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=1.670e^-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	0.001087
In_3R_P	0.003348

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	13.3571	0.0013

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2488 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
2R	13888271	2R_13888271_SNP [dm3] 2R_18000766_SNP [dm6]	A	T	5.577e^-7	0.467	INTRON dpr13
3R	9613891	3R_9613891_SNP [dm3] 3R_13788169_SNP [dm6]	T	A	5.814e^-7	0.467	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3L	16624819	3L_16624819_SNP [dm3] 3L_16631719_SNP [dm6]	T	C	1.267e^-6	0.467	INTRON Abl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	7075694	2L_7075694_MNP [dm3] 2L_7075694_MNP [dm6]	TGG	CTA	1.417e^-6	0.467	INTRON Pvf2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	7768218	3R_7768218_SNP [dm3] 3R_11942496_SNP [dm6]	A	C	1.613e^-6	0.467	INTRON Cad87A
3R	3395062	3R_3395062_SNP [dm3] 3R_7569340_SNP [dm6]	G	A	1.749e^-6	0.467	DOWNSTREAM CG34127 INTERGENIC
3R	7768547	3R_7768547_SNP [dm3] 3R_11942825_SNP [dm6]	A	T	1.823e^-6	0.467	INTRON Cad87A
2L	16552252	2L_16552252_SNP [dm3] 2L_16552252_SNP [dm6]	C	T	1.993e^-6	0.467	INTRON CG42389	TF binding site mE1_TFBS_kn mE1_TFBS_zfh1
2R	18212484	2R_18212484_SNP [dm3] 2R_22324979_SNP [dm6]	G	A	2.286e^-6	0.476	UPSTREAM Gp150 INTRON Gp150	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_sens
3R	5428755	3R_5428755_SNP [dm3] 3R_9603033_SNP [dm6]	T	C	2.903e^-6	0.525	INTRON CG8312	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	9745078	X_9745078_INS [dm3] X_9851045_INS [dm6]	A	AGACAA	3.374e^-6	0.525	UTR_3_PRIME CG32698
3R	24938557	3R_24938557_INS [dm3] 3R_29112835_INS [dm6]	C	CTCTC	3.625e^-6	0.525	UPSTREAM CG11876 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	8221792	3R_8221792_SNP [dm3] 3R_12396070_SNP [dm6]	T	G	3.860e^-6	0.525	UPSTREAM CG10096 & 1 other INTRON CG34402 EXON Cyp9f3Psi
2R	10897085	2R_10897085_SNP [dm3] 2R_15009580_SNP [dm6]	T	A	3.921e^-6	0.525	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	14904279	3R_14904279_SNP [dm3] 3R_19078557_SNP [dm6]	T	C	4.871e^-6	0.609	INTRON cdi
2R	4216491	2R_4216491_SNP [dm3] 2R_8328986_SNP [dm6]	T	C	5.747e^-6	0.623	INTRON pdm3
2R	13487738	2R_13487738_SNP [dm3] 2R_17600233_SNP [dm6]	T	C	5.891e^-6	0.623	SYNONYMOUS_CODING lack UPSTREAM CG43920 & 1 other	TF binding site mE1_TFBS_cad
2L	10355033	2L_10355033_SNP [dm3] 2L_10355033_SNP [dm6]	A	C	5.977e^-6	0.623	INTRON CG5367
3R	16494952	3R_16494952_SNP [dm3] 3R_20669230_SNP [dm6]	G	C	6.794e^-6	0.663	UPSTREAM Cpr92F INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	16552251	2L_16552251_SNP [dm3] 2L_16552251_SNP [dm6]	G	A	7.252e^-6	0.663	INTRON CG42389	TF binding site mE1_TFBS_kn mE1_TFBS_zfh1
3R	16428632	3R_16428632_SNP [dm3] 3R_20602910_SNP [dm6]	T	C	8.096e^-6	0.663	INTRON bon
3L	10542483	3L_10542483_SNP [dm3] 3L_10549383_SNP [dm6]	T	G	8.241e^-6	0.663	INTRON A2bp1
