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=6.165e^-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
In_2L_t	0.04094
In_3R_P	0.01641

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_P	5.0295	0.0809

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

3018 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	16906318	X_16906318_SNP [dm3] X_17012285_SNP [dm6]	C	A	3.538e^-9	0.004	INTRON CG45002
2L	10451494	2L_10451494_SNP [dm3] 2L_10451494_SNP [dm6]	G	T	4.999e^-9	0.004	SYNONYMOUS_CODING ppk10
2L	6157038	2L_6157038_SNP [dm3] 2L_6157038_SNP [dm6]	T	A	6.181e^-9	0.004	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
3R	26429289	3R_26429289_SNP [dm3] 3R_30603567_SNP [dm6]	C	T	1.863e^-8	0.008	NON_SYNONYMOUS_CODING CG31021 UPSTREAM PH4alphaNE3	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	18956108	2L_18956108_SNP [dm3] 2L_18956108_SNP [dm6]	C	T	2.552e^-8	0.008	NON_SYNONYMOUS_CODING CG10623
3R	26432015	3R_26432015_SNP [dm3] 3R_30606293_SNP [dm6]	G	T	2.797e^-8	0.008	NON_SYNONYMOUS_CODING CG31016 DOWNSTREAM PH4alphaNE3
2L	6157034	2L_6157034_SNP [dm3] 2L_6157034_SNP [dm6]	T	C	3.009e^-8	0.008	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
2R	12870503	2R_12870503_SNP [dm3] 2R_16982998_SNP [dm6]	T	C	3.362e^-8	0.008	INTRON Cbp53E
X	16906294	X_16906294_SNP [dm3] X_17012261_SNP [dm6]	G	A	2.288e^-7	0.047	INTRON CG45002
2L	12640743	2L_12640743_SNP [dm3] 2L_12640743_SNP [dm6]	C	A	3.471e^-7	0.063	INTRON Ref2	TF binding site mE1_TFBS_cad
2L	20840511	2L_20840511_SNP [dm3] 2L_20840511_SNP [dm6]	G	C	3.702e^-7	0.063	UPSTREAM CG31676 INTERGENIC	TF binding site mE1_TFBS_cnc mE1_TFBS_HSA
2L	6450619	2L_6450619_SNP [dm3] 2L_6450619_SNP [dm6]	C	A	7.879e^-7	0.079	INTRON retm	TF binding site mE1_TFBS_cad
3L	5551117	3L_5551117_SNP [dm3] 3L_5558017_SNP [dm6]	A	G	8.300e^-7	0.079	INTERGENIC	TF binding site mE1_TFBS_inv
3L	8796080	3L_8796080_SNP [dm3] 3L_8802980_SNP [dm6]	C	T	8.724e^-7	0.079	SYNONYMOUS_CODING CG34426 UPSTREAM CG13311 DOWNSTREAM CG32023	TF binding site mE1_TFBS_sens
2L	8362576	2L_8362576_SNP [dm3] 2L_8362576_SNP [dm6]	T	C	8.920e^-7	0.079	UPSTREAM CG7627 DOWNSTREAM RpS13 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA
3R	4038473	3R_4038473_SNP [dm3] 3R_8212751_SNP [dm6]	C	T	8.973e^-7	0.079	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	26430121	3R_26430121_SNP [dm3] 3R_30604399_SNP [dm6]	T	A	9.066e^-7	0.079	SPLICE_SITE_REGION PH4alphaNE3 DOWNSTREAM CG31021 INTRON PH4alphaNE3
