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=9.320e^-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_3R_K	0.09003

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	4.7091	0.0949

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1837 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
2L	15808926	2L_15808926_DEL [dm3] 2L_15808926_DEL [dm6]	CACATTGC	C	3.414e^-7	0.413	DOWNSTREAM CR44602 EXON CR44602
3R	23850969	3R_23850969_SNP [dm3] 3R_28025247_SNP [dm6]	G	A	4.405e^-7	0.413	INTERGENIC
X	4437888	X_4437888_SNP [dm3] X_4543855_SNP [dm6]	C	T	1.008e^-6	0.596	SYNONYMOUS_CODING CG3568 DOWNSTREAM Usf INTRON CR32773	TF binding site mE1_TFBS_sens
2R	10527378	2R_10527378_SNP [dm3] 2R_14639873_SNP [dm6]	A	G	1.358e^-6	0.596	DOWNSTREAM CG43236 & 2 others INTERGENIC	TF binding site mE1_TFBS_inv
X	4437897	X_4437897_SNP [dm3] X_4543864_SNP [dm6]	C	G	2.030e^-6	0.596	SYNONYMOUS_CODING CG3568 DOWNSTREAM Usf INTRON CR32773	TF binding site mE1_TFBS_sens
2L	5563182	2L_5563182_SNP [dm3] 2L_5563182_SNP [dm6]	G	A	2.461e^-6	0.596	INTRON GluRIIB	TF binding site mE1_TFBS_cad
3R	14829606	3R_14829606_SNP [dm3] 3R_19003884_SNP [dm6]	A	G	2.480e^-6	0.596	INTRON gukh	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	15808845	2L_15808845_SNP [dm3] 2L_15808845_SNP [dm6]	G	A	2.541e^-6	0.596	DOWNSTREAM CR44602 EXON CR44602
2R	7743542	2R_7743542_SNP [dm3] 2R_11856037_SNP [dm6]	T	C	3.221e^-6	0.671	SYNONYMOUS_CODING Mtor	TF binding site mE1_TFBS_cad
2L	10040383	2L_10040383_SNP [dm3] 2L_10040383_SNP [dm6]	T	A	3.844e^-6	0.702	INTERGENIC
2R	10527693	2R_10527693_SNP [dm3] 2R_14640188_SNP [dm6]	T	C	5.406e^-6	0.702	DOWNSTREAM CG12862 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	14337190	3L_14337190_SNP [dm3] 3L_14344090_SNP [dm6]	A	T	5.984e^-6	0.702	INTRON fz
3R	23560286	3R_23560286_SNP [dm3] 3R_27734564_SNP [dm6]	G	A	6.220e^-6	0.702	INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	3525060	3L_3525060_SNP [dm3] 3L_3525060_SNP [dm6]	A	G	6.335e^-6	0.702	INTRON Eip63E
3R	23501319	3R_23501319_SNP [dm3] 3R_27675597_SNP [dm6]	C	A	6.728e^-6	0.702	INTRON unc80	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3R	23503365	3R_23503365_SNP [dm3] 3R_27677643_SNP [dm6]	A	G	6.728e^-6	0.702	UTR_5_PRIME CG5590 DOWNSTREAM unc80	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_sens
X	17337530	X_17337530_DEL [dm3] X_17443497_DEL [dm6]	CCAAAGGC	C	6.786e^-6	0.702	INTRON CG12994
2L	9193471	2L_9193471_DEL [dm3] 2L_9193471_DEL [dm6]	TT	A	7.034e^-6	0.702	INTRON tai
2R	3812654	2R_3812654_SNP [dm3] 2R_7925149_SNP [dm6]	A	T	7.788e^-6	0.702	UPSTREAM Kdm4A INTERGENIC	TF binding site BDTNP1_TFBS_prd
2R	3812652	2R_3812652_SNP [dm3] 2R_7925147_SNP [dm6]	A	C	7.890e^-6	0.702	UPSTREAM Kdm4A INTERGENIC	TF binding site BDTNP1_TFBS_prd
X	12992159	X_12992159_SNP [dm3] X_13098126_SNP [dm6]	G	A	8.333e^-6	0.702	SYNONYMOUS_CODING CG43313	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	10838982	3R_10838982_DEL [dm3] 3R_15013260_DEL [dm6]	CC	C	8.774e^-6	0.702	INTERGENIC
3R	7906721	3R_7906721_MNP [dm3] 3R_12080999_MNP [dm6]	AGCGC	TATTA	9.385e^-6	0.702	INTRON CG14741	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
