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=6.155e^-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	0.008977

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	11.749	0.0028

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

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	11442836	2L_11442836_SNP [dm3] 2L_11442836_SNP [dm6]	G	A	4.230e^-8	0.033	INTRON salm
3R	13148567	3R_13148567_SNP [dm3] 3R_17322845_SNP [dm6]	T	C	4.364e^-8	0.033	INTRON beat-IIa
2L	11442865	2L_11442865_SNP [dm3] 2L_11442865_SNP [dm6]	A	C	5.323e^-8	0.033	INTRON salm
2L	11442866	2L_11442866_SNP [dm3] 2L_11442866_SNP [dm6]	T	C	7.247e^-8	0.034	INTRON salm
2L	11442828	2L_11442828_INS [dm3] 2L_11442828_INS [dm6]	A	AATTGAAATTATGCAC...	1.064e^-7	0.04	INTRON salm
3R	8253437	3R_8253437_SNP [dm3] 3R_12427715_SNP [dm6]	C	T	1.286e^-7	0.04	NON_SYNONYMOUS_CODING Sas DOWNSTREAM CG5641	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	11442910	2L_11442910_INS [dm3] 2L_11442910_INS [dm6]	A	ATGGCTT	2.558e^-7	0.068	INTRON salm
3R	13148362	3R_13148362_SNP [dm3] 3R_17322640_SNP [dm6]	A	G	2.904e^-7	0.068	INTRON beat-IIa
3R	7768516	3R_7768516_SNP [dm3] 3R_11942794_SNP [dm6]	T	C	4.338e^-7	0.075	INTRON Cad87A
3R	7768547	3R_7768547_SNP [dm3] 3R_11942825_SNP [dm6]	A	T	5.028e^-7	0.075	INTRON Cad87A
2L	11442891	2L_11442891_SNP [dm3] 2L_11442891_SNP [dm6]	T	G	5.159e^-7	0.075	INTRON salm
2L	11442474	2L_11442474_SNP [dm3] 2L_11442474_SNP [dm6]	C	A	5.212e^-7	0.075	INTRON salm
3R	8221792	3R_8221792_SNP [dm3] 3R_12396070_SNP [dm6]	T	G	5.226e^-7	0.075	UPSTREAM CG10096 & 1 other INTRON CG34402 EXON Cyp9f3Psi
2L	11442707	2L_11442707_SNP [dm3] 2L_11442707_SNP [dm6]	A	C	5.974e^-7	0.077	INTRON salm
2L	11442875	2L_11442875_DEL [dm3] 2L_11442875_DEL [dm6]	CAC	T	6.188e^-7	0.077	INTRON salm
3R	23900528	3R_23900528_DEL [dm3] 3R_28074806_DEL [dm6]	GCAAT	G	9.571e^-7	0.112	INTRON CG34362
3R	12861402	3R_12861402_SNP [dm3] 3R_17035680_SNP [dm6]	G	A	1.132e^-6	0.125	SYNONYMOUS_CODING CG4009 DOWNSTREAM CG18213	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	7768481	3R_7768481_SNP [dm3] 3R_11942759_SNP [dm6]	G	A	1.213e^-6	0.126	INTRON Cad87A
2L	11442809	2L_11442809_SNP [dm3] 2L_11442809_SNP [dm6]	A	C	1.302e^-6	0.126	INTRON salm
2L	11442681	2L_11442681_SNP [dm3] 2L_11442681_SNP [dm6]	A	T	1.407e^-6	0.126	INTRON salm
3R	13148379	3R_13148379_SNP [dm3] 3R_17322657_SNP [dm6]	A	G	1.416e^-6	0.126	INTRON beat-IIa
2L	11442585	2L_11442585_SNP [dm3] 2L_11442585_SNP [dm6]	A	G	1.754e^-6	0.143	INTRON salm
3R	9619209	3R_9619209_SNP [dm3] 3R_13793487_SNP [dm6]	A	T	1.824e^-6	0.143	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	12465793	3L_12465793_SNP [dm3] 3L_12472693_SNP [dm6]	T	C	1.834e^-6	0.143	INTRON CG10616
2L	11442658	2L_11442658_SNP [dm3] 2L_11442658_SNP [dm6]	C	A	1.901e^-6	0.143	INTRON salm
3R	7768218	3R_7768218_SNP [dm3] 3R_11942496_SNP [dm6]	A	C	2.128e^-6	0.154	INTRON Cad87A
3L	11892865	3L_11892865_SNP [dm3] 3L_11899765_SNP [dm6]	G	A	2.524e^-6	0.17	INTRON CG44837 & 1 other
3R	8344644	3R_8344644_SNP [dm3] 3R_12518922_SNP [dm6]	C	T	2.613e^-6	0.17	SYNONYMOUS_CODING Octbeta3R INTRON Octbeta3R	TF binding site mE1_TFBS_inv
