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=8.370e^-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
In_3R_P	0.06987

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2119 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
X	19997956	X_19997956_SNP [dm3] X_20103923_SNP [dm6]	G	A	1.211e^-6	0.629	INTERGENIC
2L	3766664	2L_3766664_SNP [dm3] 2L_3766664_SNP [dm6]	A	T	1.467e^-6	0.629	NON_SYNONYMOUS_CODING CG43707 UPSTREAM mir-1004 DOWNSTREAM CG43703 INTRON CG43707	TF binding site mE1_TFBS_Trl
X	14541580	X_14541580_SNP [dm3] X_14647547_SNP [dm6]	T	C	1.845e^-6	0.629	INTRON NetA	TF binding site BDTNP1_TFBS_twi
X	22235824	X_22235824_DEL [dm3] X_22833988_DEL [dm6]	ATA	A	2.574e^-6	0.629	UPSTREAM mir-2491 INTRON fog & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_cad mE1_TFBS_HSA
2L	3766716	2L_3766716_DEL [dm3] 2L_3766716_DEL [dm6]	AA	A	2.756e^-6	0.629	UPSTREAM mir-1004 DOWNSTREAM CG43703 INTRON CG43707	TF binding site mE1_TFBS_Trl
3R	8960769	3R_8960769_SNP [dm3] 3R_13135047_SNP [dm6]	G	A	2.809e^-6	0.629	INTRON timeout & 2 others
2L	3766861	2L_3766861_SNP [dm3] 2L_3766861_SNP [dm6]	C	A	2.916e^-6	0.629	UPSTREAM mir-1004 DOWNSTREAM CG43703 INTRON CG43707
2L	12558299	2L_12558299_SNP [dm3] 2L_12558299_SNP [dm6]	T	A	3.220e^-6	0.629	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	8960679	3R_8960679_SNP [dm3] 3R_13134957_SNP [dm6]	A	T	3.332e^-6	0.629	INTRON timeout & 2 others
3R	8954375	3R_8954375_SNP [dm3] 3R_13128653_SNP [dm6]	C	A	4.001e^-6	0.629	INTRON timeout & 1 other
X	19997869	X_19997869_SNP [dm3] X_20103836_SNP [dm6]	G	A	4.020e^-6	0.629	INTERGENIC
X	18652688	X_18652688_SNP [dm3] X_18758655_SNP [dm6]	T	C	4.058e^-6	0.629	INTERGENIC
2L	8789505	2L_8789505_SNP [dm3] 2L_8789505_SNP [dm6]	A	G	5.814e^-6	0.723	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	7126328	2R_7126328_SNP [dm3] 2R_11238823_SNP [dm6]	G	T	6.211e^-6	0.723	SYNONYMOUS_CODING CG13216 DOWNSTREAM CG13215	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_sens
3R	8960634	3R_8960634_DEL [dm3] 3R_13134912_DEL [dm6]	TCACAATTT	T	6.304e^-6	0.723	INTRON timeout & 2 others
3R	17871549	3R_17871549_DEL [dm3] 3R_22045827_DEL [dm6]	ACTGCT	A	6.579e^-6	0.723	INTRON how	TF binding site BDTNP1_TFBS_twi
2R	18504922	2R_18504922_INS [dm3] 2R_22617417_INS [dm6]	T	TGGGAGCAT	7.167e^-6	0.723	INTRON CG33143	TF binding site mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA
3R	8960669	3R_8960669_SNP [dm3] 3R_13134947_SNP [dm6]	A	G	7.304e^-6	0.723	INTRON timeout & 2 others
3L	8357024	3L_8357024_SNP [dm3] 3L_8363924_SNP [dm6]	C	A	7.380e^-6	0.723	INTERGENIC
3R	17333089	3R_17333089_SNP [dm3] 3R_21507367_SNP [dm6]	T	C	8.733e^-6	0.792	SPLICE_SITE_REGION C15 INTRON C15	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	14206844	3L_14206844_SNP [dm3] 3L_14213744_SNP [dm6]	A	G	9.142e^-6	0.792	INTRON nuf
3R	8960670	3R_8960670_SNP [dm3] 3R_13134948_SNP [dm6]	A	G	9.873e^-6	0.792	INTRON timeout & 2 others
2L	12804498	2L_12804498_DEL [dm3] 2L_12804498_DEL [dm6]	TT	T	1.044e^-5	0.792	INTERGENIC
