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=2.550e^-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
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

2151 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	8524906	2L_8524906_SNP [dm3] 2L_8524906_SNP [dm6]	C	A	3.838e^-7	0.171	UTR_3_PRIME Acer DOWNSTREAM lmgA & 2 others
3L	9583287	3L_9583287_SNP [dm3] 3L_9590187_SNP [dm6]	A	G	6.405e^-7	0.171	INTRON CG42673
2L	8524323	2L_8524323_SNP [dm3] 2L_8524323_SNP [dm6]	T	C	7.141e^-7	0.171	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8521314	2L_8521314_SNP [dm3] 2L_8521314_SNP [dm6]	G	C	7.542e^-7	0.171	NON_SYNONYMOUS_CODING CG13091 UPSTREAM Acer	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_sens mE1_TFBS_Ubx
2L	8521447	2L_8521447_SNP [dm3] 2L_8521447_SNP [dm6]	C	T	7.654e^-7	0.171	UPSTREAM Acer INTRON CG13091	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_h mE1_TFBS_sens mE1_TFBS_Ubx
2L	8521633	2L_8521633_SNP [dm3] 2L_8521633_SNP [dm6]	G	A	1.140e^-6	0.171	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	8528865	2L_8528865_SNP [dm3] 2L_8528865_SNP [dm6]	C	T	1.188e^-6	0.171	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8528881	2L_8528881_SNP [dm3] 2L_8528881_SNP [dm6]	A	G	1.188e^-6	0.171	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8521332	2L_8521332_SNP [dm3] 2L_8521332_SNP [dm6]	A	C	1.216e^-6	0.171	SYNONYMOUS_CODING CG13091 UPSTREAM Acer	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_h mE1_TFBS_sens mE1_TFBS_Ubx
2L	3589047	2L_3589047_SNP [dm3] 2L_3589047_SNP [dm6]	A	T	1.311e^-6	0.171	EXON CR43823	TF binding site BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 mE1_TFBS_HSA mE1_TFBS_sens
3R	26103195	3R_26103195_SNP [dm3] 3R_30277473_SNP [dm6]	C	T	1.390e^-6	0.171	UPSTREAM hdc INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	8523762	2L_8523762_SNP [dm3] 2L_8523762_SNP [dm6]	G	T	1.393e^-6	0.171	SYNONYMOUS_CODING Acer	TF binding site mE1_TFBS_cad
3L	3384861	3L_3384861_DEL [dm3] 3L_3384861_DEL [dm6]	ATTTTTG	A	1.480e^-6	0.171	INTERGENIC
2L	8529738	2L_8529738_SNP [dm3] 2L_8529738_SNP [dm6]	A	C	1.514e^-6	0.171	INTRON CG17834	TF binding site BDTNP1_TFBS_prd mE1_TFBS_HSA
3L	3384878	3L_3384878_DEL [dm3] 3L_3384878_DEL [dm6]	GATGGTACCCCTTA...	G	1.577e^-6	0.171	INTERGENIC
3L	3384873	3L_3384873_SNP [dm3] 3L_3384873_SNP [dm6]	A	G	1.634e^-6	0.171	INTERGENIC
3L	3384870	3L_3384870_SNP [dm3] 3L_3384870_SNP [dm6]	G	A	1.781e^-6	0.171	INTERGENIC
3L	8633004	3L_8633004_SNP [dm3] 3L_8639904_SNP [dm6]	G	A	1.782e^-6	0.171	UPSTREAM Cpr66D INTERGENIC
3L	3384895	3L_3384895_SNP [dm3] 3L_3384895_SNP [dm6]	C	A	1.804e^-6	0.171	INTERGENIC
2L	16646042	2L_16646042_SNP [dm3] 2L_16646042_SNP [dm6]	A	T	1.820e^-6	0.171	INTRON CG42389
3R	22433750	3R_22433750_SNP [dm3] 3R_26608028_SNP [dm6]	T	C	2.130e^-6	0.186	EXON CR44951
3R	10349281	3R_10349281_SNP [dm3] 3R_14523559_SNP [dm6]	T	C	2.181e^-6	0.186	SYNONYMOUS_CODING Pde6 DOWNSTREAM Cyp313a1