2L	7075777	2L_7075777_SNP [dm3] 2L_7075777_SNP [dm6]	C	T	9.260e^-6	0.663	INTRON Pvf2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	7075869	2L_7075869_SNP [dm3] 2L_7075869_SNP [dm6]	T	A	9.475e^-6	0.663	INTRON Pvf2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	14904281	3R_14904281_SNP [dm3] 3R_19078559_SNP [dm6]	T	G	9.993e^-6	0.663	INTRON cdi
X	4807838	X_4807838_SNP [dm3] X_4913805_SNP [dm6]	A	T	1.006e^-5	0.663	INTRON CG32772	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	17516808	2L_17516808_SNP [dm3] 2L_17516808_SNP [dm6]	T	A	1.016e^-5	0.663	SYNONYMOUS_CODING Dhc36C	TF binding site mE1_TFBS_cad
3L	2607345	3L_2607345_SNP [dm3] 3L_2607345_SNP [dm6]	C	T	1.102e^-5	0.663	INTRON Pxn
X	17659765	X_17659765_SNP [dm3] X_17765732_SNP [dm6]	A	T	1.126e^-5	0.663	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	19969059	3L_19969059_SNP [dm3] 3L_19975959_SNP [dm6]	G	T	1.135e^-5	0.663	INTRON Ac76E
3R	3352938	3R_3352938_SNP [dm3] 3R_7527216_SNP [dm6]	T	A	1.144e^-5	0.663	INTRON alpha-Est6 EXON alpha-Est4aPsi
3L	5342569	3L_5342569_DEL [dm3] 3L_5349469_DEL [dm6]	AAATA	A	1.234e^-5	0.663	INTRON lama
3R	3352922	3R_3352922_SNP [dm3] 3R_7527200_SNP [dm6]	C	T	1.272e^-5	0.663	INTRON alpha-Est6 EXON alpha-Est4aPsi
2L	15104877	2L_15104877_SNP [dm3] 2L_15104877_SNP [dm6]	C	T	1.293e^-5	0.663	INTERGENIC
2L	15095249	2L_15095249_SNP [dm3] 2L_15095249_SNP [dm6]	T	A	1.443e^-5	0.663	INTRON CG15270
3R	14732739	3R_14732739_SNP [dm3] 3R_18907017_SNP [dm6]	A	C	1.478e^-5	0.663	UTR_5_PRIME EndoA	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_sens
3R	4996216	3R_4996216_SNP [dm3] 3R_9170494_SNP [dm6]	T	C	1.494e^-5	0.663	INTRON pum
2R	19339263	2R_19339263_DEL [dm3] 2R_23451740_DEL [dm6]	GT	C	1.578e^-5	0.663	INTRON CG43795
3R	8163343	3R_8163343_SNP [dm3] 3R_12337621_SNP [dm6]	G	T	1.668e^-5	0.663	INTRON CR44941
3L	9649700	3L_9649700_INS [dm3] 3L_9656600_INS [dm6]	C	CAACAAAATTC...	1.672e^-5	0.663	INTRON fry & 1 other
3R	9614355	3R_9614355_SNP [dm3] 3R_13788633_SNP [dm6]	G	A	1.701e^-5	0.663	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	7768136	3R_7768136_SNP [dm3] 3R_11942414_SNP [dm6]	A	G	1.745e^-5	0.663	INTRON Cad87A
2L	9692306	2L_9692306_SNP [dm3] 2L_9692306_SNP [dm6]	T	C	1.776e^-5	0.663	INTRON Pka-C1
2L	7075833	2L_7075833_SNP [dm3] 2L_7075833_SNP [dm6]	T	C	1.782e^-5	0.663	INTRON Pvf2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	17536311	X_17536311_SNP [dm3] X_17642278_SNP [dm6]	C	A	1.789e^-5	0.663	INTRON RhoGAPp190	TF binding site mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2R	618614	2R_618614_SNP [dm3] 2R_4731109_SNP [dm6]	C	G	1.863e^-5	0.663	UPSTREAM CR41440 EXON CR40282 & 1 other
3L	6576863	3L_6576863_SNP [dm3] 3L_6583763_SNP [dm6]	G	T	1.946e^-5	0.663	INTRON CG18769 & 1 other	TF binding site mE1_TFBS_inv
2L	7075702	2L_7075702_SNP [dm3] 2L_7075702_SNP [dm6]	G	A	1.959e^-5	0.663	INTRON Pvf2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
X	7743962	X_7743962_SNP [dm3] X_7849929_SNP [dm6]	T	C	1.998e^-5	0.663	INTERGENIC
