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=2.847e^-6)
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_P	0.0002743

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	5.098	0.0782

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1907 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	8521633	2L_8521633_SNP [dm3] 2L_8521633_SNP [dm6]	G	A	1.060e^-6	0.721	UTR_3_PRIME CG13091 UPSTREAM Acer	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Ubx
2L	313440	2L_313440_SNP [dm3] 2L_313440_SNP [dm6]	A	G	1.290e^-6	0.721	INTRON Plc21C
3L	6395533	3L_6395533_SNP [dm3] 3L_6402433_SNP [dm6]	G	A	1.459e^-6	0.721	INTRON CG42747
2L	13726505	2L_13726505_SNP [dm3] 2L_13726505_SNP [dm6]	G	T	2.385e^-6	0.721	INTERGENIC
2L	13726506	2L_13726506_SNP [dm3] 2L_13726506_SNP [dm6]	G	T	2.907e^-6	0.721	INTERGENIC
3L	9137472	3L_9137472_SNP [dm3] 3L_9144372_SNP [dm6]	A	G	3.074e^-6	0.721	UTR_3_PRIME nwk UPSTREAM mir-4940 INTRON nwk	TF binding site mE1_TFBS_cad
2L	8504960	2L_8504960_SNP [dm3] 2L_8504960_SNP [dm6]	G	A	3.263e^-6	0.721	INTRON Dh31
2L	8504943	2L_8504943_SNP [dm3] 2L_8504943_SNP [dm6]	T	C	3.330e^-6	0.721	INTRON Dh31
3L	6396124	3L_6396124_SNP [dm3] 3L_6403024_SNP [dm6]	A	G	4.330e^-6	0.721	INTRON CG42747
2L	4422778	2L_4422778_SNP [dm3] 2L_4422778_SNP [dm6]	A	G	4.422e^-6	0.721	INTRON CG15431
2L	10530516	2L_10530516_SNP [dm3] 2L_10530516_SNP [dm6]	T	C	4.506e^-6	0.721	SYNONYMOUS_CODING Lip4
2L	8520157	2L_8520157_SNP [dm3] 2L_8520157_SNP [dm6]	C	A	5.584e^-6	0.721	NON_SYNONYMOUS_CODING CG13091 DOWNSTREAM CG13090	TF binding site mE1_TFBS_chinmo
2L	313403	2L_313403_SNP [dm3] 2L_313403_SNP [dm6]	A	T	5.679e^-6	0.721	INTRON Plc21C
3R	16647621	3R_16647621_SNP [dm3] 3R_20821899_SNP [dm6]	C	A	5.687e^-6	0.721	UPSTREAM RpS20 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx mE1_TFBS_zfh1
3R	23848442	3R_23848442_INS [dm3] 3R_28022720_INS [dm6]	A	AA	5.767e^-6	0.721	INTERGENIC
3R	14140329	3R_14140329_SNP [dm3] 3R_18314607_SNP [dm6]	G	C	6.863e^-6	0.761	UPSTREAM PKD INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3L	15957612	3L_15957612_SNP [dm3] 3L_15964512_SNP [dm6]	G	T	7.084e^-6	0.761	SYNONYMOUS_CODING l_3_72Ab	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8504959	2L_8504959_SNP [dm3] 2L_8504959_SNP [dm6]	T	C	8.416e^-6	0.761	INTRON Dh31
2L	313446	2L_313446_SNP [dm3] 2L_313446_SNP [dm6]	A	G	8.644e^-6	0.761	INTRON Plc21C
3L	12561460	3L_12561460_SNP [dm3] 3L_12568360_SNP [dm6]	C	A	8.676e^-6	0.761	INTRON sowah
2R	18605375	2R_18605375_SNP [dm3] 2R_22717870_SNP [dm6]	T	C	9.069e^-6	0.761	SPLICE_SITE_REGION jbug DOWNSTREAM CG30268 INTRON jbug	TF binding site mE1_TFBS_chinmo
3L	9161604	3L_9161604_SNP [dm3] 3L_9168504_SNP [dm6]	T	G	9.292e^-6	0.761	INTRON Rdl
X	10933155	X_10933155_SNP [dm3] X_11039122_SNP [dm6]	G	C	9.555e^-6	0.761	INTRON CG42339	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi
2R	18608372	2R_18608372_SNP [dm3] 2R_22720867_SNP [dm6]	G	A	1.032e^-5	0.761	SYNONYMOUS_CODING jbug	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_sens
2L	8504536	2L_8504536_SNP [dm3] 2L_8504536_SNP [dm6]	A	G	1.038e^-5	0.761	INTRON Dh31
3L	5460183	3L_5460183_SNP [dm3] 3L_5467083_SNP [dm6]	G	A	1.055e^-5	0.761	INTERGENIC
2L	15052450	2L_15052450_SNP [dm3] 2L_15052450_SNP [dm6]	T	C	1.133e^-5	0.787	INTRON ck	regulatory region REDfly_CRMs
2L	10345596	2L_10345596_SNP [dm3] 2L_10345596_SNP [dm6]	T	C	1.174e^-5	0.787	INTRON CG5022
2R	18708363	2R_18708363_DEL [dm3] 2R_22820858_DEL [dm6]	TT	T	1.281e^-5	0.809	UPSTREAM CG42284 INTRON CG30271	TF binding site mE1_TFBS_chinmo
2R	18606286	2R_18606286_SNP [dm3] 2R_22718781_SNP [dm6]	C	T	1.321e^-5	0.809	SYNONYMOUS_CODING jbug	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	23884594	3R_23884594_SNP [dm3] 3R_28058872_SNP [dm6]	G	A	1.474e^-5	0.809	INTRON CG34362
3R	25477837	3R_25477837_SNP [dm3] 3R_29652115_SNP [dm6]	A	G	1.502e^-5	0.809	INTRON Dop1R2	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	6396334	3L_6396334_SNP [dm3] 3L_6403234_SNP [dm6]	G	C	1.512e^-5	0.809	INTRON CG42747
2L	8504615	2L_8504615_SNP [dm3] 2L_8504615_SNP [dm6]	C	T	1.541e^-5	0.809	INTRON Dh31
3L	6396416	3L_6396416_SNP [dm3] 3L_6403316_SNP [dm6]	G	A	1.592e^-5	0.809	INTRON CG42747
2L	8504057	2L_8504057_SNP [dm3] 2L_8504057_SNP [dm6]	G	A	1.616e^-5	0.809	INTRON Dh31
2R	1081533	2R_1081533_DEL [dm3] 2R_5194028_DEL [dm6]	GT	G	1.706e^-5	0.809	INTRON Nipped-A	transposable element FlyBase
X	5020636	X_5020636_SNP [dm3] X_5126603_SNP [dm6]	A	T	1.721e^-5	0.809	INTRON rg & 1 other
2L	1531313	2L_1531313_SNP [dm3] 2L_1531313_SNP [dm6]	G	A	1.726e^-5	0.809	INTERGENIC
2L	5417859	2L_5417859_SNP [dm3] 2L_5417859_SNP [dm6]	T	A	1.741e^-5	0.809	INTERGENIC
3L	6396128	3L_6396128_SNP [dm3] 3L_6403028_SNP [dm6]	G	A	1.768e^-5	0.809	INTRON CG42747
2R	18369048	2R_18369048_SNP [dm3] 2R_22481543_SNP [dm6]	G	A	2.017e^-5	0.874	INTRON CG4752	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	16647645	3R_16647645_SNP [dm3] 3R_20821923_SNP [dm6]	C	A	2.042e^-5	0.874	UPSTREAM RpS20 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx mE1_TFBS_zfh1
2L	313387	2L_313387_SNP [dm3] 2L_313387_SNP [dm6]	G	A	2.106e^-5	0.874	INTRON Plc21C
3L	15957664	3L_15957664_SNP [dm3] 3L_15964564_SNP [dm6]	A	G	2.124e^-5	0.874	SYNONYMOUS_CODING l_3_72Ab	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	4896797	2L_4896797_SNP [dm3] 2L_4896797_SNP [dm6]	A	T	2.144e^-5	0.874	INTRON CG3036
X	13959259	X_13959259_SNP [dm3] X_14065226_SNP [dm6]	C	A	2.302e^-5	0.919	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	16647464	3R_16647464_SNP [dm3] 3R_20821742_SNP [dm6]	C	A	2.466e^-5	0.927	UTR_5_PRIME CG17271 UPSTREAM RpS20 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cnc mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx mE1_TFBS_zfh1
