG43175 INTERGENIC	TF binding site mE1_TFBS_cad
3R	21920766	3R_21920766_SNP [dm3] 3R_26095044_SNP [dm6]	C	T	2.678e^-5	0.486	INTRON dys	regulatory region REDfly_CRMs
3L	9054881	3L_9054881_DEL [dm3] 3L_9061781_DEL [dm6]	TAACAAAGTGC...	T	2.714e^-5	0.486	INTRON Argk
3L	7741424	3L_7741424_SNP [dm3] 3L_7748324_SNP [dm6]	C	T	2.732e^-5	0.486	SYNONYMOUS_CODING CG13685 INTRON CG32373	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	21926282	3R_21926282_SNP [dm3] 3R_26100560_SNP [dm6]	T	A	2.753e^-5	0.486	INTERGENIC	regulatory region REDfly_CRMs
3R	21926287	3R_21926287_SNP [dm3] 3R_26100565_SNP [dm6]	T	C	2.753e^-5	0.486	INTERGENIC	regulatory region REDfly_CRMs
3L	10433701	3L_10433701_SNP [dm3] 3L_10440601_SNP [dm6]	A	C	2.800e^-5	0.486	INTERGENIC
2L	16135635	2L_16135635_SNP [dm3] 2L_16135635_SNP [dm6]	G	T	2.855e^-5	0.486	UPSTREAM CG34168 EXON CR44871

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By genomic position
Variant impact
Gene name

Microbiota_OTU001 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results