2L	8524326	2L_8524326_SNP [dm3] 2L_8524326_SNP [dm6]	C	T	2.279e^-6	0.186	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8528846	2L_8528846_SNP [dm3] 2L_8528846_SNP [dm6]	T	A	2.431e^-6	0.19	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	8633024	3L_8633024_SNP [dm3] 3L_8639924_SNP [dm6]	A	G	2.583e^-6	0.191	UPSTREAM Cpr66D INTERGENIC
2L	8528886	2L_8528886_SNP [dm3] 2L_8528886_SNP [dm6]	T	C	2.650e^-6	0.191	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8529262	2L_8529262_SNP [dm3] 2L_8529262_SNP [dm6]	T	C	2.886e^-6	0.2	UTR_5_PRIME CG17834 UPSTREAM lmgA & 1 other	TF binding site BDTNP1_TFBS_dl
3R	20865586	3R_20865586_INS [dm3] 3R_25039864_INS [dm6]	A	ATA	3.222e^-6	0.202	UPSTREAM CG6422 DOWNSTREAM 5PtaseI INTRON bai	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
2L	8528842	2L_8528842_SNP [dm3] 2L_8528842_SNP [dm6]	T	G	3.223e^-6	0.202	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	8520050	2L_8520050_SNP [dm3] 2L_8520050_SNP [dm6]	T	C	3.571e^-6	0.202	DOWNSTREAM CG13090 INTRON CG13091	TF binding site mE1_TFBS_chinmo
2L	8529353	2L_8529353_DEL [dm3] 2L_8529353_DEL [dm6]	ATAAAAA	A	3.574e^-6	0.202	UTR_5_PRIME CG17834 UPSTREAM lmgA & 1 other	TF binding site BDTNP1_TFBS_prd
3L	3384899	3L_3384899_SNP [dm3] 3L_3384899_SNP [dm6]	T	A	4.271e^-6	0.202	INTERGENIC
3L	3384900	3L_3384900_SNP [dm3] 3L_3384900_SNP [dm6]	A	G	4.271e^-6	0.202	INTERGENIC
3L	3384978	3L_3384978_SNP [dm3] 3L_3384978_SNP [dm6]	A	T	4.297e^-6	0.202	INTERGENIC
2L	8520294	2L_8520294_SNP [dm3] 2L_8520294_SNP [dm6]	G	A	4.348e^-6	0.202	SYNONYMOUS_CODING CG13091	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
3L	3384840	3L_3384840_SNP [dm3] 3L_3384840_SNP [dm6]	T	G	4.380e^-6	0.202	INTERGENIC
2L	7775153	2L_7775153_DEL [dm3] 2L_7775153_DEL [dm6]	AAA	A	4.393e^-6	0.202	DOWNSTREAM CG7179 & 1 other INTERGENIC
3L	3384965	3L_3384965_SNP [dm3] 3L_3384965_SNP [dm6]	G	A	4.445e^-6	0.202	INTERGENIC
3L	3384999	3L_3384999_SNP [dm3] 3L_3384999_SNP [dm6]	C	T	4.480e^-6	0.202	INTERGENIC
2L	8527696	2L_8527696_SNP [dm3] 2L_8527696_SNP [dm6]	C	T	4.546e^-6	0.202	SYNONYMOUS_CODING lmgB UTR_3_PRIME lmgA DOWNSTREAM lmgA	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	3384985	3L_3384985_SNP [dm3] 3L_3384985_SNP [dm6]	G	C	4.605e^-6	0.202	INTERGENIC
X	4747832	X_4747832_SNP [dm3] X_4853799_SNP [dm6]	C	T	4.630e^-6	0.202	INTRON CG42594
3L	3384839	3L_3384839_SNP [dm3] 3L_3384839_SNP [dm6]	C	A	4.684e^-6	0.202	INTERGENIC
3L	3384994	3L_3384994_SNP [dm3] 3L_3384994_SNP [dm6]	T	G	4.745e^-6	0.202	INTERGENIC
3L	3384963	3L_3384963_SNP [dm3] 3L_3384963_SNP [dm6]	G	T	4.916e^-6	0.205	INTERGENIC
2L	8528825	2L_8528825_SNP [dm3] 2L_8528825_SNP [dm6]	C	T	5.118e^-6	0.208	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
2L	5792276	2L_5792276_SNP [dm3] 2L_5792276_SNP [dm6]	G	A	5.261e^-6	0.208	INTRON CG9171
2L	8527621	2L_8527621_SNP [dm3] 2L_8527621_SNP [dm6]	T	C	5.393e^-6	0.208	SYNONYMOUS_CODING lmgB UTR_3_PRIME lmgA DOWNSTREAM lmgA	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	8633026	3L_8633026_SNP [dm3] 3L_8639926_SNP [dm6]	G	A	5.430e^-6	0.208	UPSTREAM Cpr66D INTERGENIC
