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=9.078e^-7)
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_K	1.241e-10

Kruskal-Wallis test

Covariate	χ²	p-value	Significance

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2042 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	13885304	3R_13885304_SNP [dm3] 3R_18059582_SNP [dm6]	C	T	2.068e^-7	0.353	INTERGENIC
2L	15881902	2L_15881902_SNP [dm3] 2L_15881902_SNP [dm6]	A	G	8.009e^-7	0.353	DOWNSTREAM CG44475 INTERGENIC	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_HSA
2L	15881899	2L_15881899_SNP [dm3] 2L_15881899_SNP [dm6]	T	A	9.348e^-7	0.353	DOWNSTREAM CG44475 INTERGENIC	TF binding site BDTNP1_TFBS_slp1 mE1_TFBS_HSA
3L	8866515	3L_8866515_SNP [dm3] 3L_8873415_SNP [dm6]	A	G	9.361e^-7	0.353	INTRON dally	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2R	8092915	2R_8092915_SNP [dm3] 2R_12205410_SNP [dm6]	C	G	9.417e^-7	0.353	UPSTREAM CR45276 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	11442866	2L_11442866_SNP [dm3] 2L_11442866_SNP [dm6]	T	C	1.217e^-6	0.38	INTRON salm
2L	8563700	2L_8563700_SNP [dm3] 2L_8563700_SNP [dm6]	T	A	2.257e^-6	0.599	INTRON Sema-1a
3R	13871179	3R_13871179_SNP [dm3] 3R_18045457_SNP [dm6]	A	G	2.662e^-6	0.599	UTR_3_PRIME htl
2L	11442865	2L_11442865_SNP [dm3] 2L_11442865_SNP [dm6]	A	C	2.948e^-6	0.599	INTRON salm
2L	11442891	2L_11442891_SNP [dm3] 2L_11442891_SNP [dm6]	T	G	3.319e^-6	0.599	INTRON salm
2L	15881680	2L_15881680_SNP [dm3] 2L_15881680_SNP [dm6]	T	C	3.737e^-6	0.599	INTERGENIC	TF binding site BDTNP1_TFBS_slp1
2R	8092654	2R_8092654_SNP [dm3] 2R_12205149_SNP [dm6]	A	T	4.034e^-6	0.599	UPSTREAM CR45276 INTERGENIC
2R	8179522	2R_8179522_SNP [dm3] 2R_12292017_SNP [dm6]	G	C	4.511e^-6	0.599	INTRON CG42700
2L	11442910	2L_11442910_INS [dm3] 2L_11442910_INS [dm6]	A	ATGGCTT	4.692e^-6	0.599	INTRON salm
2R	8179555	2R_8179555_SNP [dm3] 2R_12292050_SNP [dm6]	T	G	5.400e^-6	0.599	INTRON CG42700
2R	8179587	2R_8179587_SNP [dm3] 2R_12292082_SNP [dm6]	A	G	5.785e^-6	0.599	INTRON CG42700
2L	11442875	2L_11442875_DEL [dm3] 2L_11442875_DEL [dm6]	CAC	T	5.842e^-6	0.599	INTRON salm
3R	14361056	3R_14361056_SNP [dm3] 3R_18535334_SNP [dm6]	G	A	6.603e^-6	0.599	INTRON fru
3R	16899333	3R_16899333_MNP [dm3] 3R_21073611_MNP [dm6]	GTC	ACT	6.732e^-6	0.599	UPSTREAM dmrt93B & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	16899318	3R_16899318_INS [dm3] 3R_21073596_INS [dm6]	T	TAC	6.976e^-6	0.599	UPSTREAM dmrt93B & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1
2R	8089970	2R_8089970_SNP [dm3] 2R_12202465_SNP [dm6]	A	G	7.420e^-6	0.599	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	17091721	3R_17091721_SNP [dm3] 3R_21265999_SNP [dm6]	T	G	7.583e^-6	0.599	DOWNSTREAM Rab1 & 1 other INTERGENIC
3R	16899327	3R_16899327_SNP [dm3] 3R_21073605_SNP [dm6]	T	C	7.995e^-6	0.599	UPSTREAM dmrt93B & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	14361245	3R_14361245_SNP [dm3] 3R_18535523_SNP [dm6]	A	T	8.049e^-6	0.599	INTRON fru