2L	11442729	2L_11442729_SNP [dm3] 2L_11442729_SNP [dm6]	C	T	2.628e^-6	0.17	INTRON salm
3R	20006816	3R_20006816_SNP [dm3] 3R_24181094_SNP [dm6]	A	C	3.082e^-6	0.193	UTR_3_PRIME CG13606 INTRON CG13606
2L	7921416	2L_7921416_SNP [dm3] 2L_7921416_SNP [dm6]	T	C	3.182e^-6	0.193	INTRON Snoo
2L	11442850	2L_11442850_SNP [dm3] 2L_11442850_SNP [dm6]	G	C	3.629e^-6	0.207	INTRON salm
2L	12089190	2L_12089190_SNP [dm3] 2L_12089190_SNP [dm6]	A	G	3.637e^-6	0.207	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	11472183	2L_11472183_SNP [dm3] 2L_11472183_SNP [dm6]	A	T	4.076e^-6	0.219	INTERGENIC	TF binding site mE1_TFBS_cad
3R	7762307	3R_7762307_SNP [dm3] 3R_11936585_SNP [dm6]	T	A	4.085e^-6	0.219	INTRON Cad87A
X	17600332	X_17600332_SNP [dm3] X_17706299_SNP [dm6]	G	T	4.208e^-6	0.219	UTR_3_PRIME par-6
2L	11442524	2L_11442524_SNP [dm3] 2L_11442524_SNP [dm6]	G	T	4.398e^-6	0.223	INTRON salm
2L	11442751	2L_11442751_SNP [dm3] 2L_11442751_SNP [dm6]	T	C	5.265e^-6	0.26	INTRON salm
2L	11442523	2L_11442523_SNP [dm3] 2L_11442523_SNP [dm6]	C	T	5.613e^-6	0.267	INTRON salm
3L	12549675	3L_12549675_SNP [dm3] 3L_12556575_SNP [dm6]	A	T	5.690e^-6	0.267	INTRON sowah
2L	16497401	2L_16497401_SNP [dm3] 2L_16497401_SNP [dm6]	A	C	6.508e^-6	0.29	INTRON Tpr2
3L	4521889	3L_4521889_SNP [dm3] 3L_4521889_SNP [dm6]	T	A	6.661e^-6	0.29	INTRON Tie
3R	7760070	3R_7760070_SNP [dm3] 3R_11934348_SNP [dm6]	A	G	6.870e^-6	0.29	DOWNSTREAM CG14731 INTRON Cad87A	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	4521888	3L_4521888_SNP [dm3] 3L_4521888_SNP [dm6]	G	A	7.007e^-6	0.29	INTRON Tie
3R	7768136	3R_7768136_SNP [dm3] 3R_11942414_SNP [dm6]	A	G	7.076e^-6	0.29	INTRON Cad87A
2L	12760060	2L_12760060_SNP [dm3] 2L_12760060_SNP [dm6]	T	A	7.176e^-6	0.29	DOWNSTREAM CG15483 INTERGENIC
2L	11442495	2L_11442495_SNP [dm3] 2L_11442495_SNP [dm6]	T	C	7.668e^-6	0.29	INTRON salm
2R	14222094	2R_14222094_SNP [dm3] 2R_18334589_SNP [dm6]	T	G	7.740e^-6	0.29	INTRON sbb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
2R	14223000	2R_14223000_SNP [dm3] 2R_18335495_SNP [dm6]	G	A	7.937e^-6	0.29	INTRON sbb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	10183556	3R_10183556_SNP [dm3] 3R_14357834_SNP [dm6]	T	C	7.945e^-6	0.29	DOWNSTREAM CG31320 INTRON NK7.1
3R	7762214	3R_7762214_SNP [dm3] 3R_11936492_SNP [dm6]	T	A	7.981e^-6	0.29	INTRON Cad87A
2R	13888271	2R_13888271_SNP [dm3] 2R_18000766_SNP [dm6]	A	T	8.032e^-6	0.29	INTRON dpr13
2R	18559286	2R_18559286_SNP [dm3] 2R_22671781_SNP [dm6]	T	C	8.427e^-6	0.298	SYNONYMOUS_CODING RYBP
3L	12475243	3L_12475243_SNP [dm3] 3L_12482143_SNP [dm6]	C	G	8.733e^-6	0.299	UPSTREAM CG33725 INTRON CG10663
X	5113577	X_5113577_SNP [dm3] X_5219544_SNP [dm6]	A	G	8.788e^-6	0.299	INTRON CG15465 & 1 other
3L	4520080	3L_4520080_SNP [dm3] 3L_4520080_SNP [dm6]	G	A	9.054e^-6	0.299	INTRON Tie
2L	16541496	2L_16541496_SNP [dm3] 2L_16541496_SNP [dm6]	A	G	9.091e^-6	0.299	INTERGENIC
2R	14222237	2R_14222237_SNP [dm3] 2R_18334732_SNP [dm6]	G	A	9.867e^-6	0.319	INTRON sbb	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3R	7757573	3R_7757573_SNP [dm3] 3R_11931851_SNP [dm6]	C	G	1.089e^-5	0.346	NON_SYNONYMOUS_CODING CG14731 INTRON Cad87A