3R	19804224	3R_19804224_SNP [dm3] 3R_23978502_SNP [dm6]	A	G	2.496e^-5	0.927	INTRON CG31140
2L	5964672	2L_5964672_SNP [dm3] 2L_5964672_SNP [dm6]	G	A	2.608e^-5	0.927	UPSTREAM psd DOWNSTREAM CG13992 INTRON psd
3L	10808001	3L_10808001_DEL [dm3] 3L_10814901_DEL [dm6]	GCG	G	2.650e^-5	0.927	UTR_5_PRIME CG42831
2L	4896786	2L_4896786_SNP [dm3] 2L_4896786_SNP [dm6]	C	T	2.698e^-5	0.927	INTRON CG3036
2R	9512213	2R_9512213_SNP [dm3] 2R_13624708_SNP [dm6]	T	G	2.702e^-5	0.927	INTRON fas
3R	19804234	3R_19804234_SNP [dm3] 3R_23978512_SNP [dm6]	A	T	2.779e^-5	0.927	INTRON CG31140
3L	6396662	3L_6396662_SNP [dm3] 3L_6403562_SNP [dm6]	A	G	2.888e^-5	0.927	INTRON CG42747
3L	9053529	3L_9053529_SNP [dm3] 3L_9060429_SNP [dm6]	C	G	3.018e^-5	0.927	INTRON Argk
2R	7379875	2R_7379875_SNP [dm3] 2R_11492370_SNP [dm6]	A	G	3.058e^-5	0.927	INTRON inv
3L	15943155	3L_15943155_DEL [dm3] 3L_15950055_DEL [dm6]	AGCCA	A	3.142e^-5	0.927	INTRON Pka-C3
3R	16650170	3R_16650170_SNP [dm3] 3R_20824448_SNP [dm6]	T	A	3.179e^-5	0.927	UPSTREAM CG17272 DOWNSTREAM AdSS INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	17829310	3L_17829310_DEL [dm3] 3L_17836210_DEL [dm6]	TTTTCCGCATGCTAAAATCG...	T	3.183e^-5	0.927	INTRON Grd
3L	17829337	3L_17829337_SNP [dm3] 3L_17836237_SNP [dm6]	T	A	3.183e^-5	0.927	INTRON Grd
3R	26616008	3R_26616008_SNP [dm3] 3R_30790286_SNP [dm6]	G	A	3.214e^-5	0.927	UTR_3_PRIME wts
3L	7611528	3L_7611528_SNP [dm3] 3L_7618428_SNP [dm6]	T	C	3.285e^-5	0.927	INTRON CG33275
3L	7604878	3L_7604878_DEL [dm3] 3L_7611778_DEL [dm6]	ACGTTGA	A	3.339e^-5	0.927	INTRON CG33275
3R	19261520	3R_19261520_SNP [dm3] 3R_23435798_SNP [dm6]	A	T	3.362e^-5	0.927	INTRON CG4374
3R	2457129	3R_2457129_SNP [dm3] 3R_6631407_SNP [dm6]	A	C	3.471e^-5	0.927	DOWNSTREAM sunz INTERGENIC
3R	15309937	3R_15309937_SNP [dm3] 3R_19484215_SNP [dm6]	A	G	3.489e^-5	0.927	SYNONYMOUS_CODING Dys INTRON Dys
2L	4039632	2L_4039632_SNP [dm3] 2L_4039632_SNP [dm6]	T	G	3.521e^-5	0.927	INTRON ed
3R	16649476	3R_16649476_SNP [dm3] 3R_20823754_SNP [dm6]	T	C	3.552e^-5	0.927	DOWNSTREAM snoRNA:Psi28S-2562 & 2 others INTRON CG17272	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA
X	14855617	X_14855617_SNP [dm3] X_14961584_SNP [dm6]	A	G	3.569e^-5	0.927	INTRON eag	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_chinmo
3R	23886018	3R_23886018_SNP [dm3] 3R_28060296_SNP [dm6]	C	T	3.606e^-5	0.927	INTRON CG34362
2L	7102505	2L_7102505_SNP [dm3] 2L_7102505_SNP [dm6]	G	C	3.643e^-5	0.927	INTRON Pvf3
3L	17819926	3L_17819926_SNP [dm3] 3L_17826826_SNP [dm6]	A	G	3.746e^-5	0.927	INTRON Grd
3L	12155380	3L_12155380_SNP [dm3] 3L_12162280_SNP [dm6]	T	C	3.774e^-5	0.927	INTRON CG9760
X	12292555	X_12292555_SNP [dm3] X_12398522_SNP [dm6]	T	A	4.086e^-5	0.927	INTERGENIC
