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=1.090e^-7)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test

Covariate	p-value	Significance
In_3R_K	0.008714

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_3R_K	12.3111	0.0021

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1985 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
X	2769334	X_2769334_SNP [dm3] X_2875301_SNP [dm6]	T	A	4.906e^-7	0.887	DOWNSTREAM CG14417 INTRON kirre
X	14065943	X_14065943_SNP [dm3] X_14171910_SNP [dm6]	G	A	3.090e^-6	0.887	SYNONYMOUS_CODING betaNACtes1 DOWNSTREAM CG12480
3L	8314568	3L_8314568_SNP [dm3] 3L_8321468_SNP [dm6]	A	G	3.706e^-6	0.887	INTRON CG13670	TF binding site mE1_TFBS_cad
X	4855898	X_4855898_SNP [dm3] X_4961865_SNP [dm6]	C	G	5.466e^-6	0.887	UPSTREAM SIP3 INTRON CR44833
3R	22294793	3R_22294793_SNP [dm3] 3R_26469071_SNP [dm6]	A	G	6.498e^-6	0.887	INTRON CG5455
2L	14545567	2L_14545567_SNP [dm3] 2L_14545567_SNP [dm6]	G	A	6.761e^-6	0.887	INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	13221413	X_13221413_SNP [dm3] X_13327380_SNP [dm6]	T	C	6.981e^-6	0.887	SYNONYMOUS_CODING IP3K2
3R	14883999	3R_14883999_INS [dm3] 3R_19058277_INS [dm6]	C	CAGTCATTC	7.220e^-6	0.887	INTRON cdi	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_chinmo mE1_TFBS_HSA
3L	8860421	3L_8860421_SNP [dm3] 3L_8867321_SNP [dm6]	G	A	7.986e^-6	0.887	INTRON dally
3L	8314503	3L_8314503_SNP [dm3] 3L_8321403_SNP [dm6]	A	T	8.156e^-6	0.887	INTRON CG13670	TF binding site mE1_TFBS_cad
X	4438150	X_4438150_SNP [dm3] X_4544117_SNP [dm6]	T	C	9.724e^-6	0.887	SYNONYMOUS_CODING CG3568 DOWNSTREAM Usf INTRON CR32773	TF binding site mE1_TFBS_sens
2L	14545086	2L_14545086_SNP [dm3] 2L_14545086_SNP [dm6]	A	T	1.046e^-5	0.887	INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
2L	15100035	2L_15100035_DEL [dm3] 2L_15100035_DEL [dm6]	CC	T	1.053e^-5	0.887	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	11177866	3L_11177866_SNP [dm3] 3L_11184766_SNP [dm6]	G	T	1.079e^-5	0.887	INTRON GlcAT-P
2R	6997655	2R_6997655_SNP [dm3] 2R_11110150_SNP [dm6]	T	A	1.222e^-5	0.887	INTRON luna
2L	4957319	2L_4957319_SNP [dm3] 2L_4957319_SNP [dm6]	C	G	1.233e^-5	0.887	SYNONYMOUS_CODING Marcal1
3L	1365195	3L_1365195_SNP [dm3] 3L_1365195_SNP [dm6]	C	T	1.246e^-5	0.887	INTRON Ptp61F	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	14545578	2L_14545578_SNP [dm3] 2L_14545578_SNP [dm6]	T	G	1.271e^-5	0.887	INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	14545079	2L_14545079_SNP [dm3] 2L_14545079_SNP [dm6]	T	C	1.323e^-5	0.887	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
3R	22294769	3R_22294769_SNP [dm3] 3R_26469047_SNP [dm6]	T	C	1.328e^-5	0.887	INTRON CG5455
2L	15560955	2L_15560955_SNP [dm3] 2L_15560955_SNP [dm6]	G	C	1.435e^-5	0.887	INTRON kek3
2R	18506259	2R_18506259_SNP [dm3] 2R_22618754_SNP [dm6]	G	A	1.443e^-5	0.887	INTRON CG33143
3R	6294504	3R_6294504_SNP [dm3] 3R_10468782_SNP [dm6]	T	A	1.591e^-5	0.887	INTERGENIC