3R	16899416	3R_16899416_SNP [dm3] 3R_21073694_SNP [dm6]	C	A	8.237e^-6	0.599	UPSTREAM dmrt93B & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	16899329	3R_16899329_SNP [dm3] 3R_21073607_SNP [dm6]	A	G	8.348e^-6	0.599	UPSTREAM dmrt93B & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	15826093	2L_15826093_SNP [dm3] 2L_15826093_SNP [dm6]	T	C	8.620e^-6	0.599	INTERGENIC
X	17620828	X_17620828_SNP [dm3] X_17726795_SNP [dm6]	A	G	1.057e^-5	0.684	INTRON CG42684
3L	15321430	3L_15321430_SNP [dm3] 3L_15328330_SNP [dm6]	T	C	1.072e^-5	0.684	INTERGENIC
2R	8157362	2R_8157362_SNP [dm3] 2R_12269857_SNP [dm6]	C	A	1.094e^-5	0.684	INTRON Cam
2R	8092581	2R_8092581_SNP [dm3] 2R_12205076_SNP [dm6]	C	T	1.195e^-5	0.692	INTERGENIC
2L	19378443	2L_19378443_SNP [dm3] 2L_19378443_SNP [dm6]	C	G	1.207e^-5	0.692	INTERGENIC	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
2R	8173649	2R_8173649_SNP [dm3] 2R_12286144_SNP [dm6]	C	G	1.217e^-5	0.692	NON_SYNONYMOUS_CODING CG42700 INTRON CG42700
3R	12136326	3R_12136326_SNP [dm3] 3R_16310604_SNP [dm6]	C	T	1.394e^-5	0.712	UTR_3_PRIME Sulf1
3L	18211423	3L_18211423_SNP [dm3] 3L_18218323_SNP [dm6]	A	C	1.513e^-5	0.712	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	16497795	2L_16497795_SNP [dm3] 2L_16497795_SNP [dm6]	A	G	1.550e^-5	0.712	INTRON Tpr2
2L	14428943	2L_14428943_SNP [dm3] 2L_14428943_SNP [dm6]	A	G	1.567e^-5	0.712	EXON CR44732	TF binding site mE1_TFBS_cnc mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens
2R	8171033	2R_8171033_SNP [dm3] 2R_12283528_SNP [dm6]	G	T	1.593e^-5	0.712	INTRON CG42700
2L	11442707	2L_11442707_SNP [dm3] 2L_11442707_SNP [dm6]	A	C	1.680e^-5	0.712	INTRON salm
2R	8172592	2R_8172592_SNP [dm3] 2R_12285087_SNP [dm6]	C	G	1.691e^-5	0.712	UPSTREAM CG42700 INTRON CG42700
2R	8172696	2R_8172696_SNP [dm3] 2R_12285191_SNP [dm6]	T	C	1.691e^-5	0.712	UPSTREAM CG42700 INTRON CG42700
2R	8178527	2R_8178527_SNP [dm3] 2R_12291022_SNP [dm6]	C	T	1.702e^-5	0.712	INTRON CG42700
2R	8157360	2R_8157360_SNP [dm3] 2R_12269855_SNP [dm6]	C	A	1.736e^-5	0.712	INTRON Cam
2R	8157692	2R_8157692_SNP [dm3] 2R_12270187_SNP [dm6]	G	A	1.747e^-5	0.712	INTRON Cam	TF binding site mE1_TFBS_zfh1
3L	12443040	3L_12443040_SNP [dm3] 3L_12449940_SNP [dm6]	C	T	1.767e^-5	0.712	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
2R	8174711	2R_8174711_SNP [dm3] 2R_12287206_SNP [dm6]	G	T	1.826e^-5	0.712	INTRON CG42700
3L	3927501	3L_3927501_SNP [dm3] 3L_3927501_SNP [dm6]	G	A	1.930e^-5	0.712	INTRON Eip63F-1
3R	16899281	3R_16899281_SNP [dm3] 3R_21073559_SNP [dm6]	A	T	1.979e^-5	0.712	UPSTREAM dmrt93B & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8697335	2L_8697335_SNP [dm3] 2L_8697335_SNP [dm6]	C	A	2.042e^-5	0.712	INTRON Hnf4
3L	8842100	3L_8842100_INS [dm3] 3L_8849000_INS [dm6]	C	CGC	2.136e^-5	0.712	INTRON dally