2L	8512075	2L_8512075_SNP [dm3] 2L_8512075_SNP [dm6]	A	T	4.089e^-5	0.927	UPSTREAM CG13096 DOWNSTREAM CG13097 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_HSA
2L	7463093	2L_7463093_INS [dm3] 2L_7463093_INS [dm6]	A	AA	4.116e^-5	0.927	UPSTREAM Gr28b INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	13516036	2R_13516036_INS [dm3] 2R_17628531_INS [dm6]	A	AGTA	4.166e^-5	0.927	UTR_3_PRIME rhi INTRON CG10936
3L	15944366	3L_15944366_SNP [dm3] 3L_15951266_SNP [dm6]	A	G	4.269e^-5	0.927	INTRON Pka-C3
2L	21725821	2L_21725821_SNP [dm3] 2L_21725821_SNP [dm6]	A	C	4.292e^-5	0.927	INTRON CG31619	transposable element FlyBase
2R	17111583	2R_17111583_SNP [dm3] 2R_21224078_SNP [dm6]	A	G	4.318e^-5	0.927	UPSTREAM ASPP INTRON ASPP
2R	8937312	2R_8937312_SNP [dm3] 2R_13049807_SNP [dm6]	G	A	4.375e^-5	0.927	UPSTREAM CG13324 INTERGENIC
3R	15907840	3R_15907840_SNP [dm3] 3R_20082118_SNP [dm6]	G	A	4.398e^-5	0.927	SYNONYMOUS_CODING Rh3	TF binding site mE1_TFBS_cad
3R	22765778	3R_22765778_SNP [dm3] 3R_26940056_SNP [dm6]	G	A	4.410e^-5	0.927	INTRON sda
2R	12887593	2R_12887593_SNP [dm3] 2R_17000088_SNP [dm6]	A	G	4.439e^-5	0.927	SYNONYMOUS_CODING ste24b DOWNSTREAM ste24a	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	4422757	2L_4422757_SNP [dm3] 2L_4422757_SNP [dm6]	T	C	4.453e^-5	0.927	INTRON CG15431
3R	25367813	3R_25367813_SNP [dm3] 3R_29542091_SNP [dm6]	T	A	4.560e^-5	0.927	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
3R	16647366	3R_16647366_SNP [dm3] 3R_20821644_SNP [dm6]	G	A	4.608e^-5	0.927	NON_SYNONYMOUS_CODING CG17271 UPSTREAM RpS20 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna mE1_TFBS_cnc mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx mE1_TFBS_zfh1
2R	9513723	2R_9513723_SNP [dm3] 2R_13626218_SNP [dm6]	G	A	4.747e^-5	0.927	INTRON fas
X	5020620	X_5020620_SNP [dm3] X_5126587_SNP [dm6]	G	T	4.861e^-5	0.927	INTRON rg & 1 other
3L	19024253	3L_19024253_SNP [dm3] 3L_19031153_SNP [dm6]	T	A	4.918e^-5	0.927	INTRON nkd	TF binding site BDTNP1_TFBS_dl
3L	6395626	3L_6395626_SNP [dm3] 3L_6402526_SNP [dm6]	A	T	4.928e^-5	0.927	INTRON CG42747
X	2277460	X_2277460_DEL [dm3] X_2383427_DEL [dm6]	AA	A	5.007e^-5	0.927	INTRON PsGEF	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	23886156	3R_23886156_INS [dm3] 3R_28060434_INS [dm6]	T	TAT	5.012e^-5	0.927	INTRON CG34362
2R	9513697	2R_9513697_SNP [dm3] 2R_13626192_SNP [dm6]	G	A	5.093e^-5	0.927	INTRON fas
2L	3210619	2L_3210619_SNP [dm3] 2L_3210619_SNP [dm6]	A	T	5.132e^-5	0.927	EXON CR45336
3L	23439912	3L_23439912_SNP [dm3] 3L_23446812_SNP [dm6]	T	A	5.166e^-5	0.927	INTERGENIC
2R	16376228	2R_16376228_SNP [dm3] 2R_20488723_SNP [dm6]	T	C	5.236e^-5	0.927	INTERGENIC
3L	18545733	3L_18545733_SNP [dm3] 3L_18552633_SNP [dm6]	A	G	5.346e^-5	0.927	INTERGENIC
2L	554099	2L_554099_SNP [dm3] 2L_554099_SNP [dm6]	C	T	5.380e^-5	0.927	SYNONYMOUS_CODING rempA