3L	15248370	3L_15248370_SNP [dm3] 3L_15255270_SNP [dm6]	T	G	1.598e^-5	0.887	INTERGENIC
3R	10692944	3R_10692944_SNP [dm3] 3R_14867222_SNP [dm6]	A	T	1.625e^-5	0.887	INTRON btsz
3L	3804882	3L_3804882_SNP [dm3] 3L_3804882_SNP [dm6]	T	C	1.630e^-5	0.887	INTRON CG32264 & 1 other
2L	12924149	2L_12924149_SNP [dm3] 2L_12924149_SNP [dm6]	A	G	1.795e^-5	0.887	INTRON ACXA	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
2R	2874740	2R_2874740_SNP [dm3] 2R_6987235_SNP [dm6]	T	A	1.812e^-5	0.887	INTRON CG17002	TF binding site mE1_TFBS_cad
3R	10692958	3R_10692958_SNP [dm3] 3R_14867236_SNP [dm6]	T	C	1.816e^-5	0.887	INTRON btsz
2R	17981620	2R_17981620_SNP [dm3] 2R_22094115_SNP [dm6]	G	A	1.828e^-5	0.887	NON_SYNONYMOUS_CODING CG11073 INTRON CG11073	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2R	18474107	2R_18474107_SNP [dm3] 2R_22586602_SNP [dm6]	G	T	1.964e^-5	0.887	INTRON dnr1
2L	15100047	2L_15100047_SNP [dm3] 2L_15100047_SNP [dm6]	T	C	2.120e^-5	0.887	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	12146903	3R_12146903_SNP [dm3] 3R_16321181_SNP [dm6]	G	A	2.172e^-5	0.887	UPSTREAM tRNA:F2:89BC & 2 others INTRON Sulf1
3R	2839925	3R_2839925_SNP [dm3] 3R_7014203_SNP [dm6]	A	T	2.196e^-5	0.887	INTERGENIC	TF binding site mE1_TFBS_HSA
3L	10294712	3L_10294712_SNP [dm3] 3L_10301612_SNP [dm6]	G	A	2.242e^-5	0.887	INTERGENIC
3R	2840027	3R_2840027_SNP [dm3] 3R_7014305_SNP [dm6]	T	A	2.309e^-5	0.887	INTERGENIC	TF binding site mE1_TFBS_HSA
X	4438547	X_4438547_SNP [dm3] X_4544514_SNP [dm6]	A	G	2.503e^-5	0.887	DOWNSTREAM Usf & 1 other INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	14545406	2L_14545406_SNP [dm3] 2L_14545406_SNP [dm6]	A	T	2.525e^-5	0.887	INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	10692957	3R_10692957_SNP [dm3] 3R_14867235_SNP [dm6]	G	C	2.540e^-5	0.887	INTRON btsz
2L	14545552	2L_14545552_SNP [dm3] 2L_14545552_SNP [dm6]	G	A	2.564e^-5	0.887	INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	3885408	2L_3885408_SNP [dm3] 2L_3885408_SNP [dm6]	A	C	2.639e^-5	0.887	INTRON capu	TF binding site mE1_TFBS_bab1
3L	10295963	3L_10295963_SNP [dm3] 3L_10302863_SNP [dm6]	C	T	2.692e^-5	0.887	INTERGENIC
2L	15100021	2L_15100021_SNP [dm3] 2L_15100021_SNP [dm6]	A	T	2.792e^-5	0.887	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	15560854	2L_15560854_SNP [dm3] 2L_15560854_SNP [dm6]	A	T	2.815e^-5	0.887	INTRON kek3
3R	2887489	3R_2887489_SNP [dm3] 3R_7061767_SNP [dm6]	G	T	2.836e^-5	0.887	NON_SYNONYMOUS_CODING djl UPSTREAM CG1988
2L	14422258	2L_14422258_SNP [dm3] 2L_14422258_SNP [dm6]	G	A	2.925e^-5	0.887	INTERGENIC	TF binding site mE1_TFBS_cad
2R	12872555	2R_12872555_SNP [dm3] 2R_16985050_SNP [dm6]	A	G	2.933e^-5	0.887	INTRON Cbp53E
2R	9974020	2R_9974020_DEL [dm3] 2R_14086515_DEL [dm6]	TA	C	3.016e^-5	0.887	INTRON Prosap
2L	4916296	2L_4916296_SNP [dm3] 2L_4916296_SNP [dm6]	C	A	3.067e^-5	0.887	UPSTREAM hoe1 INTRON hoe1