X	4252978	X_4252978_SNP [dm3] X_4358945_SNP [dm6]	C	G	9.461e^-6	0.702	INTRON norpA
3R	22979078	3R_22979078_SNP [dm3] 3R_27153356_SNP [dm6]	G	A	9.899e^-6	0.702	INTRON Men-b	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3L	3298420	3L_3298420_SNP [dm3] 3L_3298420_SNP [dm6]	A	G	1.048e^-5	0.702	SYNONYMOUS_CODING CG12009 UPSTREAM mir-955 DOWNSTREAM CG14968
3R	25065088	3R_25065088_SNP [dm3] 3R_29239366_SNP [dm6]	A	C	1.086e^-5	0.702	UPSTREAM CG11951 INTRON CG31427
2R	10528040	2R_10528040_DEL [dm3] 2R_14640535_DEL [dm6]	AA	A	1.110e^-5	0.702	DOWNSTREAM CG42715 INTRON CG12862	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	19812743	3L_19812743_SNP [dm3] 3L_19819643_SNP [dm6]	C	T	1.146e^-5	0.702	SYNONYMOUS_CODING Deaf1	TF binding site mE1_TFBS_chinmo
2R	10527990	2R_10527990_SNP [dm3] 2R_14640485_SNP [dm6]	G	T	1.243e^-5	0.702	DOWNSTREAM CG42715 INTRON CG12862	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	3077465	2R_3077465_SNP [dm3] 2R_7189960_SNP [dm6]	C	A	1.299e^-5	0.702	INTRON pk
2R	13081965	2R_13081965_SNP [dm3] 2R_17194460_SNP [dm6]	T	A	1.307e^-5	0.702	UPSTREAM CG10950 INTERGENIC
3R	23498549	3R_23498549_SNP [dm3] 3R_27672827_SNP [dm6]	C	T	1.338e^-5	0.702	INTRON unc80	TF binding site mE1_TFBS_chinmo
X	16230647	X_16230647_SNP [dm3] X_16336614_SNP [dm6]	C	T	1.351e^-5	0.702	SYNONYMOUS_CODING Dsp1	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	7728414	2R_7728414_SNP [dm3] 2R_11840909_SNP [dm6]	C	G	1.385e^-5	0.702	UPSTREAM CG34229 INTERGENIC
2R	7731660	2R_7731660_SNP [dm3] 2R_11844155_SNP [dm6]	C	A	1.385e^-5	0.702	UTR_5_PRIME S2P UPSTREAM CG43190 DOWNSTREAM CR44304
2R	7734967	2R_7734967_INS [dm3] 2R_11847462_INS [dm6]	G	GAGCAAATAG	1.385e^-5	0.702	INTRON Sln
3R	23504658	3R_23504658_SNP [dm3] 3R_27678936_SNP [dm6]	G	A	1.529e^-5	0.755	UTR_3_PRIME CG5590 UPSTREAM CG12883	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo
X	4252946	X_4252946_SNP [dm3] X_4358913_SNP [dm6]	A	G	1.635e^-5	0.786	INTRON norpA
2R	10527968	2R_10527968_SNP [dm3] 2R_14640463_SNP [dm6]	G	A	1.721e^-5	0.793	DOWNSTREAM CG42715 INTRON CG12862	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	3298448	3L_3298448_INS [dm3] 3L_3298448_INS [dm6]	G	GCAC	1.734e^-5	0.793	UPSTREAM mir-955 DOWNSTREAM CG14968
2R	7731470	2R_7731470_SNP [dm3] 2R_11843965_SNP [dm6]	T	A	1.827e^-5	0.812	UTR_5_PRIME S2P UPSTREAM CG43190 DOWNSTREAM CR44304
3R	15582957	3R_15582957_SNP [dm3] 3R_19757235_SNP [dm6]	G	A	1.873e^-5	0.812	INTRON GluClalpha
2L	10885678	2L_10885678_SNP [dm3] 2L_10885678_SNP [dm6]	T	C	1.944e^-5	0.812	UPSTREAM CR44490 INTERGENIC
2L	15808493	2L_15808493_SNP [dm3] 2L_15808493_SNP [dm6]	C	A	1.947e^-5	0.812	DOWNSTREAM CR44602 EXON CR44602
3R	6517794	3R_6517794_INS [dm3] 3R_10692072_INS [dm6]	T	TT	1.992e^-5	0.812	INTRON Skeletor	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
3R	23503177	3R_23503177_SNP [dm3] 3R_27677455_SNP [dm6]	T	C	2.044e^-5	0.816	UPSTREAM CG5590 DOWNSTREAM unc80 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_HSA
3L	12843974	3L_12843974_DEL [dm3] 3L_12850874_DEL [dm6]	AGAA	T	2.198e^-5	0.859	UPSTREAM CG10948 INTRON Wbp2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
