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=1.631e^-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
No significant result.

Kruskal-Wallis test

Covariate	χ²	p-value	Significance
In_2R_NS	4.9335	0.0849

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1873 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
2R	8089676	2R_8089676_SNP [dm3] 2R_12202171_SNP [dm6]	A	T	7.215e^-9	0.007	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	8078685	2R_8078685_SNP [dm3] 2R_12191180_SNP [dm6]	G	A	7.217e^-9	0.007	NON_SYNONYMOUS_CODING Cyp6t3 UPSTREAM Cyp6g2
2R	8072884	2R_8072884_INS [dm3] 2R_12185379_INS [dm6]	G	GAGTTACGGGTGCCTCCGTT...	1.146e^-8	0.007	UTR_3_PRIME CG13175 & 1 other UPSTREAM Cyp6g1	regulatory region REDfly_CRMs
2R	8078974	2R_8078974_SNP [dm3] 2R_12191469_SNP [dm6]	G	C	9.110e^-8	0.033	NON_SYNONYMOUS_CODING Cyp6t3 DOWNSTREAM CG8858
2R	8078684	2R_8078684_SNP [dm3] 2R_12191179_SNP [dm6]	A	G	9.558e^-8	0.033	NON_SYNONYMOUS_CODING Cyp6t3 UPSTREAM Cyp6g2
2R	8098232	2R_8098232_SNP [dm3] 2R_12210727_SNP [dm6]	G	A	1.049e^-7	0.033	SYNONYMOUS_CODING Sr-CII	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	8091687	2R_8091687_SNP [dm3] 2R_12204182_SNP [dm6]	A	G	4.576e^-7	0.123	INTERGENIC
2R	8091181	2R_8091181_SNP [dm3] 2R_12203676_SNP [dm6]	A	C	1.058e^-6	0.248	INTERGENIC
2R	8090564	2R_8090564_SNP [dm3] 2R_12203059_SNP [dm6]	G	A	1.537e^-6	0.32	INTERGENIC
2R	8100594	2R_8100594_SNP [dm3] 2R_12213089_SNP [dm6]	G	A	2.016e^-6	0.378	UPSTREAM Sr-CII & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_da
3R	18990840	3R_18990840_SNP [dm3] 3R_23165118_SNP [dm6]	A	G	2.429e^-6	0.381	INTERGENIC
3R	2991929	3R_2991929_SNP [dm3] 3R_7166207_SNP [dm6]	C	T	2.622e^-6	0.381	INTRON sas
2R	8078861	2R_8078861_SNP [dm3] 2R_12191356_SNP [dm6]	T	C	2.640e^-6	0.381	SYNONYMOUS_CODING Cyp6t3 UPSTREAM Cyp6g2
3R	9124849	3R_9124849_SNP [dm3] 3R_13299127_SNP [dm6]	C	A	3.200e^-6	0.429	SYNONYMOUS_CODING CG8774 UTR_5_PRIME CG8774 DOWNSTREAM CG8773	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA mE1_TFBS_sens
2R	8090560	2R_8090560_SNP [dm3] 2R_12203055_SNP [dm6]	A	T	3.638e^-6	0.432	INTERGENIC
2R	8091158	2R_8091158_SNP [dm3] 2R_12203653_SNP [dm6]	G	C	3.684e^-6	0.432	INTERGENIC
2R	17326783	2R_17326783_SNP [dm3] 2R_21439278_SNP [dm6]	C	A	4.279e^-6	0.447	INTRON Sdc
2R	10073791	2R_10073791_SNP [dm3] 2R_14186286_SNP [dm6]	G	T	4.915e^-6	0.447	SYNONYMOUS_CODING CG30069	TF binding site mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	17623680	2R_17623680_SNP [dm3] 2R_21736175_SNP [dm6]	C	G	5.090e^-6	0.447	INTERGENIC
2R	8101879	2R_8101879_SNP [dm3] 2R_12214374_SNP [dm6]	G	A	5.133e^-6	0.447	UTR_3_PRIME CG13171
2R	8092269	2R_8092269_SNP [dm3] 2R_12204764_SNP [dm6]	T	A	5.152e^-6	0.447	INTERGENIC
2R	8070658	2R_8070658_SNP [dm3] 2R_12183153_SNP [dm6]	T	G	5.985e^-6	0.447	NON_SYNONYMOUS_CODING CG13175 UTR_5_PRIME CG33964 DOWNSTREAM wash & 1 other	TF binding site mE1_TFBS_sens
X	15273585	X_15273585_SNP [dm3] X_15379552_SNP [dm6]	G	T	6.075e^-6	0.447	UPSTREAM acj6 DOWNSTREAM CG9164 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
2R	8101919	2R_8101919_SNP [dm3] 2R_12214414_SNP [dm6]	T	C	6.249e^-6	0.447	DOWNSTREAM CG13171 INTERGENIC
2R	8101905	2R_8101905_SNP [dm3] 2R_12214400_SNP [dm6]	T	G	6.257e^-6	0.447	DOWNSTREAM CG13171 INTERGENIC
