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=1.544e^-12)
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	0.07930

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	3.1092	0.0779

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

5424 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	9618070	3R_9618070_SNP [dm3] 3R_13792348_SNP [dm6]	T	C	3.235e^-12	6.018e^-6	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	11904523	3R_11904523_SNP [dm3] 3R_16078801_SNP [dm6]	A	G	3.508e^-11	3.263e^-5	DOWNSTREAM CG32855 INTRON Mhcl	TF binding site mE1_TFBS_chinmo
3R	10414691	3R_10414691_SNP [dm3] 3R_14588969_SNP [dm6]	C	T	8.925e^-11	5.535e^-5	INTRON stumps	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	13894166	3R_13894166_SNP [dm3] 3R_18068444_SNP [dm6]	G	T	2.450e^-10	1.140e^-4	INTERGENIC
3L	10822535	3L_10822535_INS [dm3] 3L_10829435_INS [dm6]	C	CTTAC	3.161e^-10	1.176e^-4	INTERGENIC
2L	7179238	2L_7179238_SNP [dm3] 2L_7179238_SNP [dm6]	A	G	4.881e^-10	1.513e^-4	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	8532863	X_8532863_SNP [dm3] X_8638830_SNP [dm6]	G	C	8.427e^-10	2.240e^-4	INTRON oc	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
2L	13191874	2L_13191874_SNP [dm3] 2L_13191874_SNP [dm6]	T	A	1.121e^-9	2.607e^-4	UPSTREAM Edem2 INTRON CG16974	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	9866316	3R_9866316_SNP [dm3] 3R_14040594_SNP [dm6]	G	T	1.749e^-9	3.404e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	4912742	2L_4912742_SNP [dm3] 2L_4912742_SNP [dm6]	G	A	1.830e^-9	3.404e^-4	SYNONYMOUS_CODING hoe1 UTR_5_PRIME hoe1
2L	22107382	2L_22107382_SNP [dm3] 2L_22107382_SNP [dm6]	G	A	2.130e^-9	3.457e^-4	UPSTREAM CG10834 INTERGENIC
2L	13197527	2L_13197527_DEL [dm3] 2L_13197527_DEL [dm6]	CTC	C	2.230e^-9	3.457e^-4	UTR_3_PRIME CG16972 DOWNSTREAM Edem2	TF binding site mE1_TFBS_cad
2L	7179327	2L_7179327_SNP [dm3] 2L_7179327_SNP [dm6]	T	A	2.605e^-9	3.674e^-4	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	18355682	2R_18355682_SNP [dm3] 2R_22468177_SNP [dm6]	A	G	2.765e^-9	3.674e^-4	INTRON CG10384	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo
3R	9627709	3R_9627709_SNP [dm3] 3R_13801987_SNP [dm6]	C	T	3.823e^-9	4.741e^-4	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
X	11333169	X_11333169_SNP [dm3] X_11439136_SNP [dm6]	G	A	4.258e^-9	4.800e^-4	INTRON Evi5
3R	13894150	3R_13894150_SNP [dm3] 3R_18068428_SNP [dm6]	G	A	4.386e^-9	4.800e^-4	INTERGENIC
3L	1337662	3L_1337662_SNP [dm3] 3L_1337662_SNP [dm6]	T	C	6.027e^-9	6.229e^-4	NON_SYNONYMOUS_CODING l_3_02640	TF binding site mE1_TFBS_chinmo
2L	4164647	2L_4164647_SNP [dm3] 2L_4164647_SNP [dm6]	C	A	7.503e^-9	7.347e^-4	DOWNSTREAM Or24a INTERGENIC
2L	3461450	2L_3461450_SNP [dm3] 2L_3461450_SNP [dm6]	C	T	8.209e^-9	7.636e^-4	SYNONYMOUS_CODING CG3246 DOWNSTREAM msl-2	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2R	19984272	2R_19984272_SNP [dm3] 2R_24096749_SNP [dm6]	T	A	1.214e^-8	0.001	SYNONYMOUS_CODING gek	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	13197661	2L_13197661_SNP [dm3] 2L_13197661_SNP [dm6]	G	T	1.239e^-8	0.001	SYNONYMOUS_CODING CG16972 DOWNSTREAM Edem2	TF binding site mE1_TFBS_cad