3R	15292026	3R_15292026_SNP [dm3] 3R_19466304_SNP [dm6]	C	T	9.455e^-7	0.079	INTRON Dys
3L	5359500	3L_5359500_SNP [dm3] 3L_5366400_SNP [dm6]	G	T	9.739e^-7	0.079	UPSTREAM Membrin & 1 other DOWNSTREAM CG10635 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cnc mE1_TFBS_HSA
3L	5359510	3L_5359510_SNP [dm3] 3L_5366410_SNP [dm6]	T	C	9.739e^-7	0.079	UPSTREAM Membrin & 1 other DOWNSTREAM CG10635 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cnc mE1_TFBS_HSA
3L	4395182	3L_4395182_SNP [dm3] 3L_4395182_SNP [dm6]	A	T	1.022e^-6	0.079	INTRON slow
3L	2838180	3L_2838180_SNP [dm3] 3L_2838180_SNP [dm6]	C	A	1.025e^-6	0.079	INTRON CG43444
3R	15280107	3R_15280107_DEL [dm3] 3R_19454385_DEL [dm6]	TC	T	1.186e^-6	0.079	INTRON CG31221
3R	10832807	3R_10832807_SNP [dm3] 3R_15007085_SNP [dm6]	G	T	1.212e^-6	0.079	INTERGENIC
3R	20905458	3R_20905458_SNP [dm3] 3R_25079736_SNP [dm6]	A	T	1.253e^-6	0.079	INTERGENIC
3L	3854315	3L_3854315_SNP [dm3] 3L_3854315_SNP [dm6]	T	A	1.278e^-6	0.079	INTRON Awh	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	12870497	2R_12870497_SNP [dm3] 2R_16982992_SNP [dm6]	G	A	1.290e^-6	0.079	INTRON Cbp53E
3L	11053488	3L_11053488_SNP [dm3] 3L_11060388_SNP [dm6]	T	A	1.318e^-6	0.079	DOWNSTREAM CG7888 INTRON CG6321
2L	6454786	2L_6454786_SNP [dm3] 2L_6454786_SNP [dm6]	G	T	1.327e^-6	0.079	INTRON retm	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
4	216261	4_216261_SNP [dm3] 4_195635_SNP [dm6]	C	G	1.330e^-6	0.079	EXON CR44441
2R	13483176	2R_13483176_SNP [dm3] 2R_17595671_SNP [dm6]	A	C	1.331e^-6	0.079	NON_SYNONYMOUS_CODING CG11423 INTRON lack
3L	9839120	3L_9839120_SNP [dm3] 3L_9846020_SNP [dm6]	G	A	1.450e^-6	0.079	INTRON RasGAP1	TF binding site BDTNP1_TFBS_dl
4	121889	4_121889_SNP [dm3] 4_101263_SNP [dm6]	C	A	1.457e^-6	0.079	UTR_3_PRIME pan INTRON pan	transposable element FlyBase
3L	5359558	3L_5359558_SNP [dm3] 3L_5366458_SNP [dm6]	A	C	1.469e^-6	0.079	UTR_5_PRIME Membrin UPSTREAM Uev1A DOWNSTREAM CG10635	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cnc mE1_TFBS_HSA
3R	22154942	3R_22154942_SNP [dm3] 3R_26329220_SNP [dm6]	T	A	1.488e^-6	0.079	INTRON CG33970
2L	6718240	2L_6718240_SNP [dm3] 2L_6718240_SNP [dm6]	A	T	1.527e^-6	0.079	NON_SYNONYMOUS_CODING Aatf	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	6817445	2L_6817445_INS [dm3] 2L_6817445_INS [dm6]	A	AA	1.592e^-6	0.079	INTERGENIC	TF binding site mE1_TFBS_cad
2R	13483175	2R_13483175_SNP [dm3] 2R_17595670_SNP [dm6]	G	A	1.623e^-6	0.079	SYNONYMOUS_CODING CG11423 INTRON lack