3R	14904279	3R_14904279_SNP [dm3] 3R_19078557_SNP [dm6]	T	C	1.133e^-5	0.354	INTRON cdi
X	6167713	X_6167713_SNP [dm3] X_6273680_SNP [dm6]	C	T	1.153e^-5	0.354	SYNONYMOUS_CODING Spt6	TF binding site BDTNP1_TFBS_Mad BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	14530532	3L_14530532_SNP [dm3] 3L_14537432_SNP [dm6]	G	A	1.176e^-5	0.356	UPSTREAM Mpcp DOWNSTREAM CG43246 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_bab1 mE1_TFBS_HSA
2L	11444033	2L_11444033_SNP [dm3] 2L_11444033_SNP [dm6]	C	T	1.270e^-5	0.369	INTRON salm
3R	1189231	3R_1189231_SNP [dm3] 3R_5363509_SNP [dm6]	T	C	1.291e^-5	0.369	INTRON Cerk
X	7243316	X_7243316_SNP [dm3] X_7349283_SNP [dm6]	T	C	1.316e^-5	0.369	INTRON CR44357 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	10834507	2L_10834507_SNP [dm3] 2L_10834507_SNP [dm6]	C	T	1.328e^-5	0.369	INTRON Nos
2L	11442663	2L_11442663_SNP [dm3] 2L_11442663_SNP [dm6]	A	T	1.353e^-5	0.369	INTRON salm
2L	16487919	2L_16487919_SNP [dm3] 2L_16487919_SNP [dm6]	G	T	1.354e^-5	0.369	UPSTREAM CG4580 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_ftz mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA
2R	14221804	2R_14221804_SNP [dm3] 2R_18334299_SNP [dm6]	A	T	1.386e^-5	0.369	INTRON sbb
3R	7762299	3R_7762299_SNP [dm3] 3R_11936577_SNP [dm6]	C	T	1.387e^-5	0.369	INTRON Cad87A
3R	7762171	3R_7762171_SNP [dm3] 3R_11936449_SNP [dm6]	T	C	1.398e^-5	0.369	INTRON Cad87A
3R	7762173	3R_7762173_SNP [dm3] 3R_11936451_SNP [dm6]	G	T	1.426e^-5	0.372	INTRON Cad87A
3R	15382140	3R_15382140_SNP [dm3] 3R_19556418_SNP [dm6]	C	T	1.580e^-5	0.398	INTRON Dys
X	18446528	X_18446528_SNP [dm3] X_18552495_SNP [dm6]	C	G	1.583e^-5	0.398	INTRON Bx	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	17602083	X_17602083_SNP [dm3] X_17708050_SNP [dm6]	G	A	1.590e^-5	0.398	NON_SYNONYMOUS_CODING CG8173 DOWNSTREAM par-6	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	12475285	3L_12475285_SNP [dm3] 3L_12482185_SNP [dm6]	C	G	1.655e^-5	0.399	UPSTREAM CG33725 INTRON CG10663
3R	2350038	3R_2350038_SNP [dm3] 3R_6524316_SNP [dm6]	T	C	1.672e^-5	0.399	INTERGENIC
3R	7763496	3R_7763496_SNP [dm3] 3R_11937774_SNP [dm6]	G	A	1.685e^-5	0.399	INTRON Cad87A
3R	4401213	3R_4401213_SNP [dm3] 3R_8575491_SNP [dm6]	G	A	1.704e^-5	0.399	INTERGENIC
3L	12475274	3L_12475274_SNP [dm3] 3L_12482174_SNP [dm6]	G	A	1.729e^-5	0.399	UPSTREAM CG33725 INTRON CG10663
3L	4522090	3L_4522090_SNP [dm3] 3L_4522090_SNP [dm6]	G	A	1.737e^-5	0.399	INTRON Tie
X	2997851	X_2997851_SNP [dm3] X_3103818_SNP [dm6]	A	T	1.744e^-5	0.399	INTRON kirre
3L	4223777	3L_4223777_INS [dm3] 3L_4223777_INS [dm6]	A	ACTGAACA	1.787e^-5	0.404	UTR_3_PRIME CG43367 DOWNSTREAM ImpL2	TF binding site mE1_TFBS_inv
3R	7762112	3R_7762112_SNP [dm3] 3R_11936390_SNP [dm6]	G	A	1.844e^-5	0.412	INTRON Cad87A
2L	4789096	2L_4789096_DEL [dm3] 2L_4789096_DEL [dm6]	AGGTATA	A	1.888e^-5	0.417	INTRON CG15630
2L	17872148	2L_17872148_SNP [dm3] 2L_17872148_SNP [dm6]	A	G	1.912e^-5	0.417	INTRON CadN2