2R	3243754	2R_3243754_SNP [dm3] 2R_7356249_SNP [dm6]	T	C	1.589e^-8	0.001	INTRON Dscam1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	3243772	2R_3243772_SNP [dm3] 2R_7356267_SNP [dm6]	T	C	1.589e^-8	0.001	INTRON Dscam1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	16436867	2R_16436867_SNP [dm3] 2R_20549362_SNP [dm6]	T	A	1.601e^-8	0.001	UTR_5_PRIME Obp57d UTR_3_PRIME Cpr57A DOWNSTREAM CG13430 & 1 other	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
X	8532859	X_8532859_INS [dm3] X_8638826_INS [dm6]	A	ATCCTTACTCCCTAATCCTT...	1.630e^-8	0.001	INTRON oc	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3R	12554589	3R_12554589_INS [dm3] 3R_16728867_INS [dm6]	T	TTTTTTTTTATTTTTTTA...	1.672e^-8	0.001	INTRON Ubx	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	12554591	3R_12554591_SNP [dm3] 3R_16728869_SNP [dm6]	G	A	1.672e^-8	0.001	INTRON Ubx	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_twi mE1_TFBS_HSA
X	20893443	X_20893443_SNP [dm3] X_21022416_SNP [dm6]	C	T	2.658e^-8	0.002	DOWNSTREAM r-cup INTERGENIC
3R	4245775	3R_4245775_SNP [dm3] 3R_8420053_SNP [dm6]	C	T	2.986e^-8	0.002	SYNONYMOUS_CODING Obp85a INTRON CG45263
3R	12554671	3R_12554671_SNP [dm3] 3R_16728949_SNP [dm6]	T	A	3.153e^-8	0.002	INTRON Ubx	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	8396704	3R_8396704_SNP [dm3] 3R_12570982_SNP [dm6]	A	G	3.211e^-8	0.002	INTRON Octbeta2R
3L	1343143	3L_1343143_DEL [dm3] 3L_1343143_DEL [dm6]	TC	T	3.295e^-8	0.002	UTR_3_PRIME Ptp61F UPSTREAM CG2199 DOWNSTREAM Ptp61F INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	20296567	3L_20296567_SNP [dm3] 3L_20303467_SNP [dm6]	A	G	3.332e^-8	0.002	DOWNSTREAM CG32225 INTRON CG6597	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	22107514	2L_22107514_SNP [dm3] 2L_22107514_SNP [dm6]	A	C	3.719e^-8	0.002	UPSTREAM CG10834 INTERGENIC
3L	1341596	3L_1341596_DEL [dm3] 3L_1341596_DEL [dm6]	GTATTAG	G	3.769e^-8	0.002	CODON_DELETION CG2199 DOWNSTREAM Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2L	5380242	2L_5380242_SNP [dm3] 2L_5380242_SNP [dm6]	G	A	3.976e^-8	0.002	EXON CR42850	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	10831130	X_10831130_INS [dm3] X_10937097_INS [dm6]	A	AATCCAACTCCAA...	4.204e^-8	0.002	INTRON Myo10A	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	8577690	2L_8577690_SNP [dm3] 2L_8577690_SNP [dm6]	C	A	4.523e^-8	0.002	INTRON Sema-1a	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_inv
2R	20323008	2R_20323008_SNP [dm3] 2R_24435485_SNP [dm6]	G	C	5.035e^-8	0.002	INTERGENIC
2L	9091067	2L_9091067_SNP [dm3] 2L_9091067_SNP [dm6]	T	A	5.051e^-8	0.002	INTERGENIC
2R	13682205	2R_13682205_SNP [dm3] 2R_17794700_SNP [dm6]	T	C	5.140e^-8	0.002	INTRON Dhit	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2R	13682234	2R_13682234_SNP [dm3] 2R_17794729_SNP [dm6]	A	T	5.140e^-8	0.002	INTRON Dhit	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	4289381	2L_4289381_SNP [dm3] 2L_4289381_SNP [dm6]	C	T	5.608e^-8	0.002	INTRON tutl