3L	920537	3L_920537_SNP [dm3] 3L_920537_SNP [dm6]	T	G	3.117e^-5	0.887	INTRON Glut1	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	5028335	2R_5028335_SNP [dm3] 2R_9140830_SNP [dm6]	G	A	3.307e^-5	0.887	UTR_5_PRIME CG44286 UPSTREAM CG44286 INTRON CG8788 & 1 other
2R	11808585	2R_11808585_SNP [dm3] 2R_15921080_SNP [dm6]	T	C	3.323e^-5	0.887	INTRON sli	TF binding site BDTNP1_TFBS_dl
2L	14674740	2L_14674740_SNP [dm3] 2L_14674740_SNP [dm6]	A	T	3.331e^-5	0.887	INTRON osp
X	10798126	X_10798126_SNP [dm3] X_10904093_SNP [dm6]	G	A	3.412e^-5	0.887	INTERGENIC
3L	13895902	3L_13895902_SNP [dm3] 3L_13902802_SNP [dm6]	A	T	3.527e^-5	0.887	UTR_5_PRIME dysc
3L	10298570	3L_10298570_SNP [dm3] 3L_10305470_SNP [dm6]	A	G	3.592e^-5	0.887	INTERGENIC
3R	22294891	3R_22294891_SNP [dm3] 3R_26469169_SNP [dm6]	T	A	3.623e^-5	0.887	DOWNSTREAM plum INTRON CG5455
2R	4383361	2R_4383361_SNP [dm3] 2R_8495856_SNP [dm6]	A	G	3.656e^-5	0.887	INTRON mtt
3L	12382313	3L_12382313_SNP [dm3] 3L_12389213_SNP [dm6]	C	A	3.748e^-5	0.887	INTRON Ncc69
3R	12710778	3R_12710778_SNP [dm3] 3R_16885056_SNP [dm6]	C	A	3.955e^-5	0.887	INTRON iab-8
2R	11181973	2R_11181973_SNP [dm3] 2R_15294468_SNP [dm6]	T	C	4.017e^-5	0.887	DOWNSTREAM CR44241 INTRON Trpm
3R	25115832	3R_25115832_SNP [dm3] 3R_29290110_SNP [dm6]	G	A	4.095e^-5	0.887	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
2R	17873923	2R_17873923_SNP [dm3] 2R_21986418_SNP [dm6]	C	G	4.199e^-5	0.887	DOWNSTREAM CG34370 INTRON CG30401	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2R	7512818	2R_7512818_SNP [dm3] 2R_11625313_SNP [dm6]	A	G	4.237e^-5	0.887	INTRON CG9005	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	10404253	2R_10404253_SNP [dm3] 2R_14516748_SNP [dm6]	C	A	4.244e^-5	0.887	INTERGENIC
2L	2919910	2L_2919910_SNP [dm3] 2L_2919910_SNP [dm6]	C	T	4.314e^-5	0.887	INTRON lilli
3L	18140632	3L_18140632_SNP [dm3] 3L_18147532_SNP [dm6]	T	C	4.350e^-5	0.887	INTERGENIC
X	2769361	X_2769361_DEL [dm3] X_2875328_DEL [dm6]	AGAAAACATC	A	4.466e^-5	0.887	DOWNSTREAM CG14417 INTRON kirre
3R	17066906	3R_17066906_SNP [dm3] 3R_21241184_SNP [dm6]	G	C	4.470e^-5	0.887	INTERGENIC	regulatory region REDfly_CRMs
3R	10693007	3R_10693007_INS [dm3] 3R_14867285_INS [dm6]	A	ATTCA	4.471e^-5	0.887	INTRON btsz
3L	12718139	3L_12718139_SNP [dm3] 3L_12725039_SNP [dm6]	G	A	4.508e^-5	0.887	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	13055863	3R_13055863_SNP [dm3] 3R_17230141_SNP [dm6]	C	G	4.520e^-5	0.887	INTERGENIC
X	21948706	X_21948706_SNP [dm3] X_22546870_SNP [dm6]	G	A	4.558e^-5	0.887	UPSTREAM CG17601 INTERGENIC
2R	5025853	2R_5025853_SNP [dm3] 2R_9138348_SNP [dm6]	A	G	4.632e^-5	0.887	UPSTREAM alc & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
3R	12131824	3R_12131824_SNP [dm3] 3R_16306102_SNP [dm6]	C	T	4.647e^-5	0.887	START_GAINED Zip89B UTR_5_PRIME Zip89B	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	16782062	2L_16782062_SNP [dm3] 2L_16782062_SNP [dm6]	G	A	4.780e^-5	0.887	INTRON Mhc	TF binding site mE1_TFBS_chinmo