3R	14899609	3R_14899609_SNP [dm3] 3R_19073887_SNP [dm6]	G	T	2.021e^-5	0.663	INTRON cdi	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	8223796	3R_8223796_INS [dm3] 3R_12398074_INS [dm6]	T	TA	2.047e^-5	0.663	DOWNSTREAM lig3 INTRON CG34402 & 1 other
3R	9676783	3R_9676783_DEL [dm3] 3R_13851061_DEL [dm6]	GGAAAATTAAGCTATGCGAA...	CCC	2.110e^-5	0.663	INTERGENIC
2R	9367763	2R_9367763_SNP [dm3] 2R_13480258_SNP [dm6]	T	A	2.110e^-5	0.663	INTRON arr
3R	1065952	3R_1065952_SNP [dm3] 3R_5240230_SNP [dm6]	G	T	2.224e^-5	0.663	UTR_3_PRIME CG33293 INTRON CG12163	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	24871403	3R_24871403_SNP [dm3] 3R_29045681_SNP [dm6]	C	G	2.234e^-5	0.663	SYNONYMOUS_CODING Pkc98E
3R	14380877	3R_14380877_SNP [dm3] 3R_18555155_SNP [dm6]	G	T	2.272e^-5	0.663	INTERGENIC
X	20880672	X_20880672_DEL [dm3] X_21009645_DEL [dm6]	AGATGAGGAAAAACTA...	A	2.293e^-5	0.663	INTERGENIC
3L	12247082	3L_12247082_SNP [dm3] 3L_12253982_SNP [dm6]	C	A	2.311e^-5	0.663	INTRON app
2R	17786585	2R_17786585_SNP [dm3] 2R_21899080_SNP [dm6]	C	T	2.349e^-5	0.663	INTRON Fili
2L	10355738	2L_10355738_SNP [dm3] 2L_10355738_SNP [dm6]	C	T	2.352e^-5	0.663	NON_SYNONYMOUS_CODING CG5367
3L	7448361	3L_7448361_SNP [dm3] 3L_7455261_SNP [dm6]	T	A	2.389e^-5	0.663	UPSTREAM ppk26 DOWNSTREAM CG42458 INTERGENIC
2R	11422675	2R_11422675_SNP [dm3] 2R_15535170_SNP [dm6]	G	C	2.520e^-5	0.663	SPLICE_SITE_REGION CG30471 UTR_5_PRIME CG30471
3L	12003005	3L_12003005_SNP [dm3] 3L_12009905_SNP [dm6]	G	A	2.554e^-5	0.663	SYNONYMOUS_CODING rols	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	3310370	3R_3310370_SNP [dm3] 3R_7484648_SNP [dm6]	C	A	2.563e^-5	0.663	INTERGENIC
2R	11353744	2R_11353744_SNP [dm3] 2R_15466239_SNP [dm6]	C	G	2.595e^-5	0.663	INTRON CG43729
3L	4223777	3L_4223777_INS [dm3] 3L_4223777_INS [dm6]	A	ACTGAACA	2.598e^-5	0.663	UTR_3_PRIME CG43367 DOWNSTREAM ImpL2	TF binding site mE1_TFBS_inv
3R	11028748	3R_11028748_SNP [dm3] 3R_15203026_SNP [dm6]	A	G	2.614e^-5	0.663	UTR_3_PRIME CG42542 DOWNSTREAM Spn88Ea & 1 other
3L	6589159	3L_6589159_SNP [dm3] 3L_6596059_SNP [dm6]	C	G	2.642e^-5	0.663	SYNONYMOUS_CODING ndl
2L	923850	2L_923850_SNP [dm3] 2L_923850_SNP [dm6]	C	T	2.660e^-5	0.663	INTRON CG4341	TF binding site mE1_TFBS_chinmo
2R	11354006	2R_11354006_SNP [dm3] 2R_15466501_SNP [dm6]	A	T	2.701e^-5	0.663	INTRON CG43729
2R	11354007	2R_11354007_SNP [dm3] 2R_15466502_SNP [dm6]	G	C	2.701e^-5	0.663	INTRON CG43729
3L	6945496	3L_6945496_SNP [dm3] 3L_6952396_SNP [dm6]	G	A	2.811e^-5	0.663	UTR_3_PRIME CG10077 INTRON CG10077
2R	9407245	2R_9407245_SNP [dm3] 2R_13519740_SNP [dm6]	A	T	2.830e^-5	0.663	INTRON Vmat	TF binding site mE1_TFBS_cad
3R	7768481	3R_7768481_SNP [dm3] 3R_11942759_SNP [dm6]	G	A	2.845e^-5	0.663	INTRON Cad87A
2R	9591534	2R_9591534_SNP [dm3] 2R_13704029_SNP [dm6]	T	C	2.868e^-5	0.663	INTRON fas
3R	16428653	3R_16428653_SNP [dm3] 3R_20602931_SNP [dm6]	G	A	2.989e^-5	0.663	INTRON bon