2L	20100126	2L_20100126_SNP [dm3] 2L_20100126_SNP [dm6]	T	G	1.246e^-5	0.792	INTRON Kua
2L	1861200	2L_1861200_SNP [dm3] 2L_1861200_SNP [dm6]	G	A	1.432e^-5	0.792	INTRON CG31663
X	22242287	X_22242287_SNP [dm3] X_22840451_SNP [dm6]	G	A	1.465e^-5	0.792	INTRON fog & 1 other
2L	3766924	2L_3766924_SNP [dm3] 2L_3766924_SNP [dm6]	A	T	1.477e^-5	0.792	UPSTREAM mir-1004 INTRON CG43707
2L	5141534	2L_5141534_SNP [dm3] 2L_5141534_SNP [dm6]	T	A	1.567e^-5	0.792	INTRON Msp300	TF binding site mE1_TFBS_HSA
3R	17871557	3R_17871557_SNP [dm3] 3R_22045835_SNP [dm6]	A	T	1.569e^-5	0.792	INTRON how	TF binding site BDTNP1_TFBS_twi
3L	14206838	3L_14206838_SNP [dm3] 3L_14213738_SNP [dm6]	T	A	1.589e^-5	0.792	INTRON nuf
X	14538084	X_14538084_SNP [dm3] X_14644051_SNP [dm6]	A	T	1.690e^-5	0.792	INTRON NetA
3L	14206839	3L_14206839_SNP [dm3] 3L_14213739_SNP [dm6]	A	C	1.796e^-5	0.792	INTRON nuf
3R	27122929	3R_27122929_SNP [dm3] 3R_31297207_SNP [dm6]	C	G	1.805e^-5	0.792	INTERGENIC
3L	17551432	3L_17551432_SNP [dm3] 3L_17558332_SNP [dm6]	C	G	1.868e^-5	0.792	UPSTREAM CycT DOWNSTREAM Eip74EF INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	12099275	2L_12099275_SNP [dm3] 2L_12099275_SNP [dm6]	A	T	1.915e^-5	0.792	SYNONYMOUS_CODING Ced-12	TF binding site mE1_TFBS_chinmo
3R	27164884	3R_27164884_SNP [dm3] 3R_31339162_SNP [dm6]	T	A	1.953e^-5	0.792	INTRON CG34347	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	21631228	3R_21631228_SNP [dm3] 3R_25805506_SNP [dm6]	A	C	2.024e^-5	0.792	UPSTREAM BG642167 INTERGENIC
3L	10830056	3L_10830056_SNP [dm3] 3L_10836956_SNP [dm6]	C	A	2.026e^-5	0.792	INTERGENIC
3R	17871235	3R_17871235_SNP [dm3] 3R_22045513_SNP [dm6]	C	G	2.063e^-5	0.792	INTRON how	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	17871249	3R_17871249_SNP [dm3] 3R_22045527_SNP [dm6]	T	G	2.063e^-5	0.792	INTRON how	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	16901982	X_16901982_SNP [dm3] X_17007949_SNP [dm6]	A	G	2.125e^-5	0.792	INTRON CG45002
X	22246215	X_22246215_SNP [dm3] X_22844379_SNP [dm6]	T	C	2.165e^-5	0.792	INTRON fog & 1 other	transposable element FlyBase
2L	2420815	2L_2420815_SNP [dm3] 2L_2420815_SNP [dm6]	G	C	2.273e^-5	0.792	UPSTREAM CG9886 & 1 other INTERGENIC
2L	2420681	2L_2420681_SNP [dm3] 2L_2420681_SNP [dm6]	C	A	2.572e^-5	0.792	UPSTREAM CG34447 & 1 other INTERGENIC	insulator Insulator_Class_I.mE01
2L	3562491	2L_3562491_SNP [dm3] 2L_3562491_SNP [dm6]	A	T	2.640e^-5	0.792	DOWNSTREAM CR44747 EXON CR44309
2L	2420680	2L_2420680_SNP [dm3] 2L_2420680_SNP [dm6]	C	A	2.697e^-5	0.792	UPSTREAM CG34447 & 1 other INTERGENIC	insulator Insulator_Class_I.mE01
2L	9152091	2L_9152091_INS [dm3] 2L_9152091_INS [dm6]	A	AAAGTAATATT...	2.708e^-5	0.792	INTRON CG32982	TF binding site BDTNP1_TFBS_twi
2L	11244367	2L_11244367_SNP [dm3] 2L_11244367_SNP [dm6]	T	A	2.738e^-5	0.792	INTRON ab	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11244375	2L_11244375_SNP [dm3] 2L_11244375_SNP [dm6]	A	C	2.738e^-5	0.792	INTRON ab	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11244378	2L_11244378_SNP [dm3] 2L_11244378_SNP [dm6]	A	T	2.738e^-5	0.792	INTRON ab	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	9152065	2L_9152065_SNP [dm3] 2L_9152065_SNP [dm6]	A	T	2.789e^-5	0.792	INTRON CG32982	TF binding site BDTNP1_TFBS_twi
