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=9.838e^-23)
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	<

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
wolba	124.3983	6.8922e-29
In_2L_t	9.1312	0.0104

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1875 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
2R	9201997	2R_9201997_SNP [dm3] 2R_13314492_SNP [dm6]	C	T	3.659e^-8	0.069	INTERGENIC
3R	25556588	3R_25556588_SNP [dm3] 3R_29730866_SNP [dm6]	C	G	1.045e^-7	0.098	INTRON Kul	TF binding site mE1_TFBS_cad
X	20341562	X_20341562_DEL [dm3] X_20470535_DEL [dm6]	TG	T	4.086e^-7	0.238	UTR_3_PRIME RhoGAP19D DOWNSTREAM GstT3	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	9203115	2R_9203115_SNP [dm3] 2R_13315610_SNP [dm6]	G	A	5.301e^-7	0.238	INTERGENIC
2R	9209279	2R_9209279_SNP [dm3] 2R_13321774_SNP [dm6]	G	A	6.399e^-7	0.238	INTERGENIC
X	18382068	X_18382068_SNP [dm3] X_18488035_SNP [dm6]	C	G	7.621e^-7	0.238	INTRON CG15046	TF binding site mE1_TFBS_chinmo
3R	25557404	3R_25557404_SNP [dm3] 3R_29731682_SNP [dm6]	A	G	1.042e^-6	0.279	SYNONYMOUS_CODING Kul UTR_3_PRIME Kul	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	11136911	2R_11136911_SNP [dm3] 2R_15249406_SNP [dm6]	C	T	1.577e^-6	0.331	SYNONYMOUS_CODING scb	TF binding site mE1_TFBS_cad
3L	5733948	3L_5733948_SNP [dm3] 3L_5740848_SNP [dm6]	C	G	1.588e^-6	0.331	SYNONYMOUS_CODING sif INTRON sif	TF binding site mE1_TFBS_chinmo
X	17416531	X_17416531_SNP [dm3] X_17522498_SNP [dm6]	T	C	1.978e^-6	0.371	INTRON CG43658
3L	5733936	3L_5733936_SNP [dm3] 3L_5740836_SNP [dm6]	A	G	3.116e^-6	0.531	SYNONYMOUS_CODING sif INTRON sif	TF binding site mE1_TFBS_chinmo
3R	25557449	3R_25557449_SNP [dm3] 3R_29731727_SNP [dm6]	T	C	3.803e^-6	0.594	SYNONYMOUS_CODING Kul UTR_3_PRIME Kul	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	25557524	3R_25557524_SNP [dm3] 3R_29731802_SNP [dm6]	G	A	4.506e^-6	0.598	SYNONYMOUS_CODING Kul UTR_3_PRIME Kul	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	10831410	2R_10831410_SNP [dm3] 2R_14943905_SNP [dm6]	A	G	4.660e^-6	0.598	SYNONYMOUS_CODING CG10257 DOWNSTREAM aPKC
2R	9211731	2R_9211731_SNP [dm3] 2R_13324226_SNP [dm6]	A	T	4.781e^-6	0.598	INTERGENIC
2R	9890603	2R_9890603_SNP [dm3] 2R_14003098_SNP [dm6]	T	A	5.471e^-6	0.641	INTRON mam	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11982501	2L_11982501_SNP [dm3] 2L_11982501_SNP [dm6]	G	A	7.771e^-6	0.771	NON_SYNONYMOUS_CODING CG16965
X	6693235	X_6693235_SNP [dm3] X_6799202_SNP [dm6]	C	T	7.968e^-6	0.771	INTRON C3G
2R	9795157	2R_9795157_SNP [dm3] 2R_13907652_SNP [dm6]	C	T	8.132e^-6	0.771	SYNONYMOUS_CODING shot INTRON shot	TF binding site mE1_TFBS_cad
3L	6494113	3L_6494113_SNP [dm3] 3L_6501013_SNP [dm6]	G	A	8.477e^-6	0.771	INTRON sfl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_hkb mE1_TFBS_HSA
2R	13802127	2R_13802127_SNP [dm3] 2R_17914622_SNP [dm6]	C	T	8.703e^-6	0.771	INTRON Elk
2R	9209742	2R_9209742_SNP [dm3] 2R_13322237_SNP [dm6]	T	A	9.045e^-6	0.771	INTERGENIC