3R	23470717	3R_23470717_SNP [dm3] 3R_27644995_SNP [dm6]	A	G	3.002e^-5	0.663	INTRON tau	TF binding site BDTNP1_TFBS_prd
3R	10928120	3R_10928120_SNP [dm3] 3R_15102398_SNP [dm6]	T	A	3.007e^-5	0.663	INTRON CG42788
3R	5000954	3R_5000954_DEL [dm3] 3R_9175232_DEL [dm6]	AA	A	3.037e^-5	0.663	INTRON pum
2L	15403365	2L_15403365_SNP [dm3] 2L_15403365_SNP [dm6]	C	A	3.114e^-5	0.663	INTERGENIC
2L	10459970	2L_10459970_SNP [dm3] 2L_10459970_SNP [dm6]	T	C	3.161e^-5	0.663	SYNONYMOUS_CODING LM408
3L	7307474	3L_7307474_SNP [dm3] 3L_7314374_SNP [dm6]	T	A	3.177e^-5	0.663	INTERGENIC
2L	7075819	2L_7075819_DEL [dm3] 2L_7075819_DEL [dm6]	TAT	T	3.239e^-5	0.663	INTRON Pvf2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	18711683	3R_18711683_SNP [dm3] 3R_22885961_SNP [dm6]	A	G	3.240e^-5	0.663	INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	15403367	2L_15403367_SNP [dm3] 2L_15403367_SNP [dm6]	A	G	3.241e^-5	0.663	INTERGENIC
3R	10037587	3R_10037587_SNP [dm3] 3R_14211865_SNP [dm6]	C	A	3.253e^-5	0.663	INTRON Dop1R1
3R	9677552	3R_9677552_SNP [dm3] 3R_13851830_SNP [dm6]	G	A	3.341e^-5	0.663	INTERGENIC
2L	12089190	2L_12089190_SNP [dm3] 2L_12089190_SNP [dm6]	A	G	3.351e^-5	0.663	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	11811868	2L_11811868_SNP [dm3] 2L_11811868_SNP [dm6]	T	C	3.385e^-5	0.663	SYNONYMOUS_CODING CycY	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2R	7278737	2R_7278737_SNP [dm3] 2R_11391232_SNP [dm6]	T	G	3.404e^-5	0.663	INTRON sprt
3L	14582739	3L_14582739_SNP [dm3] 3L_14589639_SNP [dm6]	G	A	3.409e^-5	0.663	INTRON HGTX
3R	13916678	3R_13916678_SNP [dm3] 3R_18090956_SNP [dm6]	T	C	3.493e^-5	0.663	UTR_5_PRIME sr	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	15403373	2L_15403373_SNP [dm3] 2L_15403373_SNP [dm6]	T	G	3.505e^-5	0.663	INTERGENIC
3R	18174376	3R_18174376_SNP [dm3] 3R_22348654_SNP [dm6]	G	T	3.571e^-5	0.663	INTERGENIC
3L	7851352	3L_7851352_SNP [dm3] 3L_7858252_SNP [dm6]	G	T	3.583e^-5	0.663	INTRON Pdp1	TF binding site mE1_TFBS_HSA
2L	5336427	2L_5336427_SNP [dm3] 2L_5336427_SNP [dm6]	G	T	3.593e^-5	0.663	UPSTREAM fusl INTRON fusl
2L	15403375	2L_15403375_SNP [dm3] 2L_15403375_SNP [dm6]	A	G	3.622e^-5	0.663	INTERGENIC
2L	5273998	2L_5273998_SNP [dm3] 2L_5273998_SNP [dm6]	C	A	3.629e^-5	0.663	UTR_3_PRIME Bsg25D INTRON Bsg25D	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_inv
2L	5336428	2L_5336428_INS [dm3] 2L_5336428_INS [dm6]	A	ATTTTTA	3.676e^-5	0.663	UPSTREAM fusl INTRON fusl
3L	18911661	3L_18911661_SNP [dm3] 3L_18918561_SNP [dm6]	G	A	3.678e^-5	0.663	SYNONYMOUS_CODING CG6839 DOWNSTREAM CG18223	TF binding site mE1_TFBS_cad mE1_TFBS_sens

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=5.875e^-13)
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	0.07407
In_3R_P	7.069e-05

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2L_t	6.4172	0.0404

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2377 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	8264461	3R_8264461_SNP [dm3] 3R_12438739_SNP [dm6]	G	A	1.880e^-7	0.163	NON_SYNONYMOUS_CODING CG17207 UPSTREAM Desat1 DOWNSTREAM Desat2	regulatory region REDfly_CRMs TF binding site mE1_TFBS_cad