2R	20166720	2R_20166720_SNP [dm3] 2R_24279197_SNP [dm6]	C	G	2.798e^-5	0.792	INTRON nvy	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_chinmo
2L	2289650	2L_2289650_SNP [dm3] 2L_2289650_SNP [dm6]	C	A	2.876e^-5	0.792	UPSTREAM CG17237 DOWNSTREAM robl22E INTERGENIC
2R	13383563	2R_13383563_SNP [dm3] 2R_17496058_SNP [dm6]	A	T	2.907e^-5	0.792	DOWNSTREAM CG30103 INTERGENIC
3R	17871262	3R_17871262_SNP [dm3] 3R_22045540_SNP [dm6]	T	A	2.929e^-5	0.792	INTRON how	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	17550217	3L_17550217_SNP [dm3] 3L_17557117_SNP [dm6]	G	A	2.950e^-5	0.792	UTR_5_PRIME CycT	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens mE1_TFBS_Trl
3R	8985034	3R_8985034_SNP [dm3] 3R_13159312_SNP [dm6]	T	G	2.964e^-5	0.792	INTRON timeout
2L	12384172	2L_12384172_SNP [dm3] 2L_12384172_SNP [dm6]	C	A	3.234e^-5	0.792	INTRON bru-2	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
X	9914472	X_9914472_SNP [dm3] X_10020439_SNP [dm6]	T	C	3.253e^-5	0.792	INTRON Cht6
X	10381386	X_10381386_SNP [dm3] X_10487353_SNP [dm6]	C	A	3.263e^-5	0.792	UPSTREAM CG32687 INTERGENIC
2L	12804007	2L_12804007_SNP [dm3] 2L_12804007_SNP [dm6]	G	T	3.318e^-5	0.792	INTERGENIC
2L	12384183	2L_12384183_SNP [dm3] 2L_12384183_SNP [dm6]	G	T	3.605e^-5	0.792	INTRON bru-2	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3R	5119239	3R_5119239_SNP [dm3] 3R_9293517_SNP [dm6]	G	A	3.893e^-5	0.792	DOWNSTREAM CG8861 INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	4309389	3L_4309389_SNP [dm3] 3L_4309389_SNP [dm6]	T	G	3.897e^-5	0.792	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	18240674	3R_18240674_SNP [dm3] 3R_22414952_SNP [dm6]	T	A	3.960e^-5	0.792	SYNONYMOUS_CODING lqfR INTRON lqfR	TF binding site mE1_TFBS_cad
X	2690048	X_2690048_SNP [dm3] X_2796015_SNP [dm6]	A	C	3.985e^-5	0.792	INTRON kirre & 1 other	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
2R	1364975	2R_1364975_SNP [dm3] 2R_5477470_SNP [dm6]	A	G	4.100e^-5	0.792	INTRON CG30440
3R	26432868	3R_26432868_SNP [dm3] 3R_30607146_SNP [dm6]	G	A	4.151e^-5	0.792	NON_SYNONYMOUS_CODING CG31016	TF binding site mE1_TFBS_HSA
2L	10800719	2L_10800719_SNP [dm3] 2L_10800719_SNP [dm6]	A	T	4.158e^-5	0.792	UTR_5_PRIME CG31869 DOWNSTREAM CR44581
2L	13123193	2L_13123193_SNP [dm3] 2L_13123193_SNP [dm6]	G	A	4.162e^-5	0.792	INTERGENIC
3L	3948230	3L_3948230_SNP [dm3] 3L_3948230_SNP [dm6]	A	T	4.209e^-5	0.792	NON_SYNONYMOUS_CODING CG10853 DOWNSTREAM CG14982 & 1 other
2L	14537178	2L_14537178_SNP [dm3] 2L_14537178_SNP [dm6]	A	G	4.251e^-5	0.792	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Ubx
3R	15833857	3R_15833857_SNP [dm3] 3R_20008135_SNP [dm6]	A	T	4.328e^-5	0.792	UPSTREAM MED25 INTRON Hs6st	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
3R	20617	3R_20617_SNP [dm3] 3R_4194895_SNP [dm6]	T	G	4.428e^-5	0.792	INTRON CR33294	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	13248987	3L_13248987_SNP [dm3] 3L_13255887_SNP [dm6]	T	A	4.466e^-5	0.792	INTRON caps