2R	9890606	2R_9890606_SNP [dm3] 2R_14003101_SNP [dm6]	A	G	1.003e^-5	0.787	INTRON mam	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	20458518	3L_20458518_SNP [dm3] 3L_20465418_SNP [dm6]	G	A	1.008e^-5	0.787	SYNONYMOUS_CODING CG42764 UPSTREAM CG5195
2R	1247208	2R_1247208_SNP [dm3] 2R_5359703_SNP [dm6]	T	C	1.086e^-5	0.815	DOWNSTREAM CG10417 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	9211496	2R_9211496_SNP [dm3] 2R_13323991_SNP [dm6]	G	A	1.174e^-5	0.833	INTERGENIC
3L	3571701	3L_3571701_SNP [dm3] 3L_3571701_SNP [dm6]	T	G	1.235e^-5	0.833	INTRON Eip63E
3R	25569204	3R_25569204_SNP [dm3] 3R_29743482_SNP [dm6]	A	G	1.315e^-5	0.833	SYNONYMOUS_CODING CG7609
3R	25555999	3R_25555999_SNP [dm3] 3R_29730277_SNP [dm6]	C	A	1.355e^-5	0.833	SYNONYMOUS_CODING Kul	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
3L	3571696	3L_3571696_SNP [dm3] 3L_3571696_SNP [dm6]	C	A	1.357e^-5	0.833	INTRON Eip63E
3R	25566947	3R_25566947_SNP [dm3] 3R_29741225_SNP [dm6]	G	A	1.446e^-5	0.833	SYNONYMOUS_CODING CG1969 DOWNSTREAM CG7609
X	20341570	X_20341570_SNP [dm3] X_20470543_SNP [dm6]	C	A	1.452e^-5	0.833	UTR_3_PRIME RhoGAP19D DOWNSTREAM GstT3	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	25556299	3R_25556299_SNP [dm3] 3R_29730577_SNP [dm6]	G	A	1.511e^-5	0.833	INTRON Kul	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	9215582	2R_9215582_SNP [dm3] 2R_13328077_SNP [dm6]	A	C	1.547e^-5	0.833	INTERGENIC
3L	6837443	3L_6837443_SNP [dm3] 3L_6844343_SNP [dm6]	G	T	1.583e^-5	0.833	INTERGENIC
X	9271917	X_9271917_SNP [dm3] X_9377884_SNP [dm6]	C	G	1.599e^-5	0.833	INTRON mgl
3L	12156141	3L_12156141_SNP [dm3] 3L_12163041_SNP [dm6]	A	T	1.678e^-5	0.833	INTRON CG9760
2R	16961070	2R_16961070_SNP [dm3] 2R_21073565_SNP [dm6]	A	G	1.688e^-5	0.833	UPSTREAM CG10527 & 1 other INTERGENIC
3L	5076045	3L_5076045_SNP [dm3] 3L_5076045_SNP [dm6]	C	T	1.791e^-5	0.85	INTRON Con
X	18966091	X_18966091_SNP [dm3] X_19072058_SNP [dm6]	C	T	1.885e^-5	0.85	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_chinmo
3R	10219205	3R_10219205_INS [dm3] 3R_14393483_INS [dm6]	A	AGGGAAATTAG...	1.891e^-5	0.85	SPLICE_SITE_REGION cv-c INTRON cv-c
2R	11380163	2R_11380163_SNP [dm3] 2R_15492658_SNP [dm6]	T	C	2.023e^-5	0.85	INTRON CG12964
3R	25557563	3R_25557563_SNP [dm3] 3R_29731841_SNP [dm6]	C	A	2.038e^-5	0.85	SYNONYMOUS_CODING Kul UTR_3_PRIME Kul	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	11376353	2R_11376353_SNP [dm3] 2R_15488848_SNP [dm6]	A	G	2.045e^-5	0.85	NON_SYNONYMOUS_CODING CG12964	TF binding site mE1_TFBS_chinmo
2R	9203443	2R_9203443_SNP [dm3] 2R_13315938_SNP [dm6]	A	C	2.182e^-5	0.85	INTERGENIC
2R	16960970	2R_16960970_SNP [dm3] 2R_21073465_SNP [dm6]	T	C	2.198e^-5	0.85	UPSTREAM CG10527 & 1 other INTERGENIC
3R	26050610	3R_26050610_SNP [dm3] 3R_30224888_SNP [dm6]	T	C	2.201e^-5	0.85	INTERGENIC
3L	15882131	3L_15882131_SNP [dm3] 3L_15889031_SNP [dm6]	G	A	2.275e^-5	0.85	INTRON pHCl
3R	25569208	3R_25569208_SNP [dm3] 3R_29743486_SNP [dm6]	C	T	2.311e^-5	0.85	SYNONYMOUS_CODING CG7609
2R	6865422	2R_6865422_DEL [dm3] 2R_10977917_DEL [dm6]	AA	A	2.311e^-5	0.85	DOWNSTREAM luna INTERGENIC