2R	13713600	2R_13713600_SNP [dm3] 2R_17826095_SNP [dm6]	A	G	1.995e^-7	0.163	INTRON grh	transposable element FlyBase
3R	8341839	3R_8341839_DEL [dm3] 3R_12516117_DEL [dm6]	AGGAACTTAAATACACAATT...	A	2.599e^-7	0.163	INTRON Octbeta3R
3R	8216558	3R_8216558_SNP [dm3] 3R_12390836_SNP [dm6]	C	T	9.111e^-7	0.365	UTR_3_PRIME CG10096 & 1 other INTRON CG34402
3L	8078005	3L_8078005_SNP [dm3] 3L_8084905_SNP [dm6]	T	C	1.017e^-6	0.365	INTRON Ect4	TF binding site BDTNP1_TFBS_sna
3R	2148209	3R_2148209_SNP [dm3] 3R_6322487_SNP [dm6]	G	A	1.464e^-6	0.365	INTRON Osi17
3L	8077974	3L_8077974_SNP [dm3] 3L_8084874_SNP [dm6]	C	T	1.602e^-6	0.365	INTRON Ect4	TF binding site BDTNP1_TFBS_sna
3L	6395533	3L_6395533_SNP [dm3] 3L_6402433_SNP [dm6]	G	A	1.796e^-6	0.365	INTRON CG42747
3R	4858700	3R_4858700_SNP [dm3] 3R_9032978_SNP [dm6]	C	T	1.974e^-6	0.365	INTRON neur	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	4040573	3R_4040573_SNP [dm3] 3R_8214851_SNP [dm6]	A	T	2.043e^-6	0.365	INTERGENIC
X	4300225	X_4300225_SNP [dm3] X_4406192_SNP [dm6]	T	C	2.262e^-6	0.365	INTRON CR32773	TF binding site mE1_TFBS_chinmo
3R	8349986	3R_8349986_SNP [dm3] 3R_12524264_SNP [dm6]	T	C	2.717e^-6	0.365	INTRON Octbeta3R
3R	7728163	3R_7728163_SNP [dm3] 3R_11902441_SNP [dm6]	A	T	2.870e^-6	0.365	INTRON Cad87A
3R	14335563	3R_14335563_SNP [dm3] 3R_18509841_SNP [dm6]	T	C	2.878e^-6	0.365	INTRON fru
3R	8350023	3R_8350023_SNP [dm3] 3R_12524301_SNP [dm6]	C	A	2.942e^-6	0.365	INTRON Octbeta3R
3R	26512851	3R_26512851_SNP [dm3] 3R_30687129_SNP [dm6]	T	A	3.118e^-6	0.365	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	13325132	3L_13325132_SNP [dm3] 3L_13332032_SNP [dm6]	A	G	4.249e^-6	0.399	INTERGENIC
2L	2526054	2L_2526054_SNP [dm3] 2L_2526054_SNP [dm6]	T	C	4.432e^-6	0.399	INTERGENIC
3R	8349787	3R_8349787_SNP [dm3] 3R_12524065_SNP [dm6]	C	A	4.679e^-6	0.399	INTRON Octbeta3R
3R	8286537	3R_8286537_SNP [dm3] 3R_12460815_SNP [dm6]	C	T	4.688e^-6	0.399	UPSTREAM CG5961 INTRON CG12267	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	735620	3L_735620_SNP [dm3] 3L_735620_SNP [dm6]	G	T	4.716e^-6	0.399	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
2R	12788320	2R_12788320_SNP [dm3] 2R_16900815_SNP [dm6]	A	C	5.016e^-6	0.399	INTRON inaC
3R	8220292	3R_8220292_SNP [dm3] 3R_12394570_SNP [dm6]	T	C	5.083e^-6	0.399	SYNONYMOUS_CODING CG10097 START_GAINED CG10096 UTR_5_PRIME CG10096 INTRON CG34402
3R	7728095	3R_7728095_SNP [dm3] 3R_11902373_SNP [dm6]	T	C	5.223e^-6	0.399	INTRON Cad87A
3R	2776414	3R_2776414_SNP [dm3] 3R_6950692_SNP [dm6]	G	A	5.436e^-6	0.399	INTRON Antp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	16861822	3R_16861822_SNP [dm3] 3R_21036100_SNP [dm6]	C	G	5.526e^-6	0.399	SYNONYMOUS_CODING Dhc93AB	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	8242073	3R_8242073_SNP [dm3] 3R_12416351_SNP [dm6]	C	A	6.727e^-6	0.446	SYNONYMOUS_CODING pps	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3R	7728045	3R_7728045_SNP [dm3] 3R_11902323_SNP [dm6]	C	A	6.914e^-6	0.446	INTRON Cad87A