2L	11442751	2L_11442751_SNP [dm3] 2L_11442751_SNP [dm6]	T	C	2.369e^-5	0.712	INTRON salm
2L	8700154	2L_8700154_SNP [dm3] 2L_8700154_SNP [dm6]	C	G	2.395e^-5	0.712	UPSTREAM Hnf4 INTRON Hnf4
3L	18231717	3L_18231717_DEL [dm3] 3L_18238617_DEL [dm6]	AA	A	2.399e^-5	0.712	INTERGENIC	TF binding site mE1_TFBS_cnc
3R	26568491	3R_26568491_SNP [dm3] 3R_30742769_SNP [dm6]	T	C	2.400e^-5	0.712	UPSTREAM CG15543 INTERGENIC
2L	11442850	2L_11442850_SNP [dm3] 2L_11442850_SNP [dm6]	G	C	2.413e^-5	0.712	INTRON salm
2R	8172504	2R_8172504_SNP [dm3] 2R_12284999_SNP [dm6]	T	A	2.437e^-5	0.712	INTRON CG42700
3R	18286355	3R_18286355_SNP [dm3] 3R_22460633_SNP [dm6]	T	G	2.513e^-5	0.712	UTR_3_PRIME CG34376 DOWNSTREAM Rpn7
3R	9721237	3R_9721237_SNP [dm3] 3R_13895515_SNP [dm6]	T	A	2.554e^-5	0.712	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	8092572	2R_8092572_SNP [dm3] 2R_12205067_SNP [dm6]	C	T	2.568e^-5	0.712	INTERGENIC
3R	7734002	3R_7734002_SNP [dm3] 3R_11908280_SNP [dm6]	A	C	2.612e^-5	0.712	INTRON Cad87A
2R	8096002	2R_8096002_SNP [dm3] 2R_12208497_SNP [dm6]	C	A	2.645e^-5	0.712	DOWNSTREAM Sr-CII INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_twi
2R	8127730	2R_8127730_SNP [dm3] 2R_12240225_SNP [dm6]	T	C	2.647e^-5	0.712	UPSTREAM CG13170 & 1 other INTERGENIC
3R	18982520	3R_18982520_SNP [dm3] 3R_23156798_SNP [dm6]	A	G	2.666e^-5	0.712	INTRON unk	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_zfh1
2L	13746070	2L_13746070_SNP [dm3] 2L_13746070_SNP [dm6]	C	A	2.808e^-5	0.712	UPSTREAM TM9SF4 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_HSA
3L	11331870	3L_11331870_SNP [dm3] 3L_11338770_SNP [dm6]	T	G	2.979e^-5	0.712	INTERGENIC
2R	8096130	2R_8096130_SNP [dm3] 2R_12208625_SNP [dm6]	G	A	3.001e^-5	0.712	DOWNSTREAM Sr-CII INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_twi mE1_TFBS_cad
2R	8157082	2R_8157082_SNP [dm3] 2R_12269577_SNP [dm6]	A	T	3.105e^-5	0.712	INTRON Cam
3L	8842090	3L_8842090_SNP [dm3] 3L_8848990_SNP [dm6]	G	T	3.146e^-5	0.712	INTRON dally
3R	23184598	3R_23184598_SNP [dm3] 3R_27358876_SNP [dm6]	C	G	3.203e^-5	0.712	UPSTREAM CG42534 INTRON CG42534
3R	23184608	3R_23184608_SNP [dm3] 3R_27358886_SNP [dm6]	A	T	3.247e^-5	0.712	UPSTREAM CG42534 INTRON CG42534
2R	8176594	2R_8176594_SNP [dm3] 2R_12289089_SNP [dm6]	C	G	3.247e^-5	0.712	INTRON CG42700
2L	7532917	2L_7532917_SNP [dm3] 2L_7532917_SNP [dm6]	G	T	3.250e^-5	0.712	INTRON RapGAP1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	12185848	3L_12185848_SNP [dm3] 3L_12192748_SNP [dm6]	T	C	3.280e^-5	0.712	SYNONYMOUS_CODING thoc6 DOWNSTREAM Est-P	TF binding site mE1_TFBS_sens
3R	17091722	3R_17091722_DEL [dm3] 3R_21266000_DEL [dm6]	CCAA	C	3.329e^-5	0.712	DOWNSTREAM Rab1 & 1 other INTERGENIC
3R	23184612	3R_23184612_SNP [dm3] 3R_27358890_SNP [dm6]	G	A	3.556e^-5	0.712	UPSTREAM CG42534 INTRON CG42534