3L	12843980	3L_12843980_INS [dm3] 3L_12850880_INS [dm6]	T	TGTCTATGTT	2.282e^-5	0.873	UPSTREAM CG10948 INTRON Wbp2	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	10885589	2L_10885589_SNP [dm3] 2L_10885589_SNP [dm6]	A	G	2.379e^-5	0.892	UPSTREAM CR44490 INTERGENIC
3R	23500564	3R_23500564_SNP [dm3] 3R_27674842_SNP [dm6]	C	T	2.576e^-5	0.915	SYNONYMOUS_CODING unc80	TF binding site BDTNP1_TFBS_sna mE1_TFBS_chinmo mE1_TFBS_HSA
3L	3298405	3L_3298405_SNP [dm3] 3L_3298405_SNP [dm6]	A	G	2.646e^-5	0.915	SYNONYMOUS_CODING CG12009 UPSTREAM mir-955 DOWNSTREAM CG14968
3R	20342127	3R_20342127_SNP [dm3] 3R_24516405_SNP [dm6]	C	T	2.729e^-5	0.915	SYNONYMOUS_CODING CG13617	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
X	3325948	X_3325948_SNP [dm3] X_3431915_SNP [dm6]	G	A	2.743e^-5	0.915	INTRON CR44999 & 1 other
X	8841578	X_8841578_SNP [dm3] X_8947545_SNP [dm6]	C	G	2.793e^-5	0.915	INTRON rdgA
2R	16732974	2R_16732974_INS [dm3] 2R_20845469_INS [dm6]	CC	AAAGGGTG	2.812e^-5	0.915	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	3330394	3L_3330394_SNP [dm3] 3L_3330394_SNP [dm6]	A	G	2.884e^-5	0.915	NON_SYNONYMOUS_CODING CG14961 DOWNSTREAM CR45380	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3L	6452915	3L_6452915_SNP [dm3] 3L_6459815_SNP [dm6]	T	C	2.888e^-5	0.915	INTRON CG42747	TF binding site BDTNP1_TFBS_twi
3R	7906712	3R_7906712_INS [dm3] 3R_12080990_INS [dm6]	A	ACATATTAC	2.984e^-5	0.915	INTRON CG14741	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	7906715	3R_7906715_MNP [dm3] 3R_12080993_MNP [dm6]	CAGCG	ATTAC	2.984e^-5	0.915	INTRON CG14741	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	7906728	3R_7906728_SNP [dm3] 3R_12081006_SNP [dm6]	A	T	2.984e^-5	0.915	INTRON CG14741	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	12558120	2L_12558120_SNP [dm3] 2L_12558120_SNP [dm6]	A	C	3.032e^-5	0.915	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	9567283	3R_9567283_SNP [dm3] 3R_13741561_SNP [dm6]	T	A	3.073e^-5	0.915	INTRON CG34383
2R	14271651	2R_14271651_SNP [dm3] 2R_18384146_SNP [dm6]	C	A	3.125e^-5	0.916	UPSTREAM IM23 & 1 other DOWNSTREAM CG15067 INTRON IM1
2L	14566781	2L_14566781_SNP [dm3] 2L_14566781_SNP [dm6]	T	G	3.380e^-5	0.953	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	3298417	3L_3298417_SNP [dm3] 3L_3298417_SNP [dm6]	A	T	3.466e^-5	0.953	SYNONYMOUS_CODING CG12009 UPSTREAM mir-955 DOWNSTREAM CG14968
X	4762076	X_4762076_SNP [dm3] X_4868043_SNP [dm6]	A	T	3.475e^-5	0.953	INTRON CG42594
3R	7906737	3R_7906737_SNP [dm3] 3R_12081015_SNP [dm6]	T	C	3.504e^-5	0.953	INTRON CG14741	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	15808495	2L_15808495_SNP [dm3] 2L_15808495_SNP [dm6]	A	G	3.525e^-5	0.953	DOWNSTREAM CR44602 EXON CR44602
3R	10838951	3R_10838951_SNP [dm3] 3R_15013229_SNP [dm6]	T	C	3.556e^-5	0.953	INTERGENIC
3R	23497086	3R_23497086_SNP [dm3] 3R_27671364_SNP [dm6]	A	C	3.627e^-5	0.958	SYNONYMOUS_CODING unc80	TF binding site mE1_TFBS_cad
2R	7404658	2R_7404658_DEL [dm3] 2R_11517153_DEL [dm6]	TGAGT	T	4.126e^-5	0.979	INTERGENIC
2R	10527509	2R_10527509_SNP [dm3] 2R_14640004_SNP [dm6]	C	A	4.161e^-5	0.979	DOWNSTREAM CG12862 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_inv
2R	3812632	2R_3812632_SNP [dm3] 2R_7925127_SNP [dm6]	A	T	4.208e^-5	0.979	UPSTREAM Kdm4A INTERGENIC	TF binding site BDTNP1_TFBS_prd