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=1.874e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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	0.02217
In_3R_P	0.02369
In_3R_Mo	0.07761

Kruskal-Wallis test

Covariate	χ²	p-value
In_2L_t	8.0817	0.0176
In_2R_NS	5.0342	0.0807
In_3R_P	5.2005	0.0743
In_3R_K	5.4414	0.0658

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1661 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	6659878	3R_6659878_SNP [dm3] 3R_10834156_SNP [dm6]	G	C	3.288e^-8	0.062	INTRON Cad86C	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	6659902	3R_6659902_DEL [dm3] 3R_10834180_DEL [dm6]	GCTCCAG	G	9.183e^-8	0.086	INTRON Cad86C	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	6659901	3R_6659901_SNP [dm3] 3R_10834179_SNP [dm6]	A	C	2.931e^-7	0.141	INTRON Cad86C	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	6669804	3R_6669804_SNP [dm3] 3R_10844082_SNP [dm6]	C	T	3.751e^-7	0.141	SYNONYMOUS_CODING Cad86C	TF binding site mE1_TFBS_cad mE1_TFBS_inv
3R	6669810	3R_6669810_SNP [dm3] 3R_10844088_SNP [dm6]	G	A	3.751e^-7	0.141	SYNONYMOUS_CODING Cad86C	TF binding site mE1_TFBS_cad mE1_TFBS_inv
2L	16388013	2L_16388013_INS [dm3] 2L_16388013_INS [dm6]	G	GG	1.292e^-6	0.384	INTERGENIC
2R	14646077	2R_14646077_SNP [dm3] 2R_18758572_SNP [dm6]	C	T	1.432e^-6	0.384	SPLICE_SITE_REGION Jabba SYNONYMOUS_CODING Jabba	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	1072336	2R_1072336_INS [dm3] 2R_5184831_INS [dm6]	C	CGCC	2.678e^-6	0.609	INTRON Nipped-A
3R	8153237	3R_8153237_SNP [dm3] 3R_12327515_SNP [dm6]	C	T	2.960e^-6	0.609	EXON CR45584
X	3422598	X_3422598_SNP [dm3] X_3528565_SNP [dm6]	T	A	3.515e^-6	0.609	INTRON CG32791
2R	1072326	2R_1072326_INS [dm3] 2R_5184821_INS [dm6]	T	TT	3.677e^-6	0.609	INTRON Nipped-A
3R	25784282	3R_25784282_SNP [dm3] 3R_29958560_SNP [dm6]	T	G	4.257e^-6	0.609	INTRON TkR99D
X	3422445	X_3422445_SNP [dm3] X_3528412_SNP [dm6]	G	A	4.459e^-6	0.609	INTRON CG32791
3R	6699278	3R_6699278_SNP [dm3] 3R_10873556_SNP [dm6]	T	C	4.545e^-6	0.609	SYNONYMOUS_CODING CG4596	TF binding site mE1_TFBS_cad
2L	8893286	2L_8893286_SNP [dm3] 2L_8893286_SNP [dm6]	G	A	7.598e^-6	0.902	INTERGENIC
X	5920643	X_5920643_SNP [dm3] X_6026610_SNP [dm6]	T	C	8.330e^-6	0.902	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	9191571	3L_9191571_SNP [dm3] 3L_9198471_SNP [dm6]	G	A	8.342e^-6	0.902	INTERGENIC
2R	14649714	2R_14649714_SNP [dm3] 2R_18762209_SNP [dm6]	C	T	8.861e^-6	0.902	UTR_5_PRIME Mctp
2L	8901240	2L_8901240_SNP [dm3] 2L_8901240_SNP [dm6]	C	T	9.135e^-6	0.902	INTRON CG34398
2R	12163788	2R_12163788_SNP [dm3] 2R_16276283_SNP [dm6]	C	A	1.075e^-5	1	NON_SYNONYMOUS_CODING CG33017
3R	6682426	3R_6682426_SNP [dm3] 3R_10856704_SNP [dm6]	G	T	1.372e^-5	1	UPSTREAM CG4570 DOWNSTREAM CG4511 INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	16145479	2R_16145479_SNP [dm3] 2R_20257974_SNP [dm6]	A	T	1.467e^-5	1	UPSTREAM Hsl & 1 other INTRON Hsl	TF binding site mE1_TFBS_cad