3R	8221499	3R_8221499_SNP [dm3] 3R_12395777_SNP [dm6]	G	A	7.020e^-6	0.446	SYNONYMOUS_CODING CG10097 UTR_5_PRIME CG10096 DOWNSTREAM Cyp9f3Psi INTRON CG34402
3R	8234140	3R_8234140_SNP [dm3] 3R_12408418_SNP [dm6]	C	G	7.131e^-6	0.446	NON_SYNONYMOUS_CODING CG5196 UPSTREAM CG5196 DOWNSTREAM CG5167	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad
2L	15104877	2L_15104877_SNP [dm3] 2L_15104877_SNP [dm6]	C	T	7.761e^-6	0.451	INTERGENIC
3R	8253437	3R_8253437_SNP [dm3] 3R_12427715_SNP [dm6]	C	T	8.277e^-6	0.451	NON_SYNONYMOUS_CODING Sas DOWNSTREAM CG5641	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	8286850	3R_8286850_SNP [dm3] 3R_12461128_SNP [dm6]	G	A	8.399e^-6	0.451	SYNONYMOUS_CODING CG12267 UPSTREAM CG5961	TF binding site mE1_TFBS_inv
3R	8235993	3R_8235993_SNP [dm3] 3R_12410271_SNP [dm6]	T	G	8.409e^-6	0.451	SPLICE_SITE_REGION CG5196 INTRON CG5196	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3R	17912729	3R_17912729_SNP [dm3] 3R_22087007_SNP [dm6]	G	A	8.514e^-6	0.451	UPSTREAM CG5791 & 1 other INTRON CG5778
3R	8234936	3R_8234936_SNP [dm3] 3R_12409214_SNP [dm6]	A	G	8.650e^-6	0.451	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	26505012	3R_26505012_SNP [dm3] 3R_30679290_SNP [dm6]	C	T	9.445e^-6	0.456	INTERGENIC
3R	26505170	3R_26505170_SNP [dm3] 3R_30679448_SNP [dm6]	C	T	9.476e^-6	0.456	INTERGENIC
3R	7728056	3R_7728056_DEL [dm3] 3R_11902334_DEL [dm6]	TT	T	9.554e^-6	0.456	INTRON Cad87A
3R	24599566	3R_24599566_INS [dm3] 3R_28773844_INS [dm6]	T	TT	9.719e^-6	0.456	INTERGENIC
3R	23509134	3R_23509134_SNP [dm3] 3R_27683412_SNP [dm6]	C	T	1.012e^-5	0.463	INTERGENIC	TF binding site mE1_TFBS_chinmo
3R	26087341	3R_26087341_SNP [dm3] 3R_30261619_SNP [dm6]	A	T	1.102e^-5	0.492	INTERGENIC	TF binding site mE1_TFBS_Kr
3L	14122277	3L_14122277_SNP [dm3] 3L_14129177_SNP [dm6]	C	A	1.141e^-5	0.497	INTRON Sox21b	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	8164413	3R_8164413_SNP [dm3] 3R_12338691_SNP [dm6]	A	C	1.269e^-5	0.54	INTRON CR44941
3R	25818024	3R_25818024_SNP [dm3] 3R_29992302_SNP [dm6]	A	G	1.295e^-5	0.54	SYNONYMOUS_CODING Acph-1	TF binding site mE1_TFBS_cad mE1_TFBS_sens
3R	4463463	3R_4463463_SNP [dm3] 3R_8637741_SNP [dm6]	G	A	1.339e^-5	0.546	INTERGENIC
3R	1795589	3R_1795589_SNP [dm3] 3R_5969867_SNP [dm6]	G	A	1.483e^-5	0.592	UPSTREAM CR44926 INTERGENIC
2R	6305228	2R_6305228_SNP [dm3] 2R_10417723_SNP [dm6]	T	C	1.624e^-5	0.62	UPSTREAM CG42732 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3R	8235953	3R_8235953_SNP [dm3] 3R_12410231_SNP [dm6]	A	G	1.651e^-5	0.62	INTRON CG5196	TF binding site BDTNP1_TFBS_da mE1_TFBS_cad mE1_TFBS_HSA
3L	6396334	3L_6396334_SNP [dm3] 3L_6403234_SNP [dm6]	G	C	1.654e^-5	0.62	INTRON CG42747
3R	15592989	3R_15592989_INS [dm3] 3R_19767267_INS [dm6]	A	ATCCTGGCACCCTGGCA...	1.763e^-5	0.634	INTRON GluClalpha