2L	8524455	2L_8524455_SNP [dm3] 2L_8524455_SNP [dm6]	T	C	5.541e^-6	0.208	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8528818	2L_8528818_SNP [dm3] 2L_8528818_SNP [dm6]	A	C	5.884e^-6	0.216	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	3384976	3L_3384976_INS [dm3] 3L_3384976_INS [dm6]	A	AC	7.034e^-6	0.254	INTERGENIC
3R	20865557	3R_20865557_SNP [dm3] 3R_25039835_SNP [dm6]	T	C	7.434e^-6	0.263	UPSTREAM CG6422 DOWNSTREAM 5PtaseI INTRON bai	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
3L	3383083	3L_3383083_SNP [dm3] 3L_3383083_SNP [dm6]	G	A	8.400e^-6	0.281	INTERGENIC
2L	8520129	2L_8520129_SNP [dm3] 2L_8520129_SNP [dm6]	C	G	8.509e^-6	0.281	SYNONYMOUS_CODING CG13091 DOWNSTREAM CG13090	TF binding site mE1_TFBS_chinmo
2L	8523852	2L_8523852_SNP [dm3] 2L_8523852_SNP [dm6]	C	G	8.639e^-6	0.281	NON_SYNONYMOUS_CODING Acer	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8510361	2L_8510361_SNP [dm3] 2L_8510361_SNP [dm6]	C	A	8.656e^-6	0.281	INTRON CG13096	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
X	4443358	X_4443358_SNP [dm3] X_4549325_SNP [dm6]	T	C	8.700e^-6	0.281	SYNONYMOUS_CODING CG15912 UPSTREAM Usf DOWNSTREAM CG11436 INTRON CR32773	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
3L	3384612	3L_3384612_SNP [dm3] 3L_3384612_SNP [dm6]	C	A	9.780e^-6	0.307	INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	8529328	2L_8529328_SNP [dm3] 2L_8529328_SNP [dm6]	G	A	9.885e^-6	0.307	UTR_5_PRIME CG17834 UPSTREAM lmgA & 1 other
2L	8524431	2L_8524431_SNP [dm3] 2L_8524431_SNP [dm6]	A	T	1.055e^-5	0.307	SYNONYMOUS_CODING Acer DOWNSTREAM lmgA & 1 other	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	8525014	2L_8525014_SNP [dm3] 2L_8525014_SNP [dm6]	A	T	1.062e^-5	0.307	UTR_3_PRIME Acer & 2 others DOWNSTREAM lmgA & 2 others
3L	3382670	3L_3382670_SNP [dm3] 3L_3382670_SNP [dm6]	G	C	1.080e^-5	0.307	INTERGENIC
2L	8529270	2L_8529270_SNP [dm3] 2L_8529270_SNP [dm6]	C	A	1.089e^-5	0.307	UTR_5_PRIME CG17834 UPSTREAM lmgA & 1 other	TF binding site BDTNP1_TFBS_dl
2L	8529430	2L_8529430_SNP [dm3] 2L_8529430_SNP [dm6]	T	A	1.125e^-5	0.307	UTR_5_PRIME CG17834 UPSTREAM lmgA & 1 other INTRON CG17834	TF binding site BDTNP1_TFBS_prd
3L	3384633	3L_3384633_SNP [dm3] 3L_3384633_SNP [dm6]	C	T	1.128e^-5	0.307	INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	20810978	3R_20810978_SNP [dm3] 3R_24985256_SNP [dm6]	G	A	1.130e^-5	0.307	UPSTREAM tnc INTRON tnc
2L	4420360	2L_4420360_SNP [dm3] 2L_4420360_SNP [dm6]	T	A	1.139e^-5	0.307	INTRON CG15431
2L	8520157	2L_8520157_SNP [dm3] 2L_8520157_SNP [dm6]	C	A	1.142e^-5	0.307	NON_SYNONYMOUS_CODING CG13091 DOWNSTREAM CG13090	TF binding site mE1_TFBS_chinmo
2L	8520273	2L_8520273_SNP [dm3] 2L_8520273_SNP [dm6]	T	C	1.162e^-5	0.307	SYNONYMOUS_CODING CG13091	TF binding site mE1_TFBS_chinmo mE1_TFBS_sens
2L	15805007	2L_15805007_SNP [dm3] 2L_15805007_SNP [dm6]	C	A	1.174e^-5	0.307	INTERGENIC
2L	18585505	2L_18585505_SNP [dm3] 2L_18585505_SNP [dm6]	T	A	1.192e^-5	0.307	INTRON Pde11
3L	3382665	3L_3382665_SNP [dm3] 3L_3382665_SNP [dm6]	A	G	1.193e^-5	0.307	INTERGENIC
3L	3384722	3L_3384722_SNP [dm3] 3L_3384722_SNP [dm6]	G	T	1.225e^-5	0.307	INTERGENIC
2R	12703280	2R_12703280_SNP [dm3] 2R_16815775_SNP [dm6]	A	C	1.238e^-5	0.307	UPSTREAM CR44380 & 1 other INTERGENIC