3R	19007077	3R_19007077_SNP [dm3] 3R_23181355_SNP [dm6]	A	G	4.567e^-5	0.792	UPSTREAM Irk1 INTRON Irk1
2L	2789832	2L_2789832_SNP [dm3] 2L_2789832_SNP [dm6]	G	C	4.582e^-5	0.792	UTR_3_PRIME Syt1 INTRON Syt1
3R	27135758	3R_27135758_INS [dm3] 3R_31310036_INS [dm6]	A	ACTGCTGCG	4.746e^-5	0.792	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	22245290	X_22245290_SNP [dm3] X_22843454_SNP [dm6]	T	G	4.751e^-5	0.792	INTRON fog & 1 other	transposable element FlyBase
3R	18241721	3R_18241721_SNP [dm3] 3R_22415999_SNP [dm6]	T	G	4.788e^-5	0.792	SYNONYMOUS_CODING lqfR INTRON lqfR
3R	18241724	3R_18241724_SNP [dm3] 3R_22416002_SNP [dm6]	C	T	4.788e^-5	0.792	SYNONYMOUS_CODING lqfR INTRON lqfR
3R	18241757	3R_18241757_SNP [dm3] 3R_22416035_SNP [dm6]	T	A	4.788e^-5	0.792	NON_SYNONYMOUS_CODING lqfR INTRON lqfR
2L	20097212	2L_20097212_INS [dm3] 2L_20097212_INS [dm6]	C	CC	4.868e^-5	0.792	UTR_5_PRIME mRpS18B UPSTREAM Kua DOWNSTREAM nesd	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
X	9914481	X_9914481_SNP [dm3] X_10020448_SNP [dm6]	A	T	4.885e^-5	0.792	INTRON Cht6
X	22203252	X_22203252_DEL [dm3] X_22801416_DEL [dm6]	AA	A	4.915e^-5	0.792	INTERGENIC
X	22203256	X_22203256_DEL [dm3] X_22801420_DEL [dm6]	ATA	A	4.915e^-5	0.792	INTERGENIC
3L	10039434	3L_10039434_SNP [dm3] 3L_10046334_SNP [dm6]	A	G	5.000e^-5	0.792	INTRON dpr6
2L	1091833	2L_1091833_SNP [dm3] 2L_1091833_SNP [dm6]	A	G	5.000e^-5	0.792	INTRON CG4629
3L	3790076	3L_3790076_SNP [dm3] 3L_3790076_SNP [dm6]	C	T	5.023e^-5	0.792	UPSTREAM CG32266 INTRON CG32264	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2L	7524871	2L_7524871_SNP [dm3] 2L_7524871_SNP [dm6]	T	C	5.073e^-5	0.792	INTRON RapGAP1
2L	12558335	2L_12558335_SNP [dm3] 2L_12558335_SNP [dm6]	G	C	5.075e^-5	0.792	INTERGENIC	TF binding site BDTNP1_TFBS_twi
3R	23434542	3R_23434542_SNP [dm3] 3R_27608820_SNP [dm6]	C	G	5.118e^-5	0.792	INTRON Tusp	TF binding site mE1_TFBS_HSA
X	22360316	X_22360316_SNP [dm3] X_22958480_SNP [dm6]	C	A	5.140e^-5	0.792	DOWNSTREAM CG40486 EXON CR45502	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	10278999	3R_10278999_SNP [dm3] 3R_14453277_SNP [dm6]	A	G	5.201e^-5	0.792	INTRON cv-c	TF binding site mE1_TFBS_inv
X	6435691	X_6435691_SNP [dm3] X_6541658_SNP [dm6]	T	C	5.254e^-5	0.792	INTRON CG34417
3L	24300131	3L_24300131_SNP [dm3] 3L_24307031_SNP [dm6]	T	C	5.300e^-5	0.792	INTERGENIC
2R	14750486	2R_14750486_SNP [dm3] 2R_18862981_SNP [dm6]	T	A	5.312e^-5	0.792	SYNONYMOUS_CODING CG43069 UPSTREAM Jheh3 & 1 other
3L	5936907	3L_5936907_SNP [dm3] 3L_5943807_SNP [dm6]	C	A	5.346e^-5	0.792	INTRON CG33993
2L	21051991	2L_21051991_SNP [dm3] 2L_21051991_SNP [dm6]	A	G	5.358e^-5	0.792	UTR_5_PRIME CG42238 UPSTREAM CG42238	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr mE1_TFBS_Trl
3L	13679051	3L_13679051_SNP [dm3] 3L_13685951_SNP [dm6]	C	T	5.477e^-5	0.792	INTRON bru-3

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By genomic position
Variant impact
Gene name

Microbiota_OTU002 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results