3L	19957640	3L_19957640_SNP [dm3] 3L_19964540_SNP [dm6]	G	A	2.010e^-5	0.433	INTRON Ac76E
2L	11443197	2L_11443197_SNP [dm3] 2L_11443197_SNP [dm6]	G	A	2.039e^-5	0.435	INTRON salm
3R	8209974	3R_8209974_SNP [dm3] 3R_12384252_SNP [dm6]	T	A	2.079e^-5	0.436	UPSTREAM GstD11 INTRON GstD11	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
X	8902108	X_8902108_SNP [dm3] X_9008075_SNP [dm6]	A	G	2.141e^-5	0.436	INTRON rdgA & 1 other
2L	11471977	2L_11471977_SNP [dm3] 2L_11471977_SNP [dm6]	G	T	2.161e^-5	0.436	INTERGENIC	TF binding site mE1_TFBS_cad
3L	8034933	3L_8034933_INS [dm3] 3L_8041833_INS [dm6]	A	AGAA	2.167e^-5	0.436	INTRON nmo
2L	11442767	2L_11442767_SNP [dm3] 2L_11442767_SNP [dm6]	T	C	2.207e^-5	0.436	INTRON salm
3R	13147915	3R_13147915_SNP [dm3] 3R_17322193_SNP [dm6]	G	A	2.236e^-5	0.436	INTRON beat-IIa	TF binding site mE1_TFBS_inv
3L	19970676	3L_19970676_SNP [dm3] 3L_19977576_SNP [dm6]	G	A	2.243e^-5	0.436	UTR_3_PRIME Ac76E
3L	6622065	3L_6622065_SNP [dm3] 3L_6628965_SNP [dm6]	C	T	2.260e^-5	0.436	SYNONYMOUS_CODING GluRIA
3R	14899338	3R_14899338_SNP [dm3] 3R_19073616_SNP [dm6]	G	T	2.281e^-5	0.436	INTRON cdi	TF binding site mE1_TFBS_chinmo
3R	10630735	3R_10630735_SNP [dm3] 3R_14805013_SNP [dm6]	A	T	2.322e^-5	0.436	UTR_3_PRIME btsz DOWNSTREAM CG14857
X	8208722	X_8208722_SNP [dm3] X_8314689_SNP [dm6]	A	C	2.327e^-5	0.436	INTRON nAChRalpha3
3R	13923480	3R_13923480_SNP [dm3] 3R_18097758_SNP [dm6]	T	G	2.353e^-5	0.436	INTRON sr

Showing 1 to 100 of 1,000 entries

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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=4.401e^-10)
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	0.03359

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	6.6206	0.0365

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2199 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

Variant impact HIGH MODERATE LOW MODIFIER

Show entries

Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3R	8220292	3R_8220292_SNP [dm3] 3R_12394570_SNP [dm6]	T	C	2.559e^-11	4.801e^-5	SYNONYMOUS_CODING CG10097 START_GAINED CG10096 UTR_5_PRIME CG10096 INTRON CG34402
3R	8221499	3R_8221499_SNP [dm3] 3R_12395777_SNP [dm6]	G	A	1.100e^-9	9.492e^-4	SYNONYMOUS_CODING CG10097 UTR_5_PRIME CG10096 DOWNSTREAM Cyp9f3Psi INTRON CG34402
3R	8242073	3R_8242073_SNP [dm3] 3R_12416351_SNP [dm6]	C	A	1.518e^-9	9.492e^-4	SYNONYMOUS_CODING pps	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3R	8235993	3R_8235993_SNP [dm3] 3R_12410271_SNP [dm6]	T	G	4.112e^-9	0.002	SPLICE_SITE_REGION CG5196 INTRON CG5196	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3R	8221349	3R_8221349_SNP [dm3] 3R_12395627_SNP [dm6]	A	G	5.009e^-9	0.002	DOWNSTREAM Cyp9f3Psi INTRON CG34402 & 2 others
3R	8235953	3R_8235953_SNP [dm3] 3R_12410231_SNP [dm6]	A	G	1.145e^-8	0.003	INTRON CG5196	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3R	8221282	3R_8221282_SNP [dm3] 3R_12395560_SNP [dm6]	A	C	1.173e^-8	0.003	NON_SYNONYMOUS_CODING CG10097 UTR_5_PRIME CG10096 DOWNSTREAM Cyp9f3Psi INTRON CG34402