3L	2835610	3L_2835610_SNP [dm3] 3L_2835610_SNP [dm6]	G	T	1.701e^-6	0.081	INTRON CG43444
3R	22886906	3R_22886906_SNP [dm3] 3R_27061184_SNP [dm6]	A	G	1.784e^-6	0.083	SPLICE_SITE_REGION Nep5 INTRON Nep5
3R	26433919	3R_26433919_SNP [dm3] 3R_30608197_SNP [dm6]	C	T	1.885e^-6	0.084	UTR_3_PRIME CG31016 DOWNSTREAM CG31016
3R	26433920	3R_26433920_SNP [dm3] 3R_30608198_SNP [dm6]	C	T	1.885e^-6	0.084	UTR_3_PRIME CG31016 DOWNSTREAM CG31016
X	16336970	X_16336970_SNP [dm3] X_16442937_SNP [dm6]	A	G	1.943e^-6	0.084	INTRON rngo	TF binding site BDTNP1_TFBS_dl
3L	3572496	3L_3572496_SNP [dm3] 3L_3572496_SNP [dm6]	T	G	2.049e^-6	0.087	INTRON Eip63E
2R	12870593	2R_12870593_SNP [dm3] 2R_16983088_SNP [dm6]	T	C	2.353e^-6	0.092	INTRON Cbp53E
3R	26429170	3R_26429170_SNP [dm3] 3R_30603448_SNP [dm6]	G	T	2.558e^-6	0.092	NON_SYNONYMOUS_CODING CG31021 UPSTREAM PH4alphaNE3	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	26429813	3R_26429813_INS [dm3] 3R_30604091_INS [dm6]	G	TCTTTA	2.558e^-6	0.092	UPSTREAM PH4alphaNE3 DOWNSTREAM CG31021 INTERGENIC
3R	26430076	3R_26430076_DEL [dm3] 3R_30604354_DEL [dm6]	CAA	TT	2.558e^-6	0.092	DOWNSTREAM CG31021 INTRON PH4alphaNE3
3R	26430097	3R_26430097_SNP [dm3] 3R_30604375_SNP [dm6]	C	A	2.558e^-6	0.092	DOWNSTREAM CG31021 INTRON PH4alphaNE3
3R	26430207	3R_26430207_SNP [dm3] 3R_30604485_SNP [dm6]	T	C	2.558e^-6	0.092	SYNONYMOUS_CODING PH4alphaNE3 DOWNSTREAM CG31021
2R	8435171	2R_8435171_DEL [dm3] 2R_12547666_DEL [dm6]	TT	T	2.578e^-6	0.092	INTRON fra
X	10202931	X_10202931_SNP [dm3] X_10308898_SNP [dm6]	C	G	2.580e^-6	0.092	UTR_5_PRIME alpha-Man-I INTRON alpha-Man-I	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sbb mE1_TFBS_Trl
2L	12640744	2L_12640744_SNP [dm3] 2L_12640744_SNP [dm6]	C	A	2.765e^-6	0.092	INTRON Ref2	TF binding site mE1_TFBS_cad
3L	10930028	3L_10930028_SNP [dm3] 3L_10936928_SNP [dm6]	G	C	2.769e^-6	0.092	INTERGENIC
2L	12640849	2L_12640849_SNP [dm3] 2L_12640849_SNP [dm6]	A	G	2.788e^-6	0.092	INTRON Ref2
3R	22883537	3R_22883537_SNP [dm3] 3R_27057815_SNP [dm6]	A	T	2.971e^-6	0.092	UTR_3_PRIME RYa-R DOWNSTREAM Nep5 & 1 other	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	22885484	3R_22885484_SNP [dm3] 3R_27059762_SNP [dm6]	G	C	2.971e^-6	0.092	SYNONYMOUS_CODING Nep5
3R	22885505	3R_22885505_SNP [dm3] 3R_27059783_SNP [dm6]	T	C	2.971e^-6	0.092	SYNONYMOUS_CODING Nep5
X	16906299	X_16906299_SNP [dm3] X_17012266_SNP [dm6]	A	T	2.972e^-6	0.092	INTRON CG45002