2R	12534007	2R_12534007_SNP [dm3] 2R_16646502_SNP [dm6]	A	G	3.611e^-5	0.712	SYNONYMOUS_CODING gprs UTR_3_PRIME gprs	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	16899289	3R_16899289_SNP [dm3] 3R_21073567_SNP [dm6]	T	C	3.641e^-5	0.712	UPSTREAM dmrt93B & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1
2L	1503746	2L_1503746_SNP [dm3] 2L_1503746_SNP [dm6]	G	A	3.650e^-5	0.712	UPSTREAM CG7420 EXON CR44064	TF binding site BDTNP1_TFBS_dl
3R	20450455	3R_20450455_SNP [dm3] 3R_24624733_SNP [dm6]	G	C	3.675e^-5	0.712	NON_SYNONYMOUS_CODING Syx18 UPSTREAM atl DOWNSTREAM mld
3R	16899407	3R_16899407_SNP [dm3] 3R_21073685_SNP [dm6]	A	G	3.764e^-5	0.712	UPSTREAM dmrt93B & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	8171228	2R_8171228_DEL [dm3] 2R_12283723_DEL [dm6]	AGAGTCCCATAAAGGAGTAT...	A	3.766e^-5	0.712	INTRON CG42700
2R	8171218	2R_8171218_SNP [dm3] 2R_12283713_SNP [dm6]	G	A	3.778e^-5	0.712	INTRON CG42700
3R	16899088	3R_16899088_SNP [dm3] 3R_21073366_SNP [dm6]	C	T	3.783e^-5	0.712	UPSTREAM dmrt93B & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_slp1 mE1_TFBS_cad
2R	8178026	2R_8178026_SNP [dm3] 2R_12290521_SNP [dm6]	T	A	3.810e^-5	0.712	UPSTREAM CG42700 INTRON CG42700
2R	8175815	2R_8175815_SNP [dm3] 2R_12288310_SNP [dm6]	A	C	3.840e^-5	0.712	INTRON CG42700
2R	8172388	2R_8172388_SNP [dm3] 2R_12284883_SNP [dm6]	C	G	3.852e^-5	0.712	INTRON CG42700
2L	11442828	2L_11442828_INS [dm3] 2L_11442828_INS [dm6]	A	AATTGAAATTATGCAC...	3.890e^-5	0.712	INTRON salm
2R	8077706	2R_8077706_SNP [dm3] 2R_12190201_SNP [dm6]	G	T	3.918e^-5	0.712	SYNONYMOUS_CODING Cyp6g2 UPSTREAM Cyp6t3	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	8173240	2R_8173240_SNP [dm3] 2R_12285735_SNP [dm6]	T	A	3.961e^-5	0.712	UPSTREAM CG42700 INTRON CG42700
3R	11283491	3R_11283491_SNP [dm3] 3R_15457769_SNP [dm6]	T	C	3.967e^-5	0.712	INTRON AdamTS-A
3R	7870210	3R_7870210_SNP [dm3] 3R_12044488_SNP [dm6]	T	C	3.988e^-5	0.712	INTERGENIC
2R	8157444	2R_8157444_SNP [dm3] 2R_12269939_SNP [dm6]	C	T	3.989e^-5	0.712	INTRON Cam
2R	8178048	2R_8178048_SNP [dm3] 2R_12290543_SNP [dm6]	G	A	3.991e^-5	0.712	UPSTREAM CG42700 INTRON CG42700
3L	6614757	3L_6614757_SNP [dm3] 3L_6621657_SNP [dm6]	T	C	4.047e^-5	0.712	INTERGENIC
3L	11042828	3L_11042828_SNP [dm3] 3L_11049728_SNP [dm6]	C	T	4.048e^-5	0.712	UPSTREAM CG43693 & 1 other INTRON CG43693
2L	10013270	2L_10013270_SNP [dm3] 2L_10013270_SNP [dm6]	A	T	4.059e^-5	0.712	UTR_3_PRIME CG13131 DOWNSTREAM Trp1
X	6170015	X_6170015_SNP [dm3] X_6275982_SNP [dm6]	G	C	4.075e^-5	0.712	UTR_3_PRIME CG3566 DOWNSTREAM Spt6 & 1 other INTRON CG3566	TF binding site mE1_TFBS_HSA
2R	8170200	2R_8170200_SNP [dm3] 2R_12282695_SNP [dm6]	T	C	4.091e^-5	0.712	INTRON CG42700
3R	7359222	3R_7359222_SNP [dm3] 3R_11533500_SNP [dm6]	T	A	4.133e^-5	0.712	UTR_3_PRIME dpr4
3R	6542850	3R_6542850_SNP [dm3] 3R_10717128_SNP [dm6]	A	G	4.145e^-5	0.712	INTERGENIC

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_3_Me_C27_C28 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results