3R	8235851	3R_8235851_SNP [dm3] 3R_12410129_SNP [dm6]	A	G	4.351e^-8	0.01	INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
3R	17682853	3R_17682853_SNP [dm3] 3R_21857131_SNP [dm6]	A	G	5.240e^-8	0.011	UPSTREAM glec INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
3R	8224915	3R_8224915_SNP [dm3] 3R_12399193_SNP [dm6]	A	T	6.633e^-8	0.012	SYNONYMOUS_CODING lig3 UPSTREAM Cyp9f3Psi INTRON CG34402	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	8234140	3R_8234140_SNP [dm3] 3R_12408418_SNP [dm6]	C	G	9.209e^-8	0.016	NON_SYNONYMOUS_CODING CG5196 UPSTREAM CG5196 DOWNSTREAM CG5167	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad
3R	8235744	3R_8235744_SNP [dm3] 3R_12410022_SNP [dm6]	C	A	1.341e^-7	0.021	INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
3R	8234276	3R_8234276_SNP [dm3] 3R_12408554_SNP [dm6]	C	G	2.315e^-7	0.033	UPSTREAM CG5196 DOWNSTREAM CG5167 INTRON CG5196	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad
3R	8219408	3R_8219408_SNP [dm3] 3R_12393686_SNP [dm6]	G	A	2.959e^-7	0.035	UTR_5_PRIME CG10096 UTR_3_PRIME CG10097 UPSTREAM CG10096 DOWNSTREAM CG10097 INTRON CG34402
3R	8231349	3R_8231349_SNP [dm3] 3R_12405627_SNP [dm6]	T	C	2.999e^-7	0.035	UPSTREAM CG5167 INTRON Cyp9f2	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	8216558	3R_8216558_SNP [dm3] 3R_12390836_SNP [dm6]	C	T	3.010e^-7	0.035	UTR_3_PRIME CG10096 & 1 other INTRON CG34402
3R	17682885	3R_17682885_SNP [dm3] 3R_21857163_SNP [dm6]	A	T	3.232e^-7	0.036	UPSTREAM glec INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
3R	8164413	3R_8164413_SNP [dm3] 3R_12338691_SNP [dm6]	A	C	3.778e^-7	0.039	INTRON CR44941
3R	8236552	3R_8236552_SNP [dm3] 3R_12410830_SNP [dm6]	T	C	4.128e^-7	0.041	SYNONYMOUS_CODING CG5196 DOWNSTREAM Dip-C	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	8253437	3R_8253437_SNP [dm3] 3R_12427715_SNP [dm6]	C	T	4.583e^-7	0.043	NON_SYNONYMOUS_CODING Sas DOWNSTREAM CG5641	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	8234219	3R_8234219_SNP [dm3] 3R_12408497_SNP [dm6]	A	T	5.892e^-7	0.053	UPSTREAM CG5196 DOWNSTREAM CG5167 INTRON CG5196	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad
3R	8234936	3R_8234936_SNP [dm3] 3R_12409214_SNP [dm6]	A	G	7.052e^-7	0.058	UTR_5_PRIME CG5196 INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	8214104	3R_8214104_SNP [dm3] 3R_12388382_SNP [dm6]	G	A	7.575e^-7	0.058	SYNONYMOUS_CODING CG33098 UTR_3_PRIME CG33098 UPSTREAM CG34402 INTRON CG34402	TF binding site mE1_TFBS_cad
2L	12226657	2L_12226657_SNP [dm3] 2L_12226657_SNP [dm6]	G	A	7.618e^-7	0.058	INTRON aret
3R	8235861	3R_8235861_SNP [dm3] 3R_12410139_SNP [dm6]	T	A	7.790e^-7	0.058	INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
3L	6490417	3L_6490417_SNP [dm3] 3L_6497317_SNP [dm6]	T	C	9.489e^-7	0.067	INTRON sfl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_inv
3R	8220563	3R_8220563_SNP [dm3] 3R_12394841_SNP [dm6]	A	G	9.858e^-7	0.067	NON_SYNONYMOUS_CODING CG10097 UTR_5_PRIME CG10096 INTRON CG34402
3R	24599566	3R_24599566_INS [dm3] 3R_28773844_INS [dm6]	T	TT	1.003e^-6	0.067	INTERGENIC