3L	10295796	3L_10295796_SNP [dm3] 3L_10302696_SNP [dm6]	A	T	4.795e^-5	0.887	INTERGENIC
3R	10692981	3R_10692981_SNP [dm3] 3R_14867259_SNP [dm6]	C	T	4.857e^-5	0.887	INTRON btsz
2R	16353598	2R_16353598_SNP [dm3] 2R_20466093_SNP [dm6]	C	A	4.875e^-5	0.887	INTRON CG12484
3R	7114154	3R_7114154_SNP [dm3] 3R_11288432_SNP [dm6]	T	G	4.970e^-5	0.887	INTRON CR31386
2R	16019746	2R_16019746_SNP [dm3] 2R_20132241_SNP [dm6]	A	G	4.975e^-5	0.887	INTERGENIC	TF binding site mE1_TFBS_inv
2L	1697095	2L_1697095_SNP [dm3] 2L_1697095_SNP [dm6]	A	G	5.030e^-5	0.887	UTR_3_PRIME chinmo	TF binding site mE1_TFBS_hkb mE1_TFBS_HSA
3R	7859559	3R_7859559_SNP [dm3] 3R_12033837_SNP [dm6]	T	C	5.199e^-5	0.887	SYNONYMOUS_CODING ssp5	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	15728466	2L_15728466_SNP [dm3] 2L_15728466_SNP [dm6]	G	A	5.229e^-5	0.887	UTR_3_PRIME CycE	TF binding site BDTNP1_TFBS_dl
3L	19686942	3L_19686942_SNP [dm3] 3L_19693842_SNP [dm6]	T	A	5.246e^-5	0.887	INTRON verm
3L	5857071	3L_5857071_SNP [dm3] 3L_5863971_SNP [dm6]	T	A	5.256e^-5	0.887	INTERGENIC
X	4438542	X_4438542_SNP [dm3] X_4544509_SNP [dm6]	A	T	5.264e^-5	0.887	DOWNSTREAM Usf & 1 other INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3R	11945356	3R_11945356_SNP [dm3] 3R_16119634_SNP [dm6]	A	T	5.316e^-5	0.887	INTRON Sb
3R	5446009	3R_5446009_SNP [dm3] 3R_9620287_SNP [dm6]	G	A	5.345e^-5	0.887	INTRON CG8312
3L	11183481	3L_11183481_SNP [dm3] 3L_11190381_SNP [dm6]	G	T	5.407e^-5	0.887	INTRON GlcAT-P
X	5030697	X_5030697_SNP [dm3] X_5136664_SNP [dm6]	G	A	5.457e^-5	0.887	INTRON rg & 1 other
3R	22294878	3R_22294878_SNP [dm3] 3R_26469156_SNP [dm6]	C	G	5.474e^-5	0.887	DOWNSTREAM plum INTRON CG5455
2R	8854994	2R_8854994_SNP [dm3] 2R_12967489_SNP [dm6]	G	C	5.479e^-5	0.887	NON_SYNONYMOUS_CODING Psc	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	2266061	2L_2266061_SNP [dm3] 2L_2266061_SNP [dm6]	G	A	5.490e^-5	0.887	UPSTREAM CG34049 INTERGENIC
2R	10404286	2R_10404286_SNP [dm3] 2R_14516781_SNP [dm6]	G	A	5.577e^-5	0.887	INTERGENIC
2L	14545413	2L_14545413_SNP [dm3] 2L_14545413_SNP [dm6]	A	G	5.659e^-5	0.887	INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	12132497	3R_12132497_SNP [dm3] 3R_16306775_SNP [dm6]	C	A	5.749e^-5	0.887	NON_SYNONYMOUS_CODING Zip89B	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	18702415	2R_18702415_SNP [dm3] 2R_22814910_SNP [dm6]	A	G	5.755e^-5	0.887	INTRON stl	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	3827109	2R_3827109_SNP [dm3] 2R_7939604_SNP [dm6]	A	G	5.771e^-5	0.887	UTR_5_PRIME CG30380 UPSTREAM CG30379 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Ubx
X	4438551	X_4438551_SNP [dm3] X_4544518_SNP [dm6]	T	C	5.796e^-5	0.887	DOWNSTREAM Usf & 1 other INTRON CR32773	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_11_9_Me_C23 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results