2L	3217460	2L_3217460_SNP [dm3] 2L_3217460_SNP [dm6]	G	C	1.480e^-5	1	INTERGENIC
2R	8113034	2R_8113034_DEL [dm3] 2R_12225529_DEL [dm6]	TGCGTAAA	T	1.533e^-5	1	INTRON CG8854
3L	8850557	3L_8850557_SNP [dm3] 3L_8857457_SNP [dm6]	T	C	1.575e^-5	1	INTRON dally
3R	6078825	3R_6078825_SNP [dm3] 3R_10253103_SNP [dm6]	C	A	1.575e^-5	1	SYNONYMOUS_CODING CG3999
2L	2287185	2L_2287185_SNP [dm3] 2L_2287185_SNP [dm6]	A	G	1.756e^-5	1	UTR_3_PRIME CG42658 UPSTREAM CG31681
2R	3909099	2R_3909099_SNP [dm3] 2R_8021594_SNP [dm6]	A	C	1.828e^-5	1	EXON CR45267	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
3L	13188602	3L_13188602_SNP [dm3] 3L_13195502_SNP [dm6]	A	G	1.923e^-5	1	INTERGENIC
3R	13364199	3R_13364199_SNP [dm3] 3R_17538477_SNP [dm6]	C	T	1.933e^-5	1	SYNONYMOUS_CODING l_3_07882	TF binding site mE1_TFBS_sens
X	9179925	X_9179925_SNP [dm3] X_9285892_SNP [dm6]	A	C	2.026e^-5	1	UTR_5_PRIME lz
3L	11741814	3L_11741814_SNP [dm3] 3L_11748714_SNP [dm6]	C	T	2.060e^-5	1	INTRON CG6024
2R	10897085	2R_10897085_SNP [dm3] 2R_15009580_SNP [dm6]	T	A	2.081e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	13133893	2R_13133893_SNP [dm3] 2R_17246388_SNP [dm6]	T	G	2.096e^-5	1	UPSTREAM CG18469 DOWNSTREAM CG12699 INTRON mbl
X	12213474	X_12213474_DEL [dm3] X_12319441_DEL [dm6]	TCAAACTGTTTATAAGTT...	T	2.133e^-5	1	INTRON Ten-a	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	18692747	2L_18692747_SNP [dm3] 2L_18692747_SNP [dm6]	C	T	2.164e^-5	1	SYNONYMOUS_CODING CG10383	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	13363712	3R_13363712_SNP [dm3] 3R_17537990_SNP [dm6]	C	T	2.448e^-5	1	NON_SYNONYMOUS_CODING l_3_07882 DOWNSTREAM P5cr-2	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	20489206	2L_20489206_SNP [dm3] 2L_20489206_SNP [dm6]	T	C	2.539e^-5	1	UPSTREAM CR45359 DOWNSTREAM CR45360 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	13364203	3R_13364203_SNP [dm3] 3R_17538481_SNP [dm6]	G	A	2.598e^-5	1	NON_SYNONYMOUS_CODING l_3_07882	TF binding site mE1_TFBS_sens
3R	9941769	3R_9941769_SNP [dm3] 3R_14116047_SNP [dm6]	C	A	2.634e^-5	1	INTRON Kif19A	TF binding site mE1_TFBS_inv
2L	8905033	2L_8905033_SNP [dm3] 2L_8905033_SNP [dm6]	A	T	2.749e^-5	1	INTRON CG34398
3L	4666097	3L_4666097_SNP [dm3] 3L_4666097_SNP [dm6]	A	T	2.796e^-5	1	NON_SYNONYMOUS_CODING CG32236 INTRON axo
X	12422708	X_12422708_SNP [dm3] X_12528675_SNP [dm6]	A	C	2.816e^-5	1	INTRON CG43921
3R	13364202	3R_13364202_SNP [dm3] 3R_17538480_SNP [dm6]	G	A	2.836e^-5	1	SYNONYMOUS_CODING l_3_07882	TF binding site mE1_TFBS_sens
2R	12822916	2R_12822916_SNP [dm3] 2R_16935411_SNP [dm6]	G	A	2.939e^-5	1	INTRON Pkc53E
3R	8114058	3R_8114058_SNP [dm3] 3R_12288336_SNP [dm6]	T	G	2.958e^-5	1	INTRON svp	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	8124047	3R_8124047_SNP [dm3] 3R_12298325_SNP [dm6]	C	T	2.958e^-5	1	INTRON svp	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	8130568	3R_8130568_SNP [dm3] 3R_12304846_SNP [dm6]	G	T	2.999e^-5	1	INTERGENIC