2L	15209849	2L_15209849_SNP [dm3] 2L_15209849_SNP [dm6]	A	C	5.682e^-8	0.002	INTERGENIC
3R	20555202	3R_20555202_SNP [dm3] 3R_24729480_SNP [dm6]	C	T	5.744e^-8	0.002	INTRON tok
3L	3754267	3L_3754267_SNP [dm3] 3L_3754267_SNP [dm6]	C	T	5.884e^-8	0.002	NON_SYNONYMOUS_CODING ppk27 INTRON CG32264
2L	994668	2L_994668_SNP [dm3] 2L_994668_SNP [dm6]	G	A	6.314e^-8	0.002	INTERGENIC
2L	995360	2L_995360_SNP [dm3] 2L_995360_SNP [dm6]	C	T	6.314e^-8	0.002	INTERGENIC	TF binding site mE1_TFBS_chinmo
2L	995690	2L_995690_SNP [dm3] 2L_995690_SNP [dm6]	A	G	6.314e^-8	0.002	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	1580861	3L_1580861_SNP [dm3] 3L_1580861_SNP [dm6]	C	A	6.314e^-8	0.002	INTRON CG13917
3L	2205149	3L_2205149_SNP [dm3] 3L_2205149_SNP [dm6]	T	A	6.314e^-8	0.002	INTERGENIC	TF binding site BDTNP1_TFBS_hb mE1_TFBS_HSA
3L	2206130	3L_2206130_SNP [dm3] 3L_2206130_SNP [dm6]	T	C	6.314e^-8	0.002	INTERGENIC
3L	2206700	3L_2206700_SNP [dm3] 3L_2206700_SNP [dm6]	C	T	6.314e^-8	0.002	INTERGENIC
3L	2207162	3L_2207162_SNP [dm3] 3L_2207162_SNP [dm6]	G	A	6.314e^-8	0.002	INTERGENIC
3L	2207299	3L_2207299_SNP [dm3] 3L_2207299_SNP [dm6]	A	C	6.314e^-8	0.002	INTERGENIC
3L	2207304	3L_2207304_SNP [dm3] 3L_2207304_SNP [dm6]	T	C	6.314e^-8	0.002	INTERGENIC
3L	2207713	3L_2207713_SNP [dm3] 3L_2207713_SNP [dm6]	G	A	6.314e^-8	0.002	INTERGENIC
3L	2207714	3L_2207714_SNP [dm3] 3L_2207714_SNP [dm6]	A	G	6.314e^-8	0.002	INTERGENIC
3L	5384649	3L_5384649_SNP [dm3] 3L_5391549_SNP [dm6]	C	T	6.314e^-8	0.002	INTERGENIC
3R	25461868	3R_25461868_SNP [dm3] 3R_29636146_SNP [dm6]	G	A	6.314e^-8	0.002	INTRON Dop1R2	TF binding site mE1_TFBS_chinmo
2L	10006758	2L_10006758_SNP [dm3] 2L_10006758_SNP [dm6]	G	A	6.347e^-8	0.002	INTRON CG4747
3L	3980922	3L_3980922_SNP [dm3] 3L_3980922_SNP [dm6]	A	G	6.746e^-8	0.002	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl
2L	6082025	2L_6082025_SNP [dm3] 2L_6082025_SNP [dm6]	T	C	6.758e^-8	0.002	UPSTREAM Kr-h1 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	9851664	2L_9851664_SNP [dm3] 2L_9851664_SNP [dm6]	C	T	6.799e^-8	0.002	INTRON nAChRalpha6
3R	13794646	3R_13794646_SNP [dm3] 3R_17968924_SNP [dm6]	T	G	6.815e^-8	0.002	INTRON cpo
2L	9086487	2L_9086487_SNP [dm3] 2L_9086487_SNP [dm6]	A	G	7.807e^-8	0.002	NON_SYNONYMOUS_CODING Toll-4
2L	9086505	2L_9086505_SNP [dm3] 2L_9086505_SNP [dm6]	A	T	7.807e^-8	0.002	NON_SYNONYMOUS_CODING Toll-4
2L	9091465	2L_9091465_SNP [dm3] 2L_9091465_SNP [dm6]	C	T	7.807e^-8	0.002	INTERGENIC
3L	2207308	3L_2207308_INS [dm3] 3L_2207308_INS [dm6]	C	TA	7.807e^-8	0.002	INTERGENIC
3L	2209117	3L_2209117_SNP [dm3] 3L_2209117_SNP [dm6]	G	C	7.807e^-8	0.002	INTERGENIC
3L	6817434	3L_6817434_SNP [dm3] 3L_6824334_SNP [dm6]	G	A	7.936e^-8	0.002	INTERGENIC	regulatory region REDfly_CRMs
3R	25461890	3R_25461890_SNP [dm3] 3R_29636168_SNP [dm6]	C	T	8.012e^-8	0.002	INTRON Dop1R2	TF binding site mE1_TFBS_chinmo
2R	18426784	2R_18426784_SNP [dm3] 2R_22539279_SNP [dm6]	T	A	8.262e^-8	0.002	INTRON px	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	25433107	3R_25433107_SNP [dm3] 3R_29607385_SNP [dm6]	A	T	8.443e^-8	0.002	INTRON alph