3R	8264461	3R_8264461_SNP [dm3] 3R_12438739_SNP [dm6]	G	A	1.106e^-6	0.07	NON_SYNONYMOUS_CODING CG17207 UPSTREAM Desat1 DOWNSTREAM Desat2	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
3R	8235840	3R_8235840_SNP [dm3] 3R_12410118_SNP [dm6]	T	C	1.142e^-6	0.07	INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
2R	13349916	2R_13349916_SNP [dm3] 2R_17462411_SNP [dm6]	C	G	1.152e^-6	0.07	UTR_5_PRIME CG14478	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_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	12518599	X_12518599_DEL [dm3] X_12624566_DEL [dm6]	TG	T	1.213e^-6	0.071	INTRON CG15728
2R	10098532	2R_10098532_DEL [dm3] 2R_14211027_DEL [dm6]	TTTGTATCT	T	1.354e^-6	0.075	INTRON Sox15	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	8236387	3R_8236387_SNP [dm3] 3R_12410665_SNP [dm6]	G	A	1.362e^-6	0.075	SYNONYMOUS_CODING CG5196	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	8349986	3R_8349986_SNP [dm3] 3R_12524264_SNP [dm6]	T	C	1.535e^-6	0.081	INTRON Octbeta3R
3R	17682926	3R_17682926_SNP [dm3] 3R_21857204_SNP [dm6]	C	T	1.549e^-6	0.081	UPSTREAM glec INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_Trl
3R	14960664	3R_14960664_SNP [dm3] 3R_19134942_SNP [dm6]	C	T	1.706e^-6	0.086	UPSTREAM Cyp12a4 DOWNSTREAM Cyp12a5 INTERGENIC
2L	13249133	2L_13249133_SNP [dm3] 2L_13249133_SNP [dm6]	T	C	1.797e^-6	0.089	NON_SYNONYMOUS_CODING CG16820
3R	8349787	3R_8349787_SNP [dm3] 3R_12524065_SNP [dm6]	C	A	1.934e^-6	0.093	INTRON Octbeta3R
3L	6490574	3L_6490574_SNP [dm3] 3L_6497474_SNP [dm6]	C	T	2.221e^-6	0.104	INTRON sfl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	8350023	3R_8350023_SNP [dm3] 3R_12524301_SNP [dm6]	C	A	2.271e^-6	0.104	INTRON Octbeta3R
3R	3550136	3R_3550136_SNP [dm3] 3R_7724414_SNP [dm6]	T	A	2.709e^-6	0.119	UTR_3_PRIME CG2616	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	6490554	3L_6490554_SNP [dm3] 3L_6497454_SNP [dm6]	T	C	2.734e^-6	0.119	INTRON sfl	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
3R	8341839	3R_8341839_DEL [dm3] 3R_12516117_DEL [dm6]	AGGAACTTAAATACACAATT...	A	2.913e^-6	0.124	INTRON Octbeta3R
2L	12226662	2L_12226662_INS [dm3] 2L_12226662_INS [dm6]	G	AA	3.153e^-6	0.131	INTRON aret
3R	2776414	3R_2776414_SNP [dm3] 3R_6950692_SNP [dm6]	G	A	3.284e^-6	0.134	INTRON Antp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	8233903	3R_8233903_SNP [dm3] 3R_12408181_SNP [dm6]	C	T	3.401e^-6	0.136	UPSTREAM CG5196 DOWNSTREAM CG5167 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3R	4040573	3R_4040573_SNP [dm3] 3R_8214851_SNP [dm6]	A	T	3.685e^-6	0.144	INTERGENIC
3R	14960689	3R_14960689_SNP [dm3] 3R_19134967_SNP [dm6]	G	A	4.046e^-6	0.155	UPSTREAM Cyp12a4 DOWNSTREAM Cyp12a5 INTERGENIC
2L	10104398	2L_10104398_SNP [dm3] 2L_10104398_SNP [dm6]	C	T	4.794e^-6	0.18	INTRON CG44153 & 1 other
3L	2273734	3L_2273734_SNP [dm3] 3L_2273734_SNP [dm6]	T	C	5.615e^-6	0.206	UPSTREAM tRNA:CR32303 & 1 other INTERGENIC
X	19003743	X_19003743_SNP [dm3] X_19109710_SNP [dm6]	G	T	5.774e^-6	0.208	INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	2670542	3R_2670542_SNP [dm3] 3R_6844820_SNP [dm6]	G	A	5.986e^-6	0.208	INTRON Scr	regulatory region FlyBase REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad
2L	18815170	2L_18815170_SNP [dm3] 2L_18815170_SNP [dm6]	C	G	6.026e^-6	0.208	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	13344923	2R_13344923_SNP [dm3] 2R_17457418_SNP [dm6]	A	C	6.109e^-6	0.208	UPSTREAM robls54B & 1 other DOWNSTREAM robl INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_kn
2R	13713600	2R_13713600_SNP [dm3] 2R_17826095_SNP [dm6]	A	G	6.493e^-6	0.216	INTRON grh	transposable element FlyBase
3R	8280154	3R_8280154_SNP [dm3] 3R_12454432_SNP [dm6]	G	A	6.684e^-6	0.216	INTRON CG18549	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad
3R	14647605	3R_14647605_SNP [dm3] 3R_18821883_SNP [dm6]	G	C	6.688e^-6	0.216	INTRON CG18208
3L	16556338	3L_16556338_SNP [dm3] 3L_16563238_SNP [dm6]	T	A	6.861e^-6	0.216	DOWNSTREAM Mipp1 INTERGENIC	TF binding site mE1_TFBS_bab1
2R	13344452	2R_13344452_SNP [dm3] 2R_17456947_SNP [dm6]	A	G	6.976e^-6	0.216	SYNONYMOUS_CODING robl UPSTREAM robls54B & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_HSA
3R	8562118	3R_8562118_SNP [dm3] 3R_12736396_SNP [dm6]	A	C	7.026e^-6	0.216	INTERGENIC
3L	6064536	3L_6064536_SNP [dm3] 3L_6071436_SNP [dm6]	T	G	7.222e^-6	0.216	UTR_3_PRIME CG42269 UPSTREAM CG6602	TF binding site mE1_TFBS_bab1
3L	5568953	3L_5568953_DEL [dm3] 3L_5575853_DEL [dm6]	CGC	C	7.310e^-6	0.216	UPSTREAM Msr-110 INTRON Msr-110
3L	1444499	3L_1444499_SNP [dm3] 3L_1444499_SNP [dm6]	T	G	7.376e^-6	0.216	INTRON Ptp61F
2L	541774	2L_541774_SNP [dm3] 2L_541774_SNP [dm6]	A	G	7.490e^-6	0.216	SYNONYMOUS_CODING lwr	TF binding site BDTNP1_TFBS_dl mE1_TFBS_sens
3R	8234000	3R_8234000_SNP [dm3] 3R_12408278_SNP [dm6]	A	G	7.671e^-6	0.218	UPSTREAM CG5196 DOWNSTREAM CG5167 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad
3L	4104457	3L_4104457_SNP [dm3] 3L_4104457_SNP [dm6]	G	A	7.783e^-6	0.218	SYNONYMOUS_CODING Fit1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2R	13344924	2R_13344924_SNP [dm3] 2R_17457419_SNP [dm6]	G	C	8.025e^-6	0.219	UPSTREAM robls54B & 1 other DOWNSTREAM robl INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_kn
3R	8237029	3R_8237029_SNP [dm3] 3R_12411307_SNP [dm6]	T	C	8.062e^-6	0.219	SYNONYMOUS_CODING CG5196 DOWNSTREAM Dip-C	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	13237887	2L_13237887_INS [dm3] 2L_13237887_INS [dm6]	T	TT	8.487e^-6	0.227	INTRON CG5867
3R	8280116	3R_8280116_SNP [dm3] 3R_12454394_SNP [dm6]	A	C	8.937e^-6	0.236	INTRON CG18549	TF binding site BDTNP1_TFBS_prd
2R	13350610	2R_13350610_SNP [dm3] 2R_17463105_SNP [dm6]	A	G	9.536e^-6	0.248	SYNONYMOUS_CODING CG14478	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_chinmo
X	10625290	X_10625290_DEL [dm3] X_10731257_DEL [dm6]	AAA	G	1.023e^-5	0.258	INTRON CG32676	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3R	8215726	3R_8215726_SNP [dm3] 3R_12390004_SNP [dm6]	T	C	1.038e^-5	0.258	SYNONYMOUS_CODING CG34402 DOWNSTREAM CG10096 & 1 other
3R	8342670	3R_8342670_DEL [dm3] 3R_12516948_DEL [dm6]	CCGACTGCGC	C	1.056e^-5	0.258	CODON_DELETION Octbeta3R INTRON Octbeta3R	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	8349830	3R_8349830_SNP [dm3] 3R_12524108_SNP [dm6]	G	T	1.057e^-5	0.258	INTRON Octbeta3R