X	11578971	X_11578971_SNP [dm3] X_11684938_SNP [dm6]	A	T	3.136e^-5	1	INTRON bif
2L	8891623	2L_8891623_SNP [dm3] 2L_8891623_SNP [dm6]	A	G	3.201e^-5	1	INTRON CG42713
3R	6692156	3R_6692156_SNP [dm3] 3R_10866434_SNP [dm6]	A	G	3.206e^-5	1	INTRON SelR
3R	10122707	3R_10122707_DEL [dm3] 3R_14296985_DEL [dm6]	AACTACAGAAA...	A	3.363e^-5	1	INTRON CG12207
3R	13368067	3R_13368067_SNP [dm3] 3R_17542345_SNP [dm6]	A	G	3.379e^-5	1	INTRON SF1
X	5920627	X_5920627_SNP [dm3] X_6026594_SNP [dm6]	G	C	3.381e^-5	1	INTERGENIC
2R	8092915	2R_8092915_SNP [dm3] 2R_12205410_SNP [dm6]	C	G	3.407e^-5	1	UPSTREAM CR45276 INTERGENIC	TF binding site BDTNP1_TFBS_dl
2R	10897126	2R_10897126_SNP [dm3] 2R_15009621_SNP [dm6]	A	G	3.420e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	20489209	2L_20489209_SNP [dm3] 2L_20489209_SNP [dm6]	T	G	3.511e^-5	1	UPSTREAM CR45359 DOWNSTREAM CR45360 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2R	8109912	2R_8109912_SNP [dm3] 2R_12222407_SNP [dm6]	C	A	3.578e^-5	1	INTERGENIC
3R	10227637	3R_10227637_SNP [dm3] 3R_14401915_SNP [dm6]	A	T	3.712e^-5	1	INTRON cv-c
2L	8223242	2L_8223242_SNP [dm3] 2L_8223242_SNP [dm6]	T	C	3.834e^-5	1	SYNONYMOUS_CODING Pvr
X	6952627	X_6952627_SNP [dm3] X_7058594_SNP [dm6]	T	C	3.934e^-5	1	INTRON CG12541	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_eve mE1_TFBS_HSA
3R	8143710	3R_8143710_SNP [dm3] 3R_12317988_SNP [dm6]	C	A	3.962e^-5	1	INTERGENIC
3L	17591663	3L_17591663_SNP [dm3] 3L_17598563_SNP [dm6]	G	A	3.962e^-5	1	INTRON Eip74EF
2R	8109725	2R_8109725_SNP [dm3] 2R_12222220_SNP [dm6]	G	C	3.969e^-5	1	INTERGENIC
3L	13188081	3L_13188081_SNP [dm3] 3L_13194981_SNP [dm6]	C	A	4.064e^-5	1	INTERGENIC
3L	5461884	3L_5461884_SNP [dm3] 3L_5468784_SNP [dm6]	A	C	4.143e^-5	1	INTERGENIC
X	12213531	X_12213531_SNP [dm3] X_12319498_SNP [dm6]	A	T	4.156e^-5	1	INTRON Ten-a	TF binding site mE1_TFBS_cad
3L	13188650	3L_13188650_SNP [dm3] 3L_13195550_SNP [dm6]	T	A	4.237e^-5	1	INTERGENIC
3L	14581113	3L_14581113_SNP [dm3] 3L_14588013_SNP [dm6]	G	A	4.307e^-5	1	INTRON HGTX	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	10092491	2L_10092491_SNP [dm3] 2L_10092491_SNP [dm6]	A	T	4.321e^-5	1	UPSTREAM CG13133 INTRON CG44153
3L	21293251	3L_21293251_SNP [dm3] 3L_21300151_SNP [dm6]	T	A	4.483e^-5	1	UPSTREAM Cpr78Cc INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	3310241	2R_3310241_SNP [dm3] 2R_7422736_SNP [dm6]	A	G	4.515e^-5	1	INTRON so EXON CR44202	regulatory region REDfly_CRMs TF binding site mE1_TFBS_sens
3L	3076551	3L_3076551_SNP [dm3] 3L_3076551_SNP [dm6]	T	C	4.537e^-5	1	INTRON CG11486	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA
3L	4527306	3L_4527306_SNP [dm3] 3L_4527306_SNP [dm6]	C	A	4.599e^-5	1	INTRON Tie