3R	8234276	3R_8234276_SNP [dm3] 3R_12408554_SNP [dm6]	C	G	1.788e^-5	0.634	UPSTREAM CG5196 DOWNSTREAM CG5167 INTRON CG5196	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad
3R	8083034	3R_8083034_SNP [dm3] 3R_12257312_SNP [dm6]	A	T	1.798e^-5	0.634	DOWNSTREAM CG3942 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Kr
3R	14960664	3R_14960664_SNP [dm3] 3R_19134942_SNP [dm6]	C	T	1.932e^-5	0.634	UPSTREAM Cyp12a4 DOWNSTREAM Cyp12a5 INTERGENIC
3R	8164613	3R_8164613_SNP [dm3] 3R_12338891_SNP [dm6]	T	A	2.018e^-5	0.634	EXON CR44941
3L	2278086	3L_2278086_SNP [dm3] 3L_2278086_SNP [dm6]	T	G	2.039e^-5	0.634	DOWNSTREAM yellow-g2 INTERGENIC
3L	6396124	3L_6396124_SNP [dm3] 3L_6403024_SNP [dm6]	A	G	2.042e^-5	0.634	INTRON CG42747
3L	2278285	3L_2278285_SNP [dm3] 3L_2278285_SNP [dm6]	C	A	2.047e^-5	0.634	DOWNSTREAM yellow-g2 INTERGENIC	TF binding site mE1_TFBS_inv
3R	8235851	3R_8235851_SNP [dm3] 3R_12410129_SNP [dm6]	A	G	2.062e^-5	0.634	INTRON CG5196	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_HSA
X	13977568	X_13977568_SNP [dm3] X_14083535_SNP [dm6]	G	T	2.088e^-5	0.634	INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
3R	1756602	3R_1756602_SNP [dm3] 3R_5930880_SNP [dm6]	A	G	2.122e^-5	0.634	INTRON CG34113
3R	9654654	3R_9654654_SNP [dm3] 3R_13828932_SNP [dm6]	T	A	2.135e^-5	0.634	UPSTREAM Mst87F DOWNSTREAM CR43300 INTERGENIC
3R	3550136	3R_3550136_SNP [dm3] 3R_7724414_SNP [dm6]	T	A	2.205e^-5	0.634	UTR_3_PRIME CG2616	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	12561460	3L_12561460_SNP [dm3] 3L_12568360_SNP [dm6]	C	A	2.245e^-5	0.634	INTRON sowah
X	4878527	X_4878527_SNP [dm3] X_4984494_SNP [dm6]	G	A	2.262e^-5	0.634	INTRON CR44833	regulatory region REDfly_CRMs
2R	12887593	2R_12887593_SNP [dm3] 2R_17000088_SNP [dm6]	A	G	2.278e^-5	0.634	SYNONYMOUS_CODING ste24b DOWNSTREAM ste24a	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	20006816	3R_20006816_SNP [dm3] 3R_24181094_SNP [dm6]	A	C	2.372e^-5	0.634	UTR_3_PRIME CG13606 INTRON CG13606
3R	3497440	3R_3497440_SNP [dm3] 3R_7671718_SNP [dm6]	C	T	2.376e^-5	0.634	INTRON Nlg1
3L	1444499	3L_1444499_SNP [dm3] 3L_1444499_SNP [dm6]	T	G	2.377e^-5	0.634	INTRON Ptp61F
3L	2278080	3L_2278080_SNP [dm3] 3L_2278080_SNP [dm6]	G	C	2.498e^-5	0.634	DOWNSTREAM yellow-g2 INTERGENIC
2R	13344923	2R_13344923_SNP [dm3] 2R_17457418_SNP [dm6]	A	C	2.524e^-5	0.634	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
X	9753967	X_9753967_SNP [dm3] X_9859934_SNP [dm6]	G	C	2.550e^-5	0.634	INTERGENIC
3R	3219936	3R_3219936_SNP [dm3] 3R_7394214_SNP [dm6]	G	A	2.568e^-5	0.634	INTERGENIC	TF binding site mE1_TFBS_inv
2R	19122571	2R_19122571_SNP [dm3] 2R_23235048_SNP [dm6]	T	C	2.585e^-5	0.634	INTERGENIC
3R	8280154	3R_8280154_SNP [dm3] 3R_12454432_SNP [dm6]	G	A	2.615e^-5	0.634	INTRON CG18549	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad
3L	6396814	3L_6396814_SNP [dm3] 3L_6403714_SNP [dm6]	T	A	2.616e^-5	0.634	INTRON CG42747