2R	10582183	2R_10582183_SNP [dm3] 2R_14694678_SNP [dm6]	G	A	4.294e^-5	0.979	INTRON mspo
3L	14342414	3L_14342414_SNP [dm3] 3L_14349314_SNP [dm6]	T	C	4.300e^-5	0.979	INTRON fz	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3R	26689630	3R_26689630_SNP [dm3] 3R_30863908_SNP [dm6]	C	T	4.387e^-5	0.979	INTERGENIC
X	20008226	X_20008226_SNP [dm3] X_20114193_SNP [dm6]	G	A	4.405e^-5	0.979	INTERGENIC
3R	17836172	3R_17836172_SNP [dm3] 3R_22010450_SNP [dm6]	C	T	4.417e^-5	0.979	UTR_3_PRIME Eip93F
3R	23502700	3R_23502700_SNP [dm3] 3R_27676978_SNP [dm6]	A	T	4.459e^-5	0.979	UTR_3_PRIME unc80 UPSTREAM CG5590	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_sna mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA
3L	11661059	3L_11661059_SNP [dm3] 3L_11667959_SNP [dm6]	C	T	4.466e^-5	0.979	INTRON CG32085
2R	10527810	2R_10527810_INS [dm3] 2R_14640305_INS [dm6]	T	TACCT	4.519e^-5	0.979	FRAME_SHIFT CG12862 DOWNSTREAM CG42715	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	2603182	X_2603182_SNP [dm3] X_2709149_SNP [dm6]	A	G	4.612e^-5	0.979	NON_SYNONYMOUS_CODING CG2681	TF binding site mE1_TFBS_chinmo
2L	2925264	2L_2925264_SNP [dm3] 2L_2925264_SNP [dm6]	C	G	4.671e^-5	0.979	INTRON lilli
3R	20718349	3R_20718349_SNP [dm3] 3R_24892627_SNP [dm6]	G	A	4.791e^-5	0.979	UPSTREAM CG31121 INTRON CG31121
3L	9839177	3L_9839177_DEL [dm3] 3L_9846077_DEL [dm6]	GCCCATATGTGTTTAGTATT...	G	4.897e^-5	0.979	INTRON RasGAP1	TF binding site BDTNP1_TFBS_dl
3L	13196500	3L_13196500_SNP [dm3] 3L_13203400_SNP [dm6]	T	C	5.063e^-5	0.979	INTERGENIC
3L	11669094	3L_11669094_SNP [dm3] 3L_11675994_SNP [dm6]	A	C	5.070e^-5	0.979	INTRON CG32085
3R	23513457	3R_23513457_SNP [dm3] 3R_27687735_SNP [dm6]	G	A	5.088e^-5	0.979	NON_SYNONYMOUS_CODING CG31055 INTRON CG12880	TF binding site mE1_TFBS_chinmo
3R	9567301	3R_9567301_SNP [dm3] 3R_13741579_SNP [dm6]	T	C	5.183e^-5	0.979	INTRON CG34383
3R	17836173	3R_17836173_SNP [dm3] 3R_22010451_SNP [dm6]	A	T	5.217e^-5	0.979	UTR_3_PRIME Eip93F
3R	6562609	3R_6562609_SNP [dm3] 3R_10736887_SNP [dm6]	C	G	5.244e^-5	0.979	UPSTREAM tomboy20 DOWNSTREAM TkR86C INTERGENIC
2L	3435288	2L_3435288_SNP [dm3] 2L_3435288_SNP [dm6]	T	G	5.262e^-5	0.979	INTERGENIC
2R	15449650	2R_15449650_DEL [dm3] 2R_19562145_DEL [dm6]	AA	A	5.398e^-5	0.979	INTRON sm
3R	17836178	3R_17836178_INS [dm3] 3R_22010456_INS [dm6]	A	TAAT	5.408e^-5	0.979	UTR_3_PRIME Eip93F
2L	6021795	2L_6021795_SNP [dm3] 2L_6021795_SNP [dm6]	A	T	5.414e^-5	0.979	DOWNSTREAM CG13996 INTERGENIC	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
3R	24732189	3R_24732189_SNP [dm3] 3R_28906467_SNP [dm6]	T	G	5.445e^-5	0.979	SYNONYMOUS_CODING Doa INTRON Doa	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	18450260	3R_18450260_SNP [dm3] 3R_22624538_SNP [dm6]	G	A	5.447e^-5	0.979	INTRON loco	regulatory region REDfly_CRMs TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
3R	16615462	3R_16615462_SNP [dm3] 3R_20789740_SNP [dm6]	T	C	5.476e^-5	0.979	UPSTREAM Syp INTRON Syp
3R	17836180	3R_17836180_SNP [dm3] 3R_22010458_SNP [dm6]	G	A	5.591e^-5	0.979	UTR_3_PRIME Eip93F

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_7_C24_1 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results