3R	7865757	3R_7865757_SNP [dm3] 3R_12040035_SNP [dm6]	G	T	1.256e^-5	0.307	UPSTREAM CG14736 INTERGENIC
X	18445697	X_18445697_SNP [dm3] X_18551664_SNP [dm6]	G	A	1.260e^-5	0.307	INTRON Bx
3R	10811812	3R_10811812_SNP [dm3] 3R_14986090_SNP [dm6]	C	A	1.288e^-5	0.309	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_Trl
2L	11576925	2L_11576925_INS [dm3] 2L_11576925_INS [dm6]	G	GAG	1.303e^-5	0.309	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	8529077	2L_8529077_SNP [dm3] 2L_8529077_SNP [dm6]	G	C	1.338e^-5	0.314	UPSTREAM CG17834 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	20865590	3R_20865590_SNP [dm3] 3R_25039868_SNP [dm6]	G	C	1.448e^-5	0.332	UPSTREAM CG6422 DOWNSTREAM 5PtaseI INTRON bai	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_sens
X	9884642	X_9884642_SNP [dm3] X_9990609_SNP [dm6]	A	G	1.487e^-5	0.332	INTRON CG32694
3R	11086034	3R_11086034_SNP [dm3] 3R_15260312_SNP [dm6]	A	G	1.496e^-5	0.332	SYNONYMOUS_CODING Su_var_3-9 INTRON eIF-2gamma
X	11412964	X_11412964_DEL [dm3] X_11518931_DEL [dm6]	CAA	C	1.506e^-5	0.332	INTRON Drak
2L	8371525	2L_8371525_INS [dm3] 2L_8371525_INS [dm6]	A	ATGGGCCTCAAAAA...	1.585e^-5	0.332	UPSTREAM CR45341 & 1 other INTRON CG17292
3L	3384714	3L_3384714_SNP [dm3] 3L_3384714_SNP [dm6]	G	A	1.593e^-5	0.332	INTERGENIC
2L	8522458	2L_8522458_SNP [dm3] 2L_8522458_SNP [dm6]	T	C	1.644e^-5	0.332	SYNONYMOUS_CODING Acer DOWNSTREAM CG13091	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	8529408	2L_8529408_SNP [dm3] 2L_8529408_SNP [dm6]	G	A	1.646e^-5	0.332	UTR_5_PRIME CG17834 UPSTREAM lmgA & 1 other INTRON CG17834	TF binding site BDTNP1_TFBS_prd
2L	8529062	2L_8529062_SNP [dm3] 2L_8529062_SNP [dm6]	C	T	1.659e^-5	0.332	UPSTREAM lmgB & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
3L	3383210	3L_3383210_SNP [dm3] 3L_3383210_SNP [dm6]	T	G	1.660e^-5	0.332	INTERGENIC
3L	3384043	3L_3384043_SNP [dm3] 3L_3384043_SNP [dm6]	C	T	1.662e^-5	0.332	INTERGENIC	TF binding site BDTNP1_TFBS_da
2R	5232407	2R_5232407_SNP [dm3] 2R_9344902_SNP [dm6]	T	A	1.688e^-5	0.332	UPSTREAM Or45a INTRON CG13954 & 1 other
3L	9579123	3L_9579123_SNP [dm3] 3L_9586023_SNP [dm6]	G	A	1.696e^-5	0.332	INTRON CG42673
3L	9579125	3L_9579125_SNP [dm3] 3L_9586025_SNP [dm6]	G	A	1.696e^-5	0.332	INTRON CG42673
2L	8529069	2L_8529069_SNP [dm3] 2L_8529069_SNP [dm6]	T	C	1.707e^-5	0.332	UPSTREAM CG17834 & 2 others INTERGENIC	TF binding site BDTNP1_TFBS_dl
3R	23285239	3R_23285239_SNP [dm3] 3R_27459517_SNP [dm6]	C	T	1.723e^-5	0.332	INTERGENIC
3R	26488840	3R_26488840_SNP [dm3] 3R_30663118_SNP [dm6]	G	A	1.726e^-5	0.332	INTERGENIC
2R	4530115	2R_4530115_SNP [dm3] 2R_8642610_SNP [dm6]	C	A	1.733e^-5	0.332	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad
2L	14861836	2L_14861836_SNP [dm3] 2L_14861836_SNP [dm6]	G	A	1.801e^-5	0.334	INTERGENIC
2L	16646040	2L_16646040_SNP [dm3] 2L_16646040_SNP [dm6]	G	T	1.815e^-5	0.334	INTRON CG42389

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Missing results

By genomic position
Variant impact
Gene name

Cuticul_3_Me_C23 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results