2R	17464624	2R_17464624_SNP [dm3] 2R_21577119_SNP [dm6]	G	A	2.320e^-5	0.85	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	13007111	X_13007111_SNP [dm3] X_13113078_SNP [dm6]	T	C	2.356e^-5	0.85	UPSTREAM CG43313 INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Ubx
2L	7754680	2L_7754680_SNP [dm3] 2L_7754680_SNP [dm6]	G	A	2.511e^-5	0.866	INTRON CG7196
2R	16921250	2R_16921250_SNP [dm3] 2R_21033745_SNP [dm6]	T	G	2.548e^-5	0.866	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13149224	3L_13149224_SNP [dm3] 3L_13156124_SNP [dm6]	G	C	2.647e^-5	0.866	INTERGENIC
2L	9550783	2L_9550783_SNP [dm3] 2L_9550783_SNP [dm6]	A	G	2.795e^-5	0.866	UTR_5_PRIME jp INTRON jp	TF binding site mE1_TFBS_cad
2L	4455150	2L_4455150_SNP [dm3] 2L_4455150_SNP [dm6]	G	A	2.831e^-5	0.866	UTR_3_PRIME Gs1l & 1 other UPSTREAM CG15440 DOWNSTREAM Gs1l	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	4058938	2L_4058938_SNP [dm3] 2L_4058938_SNP [dm6]	T	G	2.883e^-5	0.866	INTRON ed	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	9203429	2R_9203429_SNP [dm3] 2R_13315924_SNP [dm6]	T	A	2.887e^-5	0.866	INTERGENIC
3L	13094196	3L_13094196_SNP [dm3] 3L_13101096_SNP [dm6]	T	A	2.902e^-5	0.866	DOWNSTREAM CR44554 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	1085153	2L_1085153_SNP [dm3] 2L_1085153_SNP [dm6]	G	A	2.990e^-5	0.866	UTR_3_PRIME Atg4a INTRON CG4629	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	11377499	2R_11377499_SNP [dm3] 2R_15489994_SNP [dm6]	C	A	3.000e^-5	0.866	INTRON CG12964
3L	4083000	3L_4083000_SNP [dm3] 3L_4083000_SNP [dm6]	C	T	3.010e^-5	0.866	INTRON Gad1
3L	8792498	3L_8792498_SNP [dm3] 3L_8799398_SNP [dm6]	C	G	3.076e^-5	0.866	SYNONYMOUS_CODING CG13310 DOWNSTREAM Fhos
2R	9890438	2R_9890438_SNP [dm3] 2R_14002933_SNP [dm6]	C	G	3.087e^-5	0.866	INTRON mam	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	9890522	2R_9890522_DEL [dm3] 2R_14003017_DEL [dm6]	TAAAAGCATTTCCTTTTAT...	T	3.087e^-5	0.866	INTRON mam	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	11963728	2R_11963728_SNP [dm3] 2R_16076223_SNP [dm6]	A	G	3.125e^-5	0.866	INTERGENIC	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	4090390	3L_4090390_SNP [dm3] 3L_4090390_SNP [dm6]	A	T	3.140e^-5	0.866	NON_SYNONYMOUS_CODING CG14989	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	9215849	2R_9215849_DEL [dm3] 2R_13328344_DEL [dm6]	AT	A	3.226e^-5	0.873	INTERGENIC
2R	9891838	2R_9891838_SNP [dm3] 2R_14004333_SNP [dm6]	G	C	3.271e^-5	0.873	INTRON mam	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
3L	1920862	3L_1920862_SNP [dm3] 3L_1920862_SNP [dm6]	C	T	3.312e^-5	0.873	UPSTREAM Dbx INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
X	18281098	X_18281098_SNP [dm3] X_18387065_SNP [dm6]	G	T	3.476e^-5	0.873	UPSTREAM Tsf1 INTERGENIC
X	6134306	X_6134306_SNP [dm3] X_6240273_SNP [dm6]	T	C	3.543e^-5	0.873	UTR_3_PRIME CG14445 DOWNSTREAM Rbcn-3A
2R	3591031	2R_3591031_SNP [dm3] 2R_7703526_SNP [dm6]	T	C	3.603e^-5	0.873	UTR_3_PRIME CG34216 DOWNSTREAM CG30493
2R	17756124	2R_17756124_SNP [dm3] 2R_21868619_SNP [dm6]	G	T	3.618e^-5	0.873	INTERGENIC