2L	2925901	2L_2925901_SNP [dm3] 2L_2925901_SNP [dm6]	G	A	3.059e^-6	0.092	INTRON lilli
2L	8371471	2L_8371471_SNP [dm3] 2L_8371471_SNP [dm6]	T	C	3.077e^-6	0.092	UPSTREAM CR45341 INTRON CG17292
3R	26429490	3R_26429490_SNP [dm3] 3R_30603768_SNP [dm6]	G	C	3.156e^-6	0.092	NON_SYNONYMOUS_CODING CG31021 UPSTREAM PH4alphaNE3	TF binding site mE1_TFBS_HSA
3R	26430090	3R_26430090_SNP [dm3] 3R_30604368_SNP [dm6]	G	C	3.156e^-6	0.092	DOWNSTREAM CG31021 INTRON PH4alphaNE3
3R	26431706	3R_26431706_SNP [dm3] 3R_30605984_SNP [dm6]	C	G	3.156e^-6	0.092	UTR_3_PRIME PH4alphaNE3 UPSTREAM CG31016
3R	26432390	3R_26432390_SNP [dm3] 3R_30606668_SNP [dm6]	G	A	3.245e^-6	0.093	NON_SYNONYMOUS_CODING CG31016 DOWNSTREAM PH4alphaNE3
3L	2838330	3L_2838330_SNP [dm3] 3L_2838330_SNP [dm6]	C	A	3.373e^-6	0.093	INTRON CG43444
X	16414137	X_16414137_DEL [dm3] X_16520104_DEL [dm6]	AGATTTGCTAAA...	A	3.393e^-6	0.093	INTRON para
2L	6717559	2L_6717559_SNP [dm3] 2L_6717559_SNP [dm6]	C	T	3.403e^-6	0.093	UPSTREAM Aatf INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	22884932	3R_22884932_SNP [dm3] 3R_27059210_SNP [dm6]	C	A	3.589e^-6	0.097	INTRON Nep5
2L	10946006	2L_10946006_SNP [dm3] 2L_10946006_SNP [dm6]	A	C	3.824e^-6	0.101	INTRON dpr2
2L	7990409	2L_7990409_DEL [dm3] 2L_7990409_DEL [dm6]	AGATATCGAGAAACCCATTG...	A	3.918e^-6	0.101	DOWNSTREAM pes INTRON pes	TF binding site mE1_TFBS_inv
3R	26769990	3R_26769990_SNP [dm3] 3R_30944268_SNP [dm6]	G	A	4.000e^-6	0.101	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	12079046	3R_12079046_SNP [dm3] 3R_16253324_SNP [dm6]	T	C	4.010e^-6	0.101	INTRON tara	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	18807253	3R_18807253_SNP [dm3] 3R_22981531_SNP [dm6]	A	C	4.020e^-6	0.101	UTR_3_PRIME Nha2
3R	26430095	3R_26430095_SNP [dm3] 3R_30604373_SNP [dm6]	C	T	4.124e^-6	0.102	DOWNSTREAM CG31021 INTRON PH4alphaNE3
3R	4311420	3R_4311420_SNP [dm3] 3R_8485698_SNP [dm6]	G	A	4.183e^-6	0.102	INTERGENIC
2L	11288419	2L_11288419_SNP [dm3] 2L_11288419_SNP [dm6]	A	G	4.218e^-6	0.102	INTERGENIC
3L	18254696	3L_18254696_SNP [dm3] 3L_18261596_SNP [dm6]	A	T	4.340e^-6	0.103	INTERGENIC
2R	7130028	2R_7130028_SNP [dm3] 2R_11242523_SNP [dm6]	T	C	4.420e^-6	0.103	UPSTREAM Listericin INTERGENIC
3L	5200636	3L_5200636_SNP [dm3] 3L_5207536_SNP [dm6]	A	G	4.518e^-6	0.103	INTRON shep
2L	12266907	2L_12266907_SNP [dm3] 2L_12266907_SNP [dm6]	C	G	4.603e^-6	0.103	INTRON aret
2R	3618313	2R_3618313_SNP [dm3] 2R_7730808_SNP [dm6]	G	A	4.624e^-6	0.103	INTRON CG18812