3R	23493101	3R_23493101_SNP [dm3] 3R_27667379_SNP [dm6]	C	G	1.061e^-5	0.258	SYNONYMOUS_CODING unc80
3R	8239628	3R_8239628_SNP [dm3] 3R_12413906_SNP [dm6]	A	C	1.087e^-5	0.258	UTR_5_PRIME pps UPSTREAM snmRNA:649 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_ttk
3R	8164613	3R_8164613_SNP [dm3] 3R_12338891_SNP [dm6]	T	A	1.088e^-5	0.258	EXON CR44941
2R	13349884	2R_13349884_DEL [dm3] 2R_17462379_DEL [dm6]	GAG	G	1.154e^-5	0.268	UTR_5_PRIME CG14478	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_D mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3R	8233837	3R_8233837_INS [dm3] 3R_12408115_INS [dm6]	T	TGT	1.157e^-5	0.268	UPSTREAM CG5196 DOWNSTREAM CG5167 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad
3R	15636850	3R_15636850_SNP [dm3] 3R_19811128_SNP [dm6]	A	G	1.381e^-5	0.316	INTRON bnl
3R	15354270	3R_15354270_SNP [dm3] 3R_19528548_SNP [dm6]	A	G	1.435e^-5	0.324	INTRON Dys
X	7883552	X_7883552_SNP [dm3] X_7989519_SNP [dm6]	T	C	1.505e^-5	0.334	INTERGENIC
2R	13344958	2R_13344958_SNP [dm3] 2R_17457453_SNP [dm6]	C	T	1.513e^-5	0.334	UPSTREAM CG14478 DOWNSTREAM robl INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_kn
2L	12226755	2L_12226755_SNP [dm3] 2L_12226755_SNP [dm6]	A	G	1.533e^-5	0.334	INTRON aret
3R	2219719	3R_2219719_SNP [dm3] 3R_6393997_SNP [dm6]	G	C	1.596e^-5	0.344	INTRON Dmtn
3R	8221724	3R_8221724_SNP [dm3] 3R_12396002_SNP [dm6]	G	A	1.635e^-5	0.348	UPSTREAM CG10096 & 1 other DOWNSTREAM Cyp9f3Psi INTRON CG34402
3L	9298307	3L_9298307_SNP [dm3] 3L_9305207_SNP [dm6]	G	T	1.678e^-5	0.352	INTERGENIC
2R	12788320	2R_12788320_SNP [dm3] 2R_16900815_SNP [dm6]	A	C	1.689e^-5	0.352	INTRON inaC
3L	11838216	3L_11838216_SNP [dm3] 3L_11845116_SNP [dm6]	C	G	1.721e^-5	0.352	INTERGENIC
2R	13449183	2R_13449183_SNP [dm3] 2R_17561678_SNP [dm6]	C	A	1.725e^-5	0.352	INTRON Klp54D
3R	8210917	3R_8210917_SNP [dm3] 3R_12385195_SNP [dm6]	T	G	1.772e^-5	0.357	INTRON GstD11
3R	2799335	3R_2799335_SNP [dm3] 3R_6973613_SNP [dm6]	G	A	1.822e^-5	0.362	INTRON Antp	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
3L	735620	3L_735620_SNP [dm3] 3L_735620_SNP [dm6]	G	T	1.863e^-5	0.362	INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
3R	4243195	3R_4243195_SNP [dm3] 3R_8417473_SNP [dm6]	G	T	1.869e^-5	0.362	INTRON CG45263
3R	8289146	3R_8289146_SNP [dm3] 3R_12463424_SNP [dm6]	C	A	1.871e^-5	0.362	NON_SYNONYMOUS_CODING CG5608	TF binding site mE1_TFBS_inv
3R	3984938	3R_3984938_SNP [dm3] 3R_8159216_SNP [dm6]	G	A	1.920e^-5	0.366	INTRON grn
3R	10183644	3R_10183644_SNP [dm3] 3R_14357922_SNP [dm6]	C	T	1.939e^-5	0.366	DOWNSTREAM CG31320 INTRON NK7.1
3L	17237883	3L_17237883_SNP [dm3] 3L_17244783_SNP [dm6]	A	G	1.953e^-5	0.366	DOWNSTREAM CG7707 INTERGENIC

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Cuticul_n_C26 phenotype

Phenotype distribution and association to known covariates

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GWAS results

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results