3R	14541261	3R_14541261_DEL [dm3] 3R_18715539_DEL [dm6]	TC	T	2.617e^-5	0.634	UTR_3_PRIME VAChT INTRON Cha
3R	8280116	3R_8280116_SNP [dm3] 3R_12454394_SNP [dm6]	A	C	2.638e^-5	0.634	INTRON CG18549	TF binding site BDTNP1_TFBS_prd
2R	6305220	2R_6305220_SNP [dm3] 2R_10417715_SNP [dm6]	G	T	2.762e^-5	0.635	UPSTREAM CG42732 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_zfh1
3L	571997	3L_571997_SNP [dm3] 3L_571997_SNP [dm6]	G	A	2.769e^-5	0.635	INTRON hipk	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	7087114	3L_7087114_SNP [dm3] 3L_7094014_SNP [dm6]	C	T	2.815e^-5	0.635	UPSTREAM form3 DOWNSTREAM Cpr65Ec INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
3R	25635394	3R_25635394_SNP [dm3] 3R_29809672_SNP [dm6]	T	G	2.901e^-5	0.635	NON_SYNONYMOUS_CODING ca	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2R	13344924	2R_13344924_SNP [dm3] 2R_17457419_SNP [dm6]	G	C	3.046e^-5	0.635	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	8164617	3R_8164617_SNP [dm3] 3R_12338895_SNP [dm6]	T	C	3.100e^-5	0.635	EXON CR44941
X	13977711	X_13977711_SNP [dm3] X_14083678_SNP [dm6]	C	T	3.140e^-5	0.635	INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
3R	8234000	3R_8234000_SNP [dm3] 3R_12408278_SNP [dm6]	A	G	3.143e^-5	0.635	UPSTREAM CG5196 DOWNSTREAM CG5167 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad
2L	15077112	2L_15077112_SNP [dm3] 2L_15077112_SNP [dm6]	G	T	3.170e^-5	0.635	INTRON CG15270
3R	26513130	3R_26513130_SNP [dm3] 3R_30687408_SNP [dm6]	G	A	3.204e^-5	0.635	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	23000258	3R_23000258_DEL [dm3] 3R_27174536_DEL [dm6]	AT	A	3.208e^-5	0.635	INTRON Ser	TF binding site mE1_TFBS_cad
3L	6585791	3L_6585791_SNP [dm3] 3L_6592691_SNP [dm6]	G	T	3.212e^-5	0.635	UTR_3_PRIME CG18769 DOWNSTREAM CG18769
3L	13326315	3L_13326315_SNP [dm3] 3L_13333215_SNP [dm6]	T	A	3.229e^-5	0.635	INTERGENIC
X	13977559	X_13977559_SNP [dm3] X_14083526_SNP [dm6]	T	A	3.289e^-5	0.635	INTERGENIC	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA
3R	24844793	3R_24844793_INS [dm3] 3R_29019071_INS [dm6]	A	AA	3.311e^-5	0.635	INTRON wat
3R	8350126	3R_8350126_SNP [dm3] 3R_12524404_SNP [dm6]	C	T	3.344e^-5	0.635	INTRON Octbeta3R
2L	19637775	2L_19637775_DEL [dm3] 2L_19637775_DEL [dm6]	ATAAATAA	A	3.404e^-5	0.635	INTRON Lar
X	14518170	X_14518170_SNP [dm3] X_14624137_SNP [dm6]	A	T	3.411e^-5	0.635	INTRON NetA
3R	15596110	3R_15596110_SNP [dm3] 3R_19770388_SNP [dm6]	G	T	3.420e^-5	0.635	UTR_3_PRIME GluClalpha DOWNSTREAM CG6300 INTRON GluClalpha
X	4362481	X_4362481_SNP [dm3] X_4468448_SNP [dm6]	A	C	3.433e^-5	0.635	INTRON bi & 1 other	TF binding site mE1_TFBS_chinmo
3R	10119268	3R_10119268_SNP [dm3] 3R_14293546_SNP [dm6]	G	C	3.457e^-5	0.635	INTRON CG12207
3R	17874708	3R_17874708_INS [dm3] 3R_22048986_INS [dm6]	C	CAGGC	3.469e^-5	0.635	INTRON how	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi

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Cuticul_n_C28 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