3R	25556597	3R_25556597_SNP [dm3] 3R_29730875_SNP [dm6]	G	C	3.683e^-5	0.873	INTRON Kul	TF binding site mE1_TFBS_cad
2L	10423139	2L_10423139_SNP [dm3] 2L_10423139_SNP [dm6]	T	A	3.793e^-5	0.873	UPSTREAM CG5168 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3R	26879883	3R_26879883_SNP [dm3] 3R_31054161_SNP [dm6]	G	A	3.827e^-5	0.873	UTR_3_PRIME dco UPSTREAM l_3_03670	TF binding site BDTNP1_TFBS_dl mE1_TFBS_eve mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
2R	9199782	2R_9199782_SNP [dm3] 2R_13312277_SNP [dm6]	A	C	3.833e^-5	0.873	INTERGENIC
3L	9667388	3L_9667388_SNP [dm3] 3L_9674288_SNP [dm6]	G	A	3.839e^-5	0.873	INTRON fry
2R	19705652	2R_19705652_SNP [dm3] 2R_23818129_SNP [dm6]	T	C	3.857e^-5	0.873	UTR_5_PRIME CG4797
2R	9204794	2R_9204794_SNP [dm3] 2R_13317289_SNP [dm6]	C	T	3.932e^-5	0.873	INTERGENIC
X	18281090	X_18281090_DEL [dm3] X_18387057_DEL [dm6]	AGGCACC	A	3.932e^-5	0.873	UPSTREAM Tsf1 INTERGENIC
3R	25556592	3R_25556592_SNP [dm3] 3R_29730870_SNP [dm6]	C	T	4.157e^-5	0.873	INTRON Kul	TF binding site mE1_TFBS_cad
3L	6837432	3L_6837432_SNP [dm3] 3L_6844332_SNP [dm6]	G	T	4.179e^-5	0.873	INTERGENIC
2L	16733776	2L_16733776_SNP [dm3] 2L_16733776_SNP [dm6]	C	A	4.219e^-5	0.873	UTR_3_PRIME glu DOWNSTREAM CG17904
2L	3303897	2L_3303897_SNP [dm3] 2L_3303897_SNP [dm6]	T	A	4.259e^-5	0.873	UPSTREAM CG3277 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl
2R	11375587	2R_11375587_SNP [dm3] 2R_15488082_SNP [dm6]	G	T	4.269e^-5	0.873	SYNONYMOUS_CODING CG12964	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	6506836	3R_6506836_SNP [dm3] 3R_10681114_SNP [dm6]	C	G	4.282e^-5	0.873	UPSTREAM CG14688 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
2R	11381465	2R_11381465_SNP [dm3] 2R_15493960_SNP [dm6]	A	G	4.289e^-5	0.873	INTRON CG12964
3L	6837454	3L_6837454_SNP [dm3] 3L_6844354_SNP [dm6]	G	T	4.427e^-5	0.873	INTERGENIC
2R	9209730	2R_9209730_SNP [dm3] 2R_13322225_SNP [dm6]	A	G	4.434e^-5	0.873	INTERGENIC
3R	25570319	3R_25570319_SNP [dm3] 3R_29744597_SNP [dm6]	A	G	4.487e^-5	0.873	SYNONYMOUS_CODING CG7609 UPSTREAM IntS11	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	9203452	2R_9203452_SNP [dm3] 2R_13315947_SNP [dm6]	C	A	4.508e^-5	0.873	INTERGENIC
3R	25556595	3R_25556595_SNP [dm3] 3R_29730873_SNP [dm6]	A	C	4.595e^-5	0.873	INTRON Kul	TF binding site mE1_TFBS_cad
3L	6837494	3L_6837494_SNP [dm3] 3L_6844394_SNP [dm6]	T	G	4.616e^-5	0.873	INTERGENIC
X	18496526	X_18496526_SNP [dm3] X_18602493_SNP [dm6]	G	A	4.679e^-5	0.873	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	11828964	3R_11828964_SNP [dm3] 3R_16003242_SNP [dm6]	C	T	4.747e^-5	0.873	SYNONYMOUS_CODING srp UTR_3_PRIME srp	TF binding site mE1_TFBS_cad
2R	9217036	2R_9217036_SNP [dm3] 2R_13329531_SNP [dm6]	T	G	4.773e^-5	0.873	UPSTREAM mir-184 EXON CR44206	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	9203492	2R_9203492_SNP [dm3] 2R_13315987_SNP [dm6]	G	A	4.775e^-5	0.873	INTERGENIC

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By genomic position
Variant impact
Gene name

Wolbachi_Breadth_Cov phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results