3R	5662272	3R_5662272_SNP [dm3] 3R_9836550_SNP [dm6]	A	C	8.462e^-8	0.002	INTRON Teh1
3R	13794833	3R_13794833_SNP [dm3] 3R_17969111_SNP [dm6]	A	G	8.941e^-8	0.002	INTRON cpo
3L	4532404	3L_4532404_SNP [dm3] 3L_4532404_SNP [dm6]	A	G	9.202e^-8	0.002	UPSTREAM Tie & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	2207660	3L_2207660_SNP [dm3] 3L_2207660_SNP [dm6]	C	G	9.530e^-8	0.002	INTERGENIC
3L	11320143	3L_11320143_SNP [dm3] 3L_11327043_SNP [dm6]	A	T	9.743e^-8	0.002	INTERGENIC
3R	12673660	3R_12673660_SNP [dm3] 3R_16847938_SNP [dm6]	A	G	9.857e^-8	0.002	INTRON iab-8	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad
3R	12674774	3R_12674774_SNP [dm3] 3R_16849052_SNP [dm6]	T	A	9.857e^-8	0.002	UPSTREAM iab-8 & 1 other INTRON iab-8	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	12674810	3R_12674810_SNP [dm3] 3R_16849088_SNP [dm6]	A	G	9.857e^-8	0.002	UPSTREAM iab-8 & 1 other INTRON iab-8	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	12675040	3R_12675040_SNP [dm3] 3R_16849318_SNP [dm6]	G	A	9.857e^-8	0.002	UPSTREAM iab-8 & 1 other INTRON iab-8	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_ftz BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	11319920	3L_11319920_SNP [dm3] 3L_11326820_SNP [dm6]	T	A	1.031e^-7	0.002	INTERGENIC
2L	10979332	2L_10979332_SNP [dm3] 2L_10979332_SNP [dm6]	G	A	1.046e^-7	0.002	INTRON SCAR
2R	6621377	2R_6621377_SNP [dm3] 2R_10733872_SNP [dm6]	G	T	1.046e^-7	0.002	INTRON CG7220
2L	12173026	2L_12173026_SNP [dm3] 2L_12173026_SNP [dm6]	A	T	1.052e^-7	0.002	UTR_5_PRIME crok UPSTREAM CG6583	TF binding site BDTNP1_TFBS_hb mE1_TFBS_HSA mE1_TFBS_Ubx
2R	9582178	2R_9582178_SNP [dm3] 2R_13694673_SNP [dm6]	C	A	1.081e^-7	0.002	INTRON fas
3L	20277252	3L_20277252_SNP [dm3] 3L_20284152_SNP [dm6]	A	G	1.083e^-7	0.002	INTRON gogo
3L	2699017	3L_2699017_SNP [dm3] 3L_2699017_SNP [dm6]	A	C	1.098e^-7	0.002	INTRON Fife
3L	2699137	3L_2699137_SNP [dm3] 3L_2699137_SNP [dm6]	C	A	1.098e^-7	0.002	INTRON Fife
2L	9446178	2L_9446178_SNP [dm3] 2L_9446178_SNP [dm6]	G	C	1.107e^-7	0.002	INTRON numb	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	17908928	2R_17908928_SNP [dm3] 2R_22021423_SNP [dm6]	T	C	1.120e^-7	0.002	INTRON CG34370
2R	17294578	2R_17294578_SNP [dm3] 2R_21407073_SNP [dm6]	C	T	1.169e^-7	0.002	INTRON Sdc
3L	11319883	3L_11319883_SNP [dm3] 3L_11326783_SNP [dm6]	G	A	1.223e^-7	0.002	INTERGENIC
3L	10889985	3L_10889985_SNP [dm3] 3L_10896885_SNP [dm6]	G	T	1.237e^-7	0.002	SPLICE_SITE_REGION Aps INTRON Aps
3R	12069216	3R_12069216_SNP [dm3] 3R_16243494_SNP [dm6]	A	T	1.253e^-7	0.002	INTRON tara	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	12040967	3R_12040967_SNP [dm3] 3R_16215245_SNP [dm6]	C	T	1.278e^-7	0.002	DOWNSTREAM CR45641 INTERGENIC
2L	5106629	2L_5106629_SNP [dm3] 2L_5106629_SNP [dm6]	A	G	1.284e^-7	0.002	INTRON Msp300

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By genomic position
Variant impact
Gene name

Microbiota_OTU018 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results