X	8429489	X_8429489_SNP [dm3] X_8535456_SNP [dm6]	C	T	4.634e^-6	0.103	INTRON Nrg
3R	7121991	3R_7121991_SNP [dm3] 3R_11296269_SNP [dm6]	T	G	4.692e^-6	0.103	INTRON CR31386	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	5199993	3L_5199993_SNP [dm3] 3L_5206893_SNP [dm6]	G	A	4.751e^-6	0.103	INTRON shep
3R	19022468	3R_19022468_SNP [dm3] 3R_23196746_SNP [dm6]	C	G	4.765e^-6	0.103	INTRON cnc	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	6457384	2L_6457384_SNP [dm3] 2L_6457384_SNP [dm6]	T	G	5.045e^-6	0.108	SYNONYMOUS_CODING frj	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	2835602	3L_2835602_SNP [dm3] 3L_2835602_SNP [dm6]	C	A	5.150e^-6	0.109	INTRON CG43444
3R	22883678	3R_22883678_SNP [dm3] 3R_27057956_SNP [dm6]	C	A	5.191e^-6	0.109	UTR_3_PRIME Nep5 DOWNSTREAM RYa-R	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	26431721	3R_26431721_SNP [dm3] 3R_30605999_SNP [dm6]	G	A	5.367e^-6	0.111	UTR_3_PRIME PH4alphaNE3 UPSTREAM CG31016
3R	10392184	3R_10392184_SNP [dm3] 3R_14566462_SNP [dm6]	A	G	5.406e^-6	0.111	NON_SYNONYMOUS_CODING CG14852 UTR_3_PRIME CG31313 DOWNSTREAM CG31313
2L	7531414	2L_7531414_SNP [dm3] 2L_7531414_SNP [dm6]	G	A	5.614e^-6	0.113	UPSTREAM RapGAP1 INTRON RapGAP1	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
3R	26090610	3R_26090610_INS [dm3] 3R_30264888_INS [dm6]	T	TTGGG	5.630e^-6	0.113	INTERGENIC	silencer mE1_HDAC_PRE
2R	16665648	2R_16665648_SNP [dm3] 2R_20778143_SNP [dm6]	A	T	5.841e^-6	0.116	UPSTREAM CG43710 DOWNSTREAM CG43711 INTERGENIC
3R	26429351	3R_26429351_SNP [dm3] 3R_30603629_SNP [dm6]	T	C	5.986e^-6	0.117	SPLICE_SITE_REGION CG31021 UPSTREAM PH4alphaNE3 INTRON CG31021	TF binding site mE1_TFBS_HSA
X	16332855	X_16332855_SNP [dm3] X_16438822_SNP [dm6]	C	G	6.196e^-6	0.119	UTR_3_PRIME CG9947 DOWNSTREAM CG9947 & 1 other
2L	13233926	2L_13233926_SNP [dm3] 2L_13233926_SNP [dm6]	C	A	6.206e^-6	0.119	UTR_3_PRIME CG15479 DOWNSTREAM Prosalpha6T	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	8804474	3L_8804474_SNP [dm3] 3L_8811374_SNP [dm6]	G	T	6.314e^-6	0.12	DOWNSTREAM CG13309 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	8805867	3L_8805867_SNP [dm3] 3L_8812767_SNP [dm6]	T	C	6.426e^-6	0.121	INTERGENIC
3R	26432099	3R_26432099_SNP [dm3] 3R_30606377_SNP [dm6]	C	T	6.598e^-6	0.123	SYNONYMOUS_CODING CG31016 DOWNSTREAM PH4alphaNE3

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By genomic position
Variant impact
Gene name

Microbiota_OTU053 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results