3R	20351934	3R_20351934_SNP [dm3] 3R_24526212_SNP [dm6]	C	A	4.729e^-5	1	INTRON CG13618
3L	2367629	3L_2367629_SNP [dm3] 3L_2367629_SNP [dm6]	A	T	4.752e^-5	1	DOWNSTREAM CG1317 INTERGENIC
3R	11507903	3R_11507903_SNP [dm3] 3R_15682181_SNP [dm6]	C	T	4.780e^-5	1	INTRON pxb
2R	10897097	2R_10897097_DEL [dm3] 2R_15009592_DEL [dm6]	TCGCTATAATATACATAT...	T	4.819e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	19563393	3R_19563393_SNP [dm3] 3R_23737671_SNP [dm6]	A	G	4.917e^-5	1	INTRON Hmgcr
3R	26914130	3R_26914130_SNP [dm3] 3R_31088408_SNP [dm6]	A	C	4.933e^-5	1	INTERGENIC
2L	13842350	2L_13842350_DEL [dm3] 2L_13842350_DEL [dm6]	CAAAT	C	4.934e^-5	1	UPSTREAM CG33307 DOWNSTREAM CG33306 INTRON CenG1A	TF binding site mE1_TFBS_bab1
2L	8893427	2L_8893427_SNP [dm3] 2L_8893427_SNP [dm6]	A	C	4.943e^-5	1	INTERGENIC
3L	12327350	3L_12327350_SNP [dm3] 3L_12334250_SNP [dm6]	G	A	4.974e^-5	1	SYNONYMOUS_CODING CG32105	TF binding site mE1_TFBS_chinmo
2L	15400980	2L_15400980_SNP [dm3] 2L_15400980_SNP [dm6]	A	G	5.028e^-5	1	UPSTREAM CR45374 INTERGENIC
X	12213509	X_12213509_SNP [dm3] X_12319476_SNP [dm6]	C	T	5.075e^-5	1	INTRON Ten-a	TF binding site mE1_TFBS_cad
2L	12383045	2L_12383045_SNP [dm3] 2L_12383045_SNP [dm6]	C	T	5.100e^-5	1	INTRON bru-2
2R	15430575	2R_15430575_SNP [dm3] 2R_19543070_SNP [dm6]	A	G	5.172e^-5	1	INTRON sm	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	13188174	3L_13188174_SNP [dm3] 3L_13195074_SNP [dm6]	C	G	5.190e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	13188077	3L_13188077_SNP [dm3] 3L_13194977_SNP [dm6]	A	G	5.258e^-5	1	INTERGENIC
3L	13188083	3L_13188083_SNP [dm3] 3L_13194983_SNP [dm6]	C	T	5.258e^-5	1	INTERGENIC
3L	13188084	3L_13188084_SNP [dm3] 3L_13194984_SNP [dm6]	C	T	5.258e^-5	1	INTERGENIC
3R	6701073	3R_6701073_SNP [dm3] 3R_10875351_SNP [dm6]	A	T	5.292e^-5	1	UTR_3_PRIME CG4596
2L	9289503	2L_9289503_SNP [dm3] 2L_9289503_SNP [dm6]	A	T	5.313e^-5	1	INTRON Ggamma30A
2R	6407818	2R_6407818_SNP [dm3] 2R_10520313_SNP [dm6]	A	C	5.333e^-5	1	UTR_3_PRIME lola INTRON lola	TF binding site BDTNP1_TFBS_sna
3R	11507907	3R_11507907_SNP [dm3] 3R_15682185_SNP [dm6]	C	A	5.377e^-5	1	INTRON pxb	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	8223236	2L_8223236_SNP [dm3] 2L_8223236_SNP [dm6]	G	A	5.500e^-5	1	SYNONYMOUS_CODING Pvr
2R	13877321	2R_13877321_SNP [dm3] 2R_17989816_SNP [dm6]	G	A	5.610e^-5	1	SYNONYMOUS_CODING dpr13
3L	13188049	3L_13188049_SNP [dm3] 3L_13194949_SNP [dm6]	C	A	5.770e^-5	1	INTERGENIC
3L	6171907	3L_6171907_SNP [dm3] 3L_6178807_SNP [dm6]	C	T	5.771e^-5	1	UTR_3_PRIME CG7376 & 1 other DOWNSTREAM CG7376
3L	8811821	3L_8811821_SNP [dm3] 3L_8818721_SNP [dm6]	G	T	5.823e^-5	1	INTERGENIC

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By genomic position
Variant impact
Gene name

Cuticul_2_Me_C28_C29 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results