2R	15116706	2R_15116706_SNP [dm3] 2R_19229201_SNP [dm6]	G	A	6.440e^-6	0.447	DOWNSTREAM CG7137 INTRON cora	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2R	8092306	2R_8092306_SNP [dm3] 2R_12204801_SNP [dm6]	C	T	6.769e^-6	0.447	INTERGENIC
2R	8077982	2R_8077982_SNP [dm3] 2R_12190477_SNP [dm6]	A	G	7.042e^-6	0.447	UPSTREAM Cyp6t3 & 1 other INTERGENIC	TF binding site mE1_TFBS_cad
2R	15116732	2R_15116732_SNP [dm3] 2R_19229227_SNP [dm6]	G	A	7.472e^-6	0.447	DOWNSTREAM CG7137 INTRON cora	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	14154208	X_14154208_SNP [dm3] X_14260175_SNP [dm6]	C	A	8.300e^-6	0.447	INTERGENIC
3R	26575911	3R_26575911_DEL [dm3] 3R_30750189_DEL [dm6]	TCCTGTTT	T	8.404e^-6	0.447	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	14154195	X_14154195_SNP [dm3] X_14260162_SNP [dm6]	C	T	8.547e^-6	0.447	INTERGENIC
3L	12357305	3L_12357305_DEL [dm3] 3L_12364205_DEL [dm6]	GATAACAGTT	G	8.687e^-6	0.447	INTERGENIC
3L	12929607	3L_12929607_SNP [dm3] 3L_12936507_SNP [dm6]	C	G	8.701e^-6	0.447	INTERGENIC
X	14154166	X_14154166_SNP [dm3] X_14260133_SNP [dm6]	A	G	8.754e^-6	0.447	INTERGENIC
2R	8095372	2R_8095372_INS [dm3] 2R_12207867_INS [dm6]	T	TT	8.770e^-6	0.447	DOWNSTREAM CR45276 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad
2R	8079280	2R_8079280_SNP [dm3] 2R_12191775_SNP [dm6]	G	A	8.827e^-6	0.447	SYNONYMOUS_CODING Cyp6t3 DOWNSTREAM CG8858
X	14154213	X_14154213_SNP [dm3] X_14260180_SNP [dm6]	A	T	1.037e^-5	0.484	INTERGENIC
X	16674396	X_16674396_SNP [dm3] X_16780363_SNP [dm6]	C	G	1.038e^-5	0.484	INTRON if	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	5518333	3L_5518333_SNP [dm3] 3L_5525233_SNP [dm6]	G	T	1.043e^-5	0.484	INTRON Lkr
2L	3819600	2L_3819600_SNP [dm3] 2L_3819600_SNP [dm6]	A	G	1.105e^-5	0.484	INTERGENIC	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	13132036	2R_13132036_SNP [dm3] 2R_17244531_SNP [dm6]	T	A	1.142e^-5	0.484	INTRON mbl	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2R	8101945	2R_8101945_SNP [dm3] 2R_12214440_SNP [dm6]	G	T	1.164e^-5	0.484	DOWNSTREAM CG13171 INTERGENIC
2R	8085097	2R_8085097_SNP [dm3] 2R_12197592_SNP [dm6]	T	C	1.181e^-5	0.484	SYNONYMOUS_CODING CG8858	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2R	8091180	2R_8091180_SNP [dm3] 2R_12203675_SNP [dm6]	C	A	1.181e^-5	0.484	INTERGENIC
X	14154154	X_14154154_INS [dm3] X_14260121_INS [dm6]	T	TCTGAATCAAAAATGCTTGT...	1.196e^-5	0.484	INTERGENIC
3R	8988335	3R_8988335_SNP [dm3] 3R_13162613_SNP [dm6]	C	G	1.213e^-5	0.484	NON_SYNONYMOUS_CODING timeout
X	14154204	X_14154204_SNP [dm3] X_14260171_SNP [dm6]	T	G	1.307e^-5	0.489	INTERGENIC
2R	8061931	2R_8061931_SNP [dm3] 2R_12174426_SNP [dm6]	C	A	1.322e^-5	0.489	UPSTREAM Cct5 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_GATAe mE1_TFBS_HSA mE1_TFBS_Ubx
3L	5002002	3L_5002002_SNP [dm3] 3L_5002002_SNP [dm6]	G	A	1.327e^-5	0.489	INTRON Con	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	9114055	3R_9114055_SNP [dm3] 3R_13288333_SNP [dm6]	A	T	1.338e^-5	0.489	INTRON CG15887	TF binding site mE1_TFBS_inv
3R	18784574	3R_18784574_SNP [dm3] 3R_22958852_SNP [dm6]	T	G	1.397e^-5	0.489	INTRON klg	TF binding site mE1_TFBS_cad
2R	8077706	2R_8077706_SNP [dm3] 2R_12190201_SNP [dm6]	G	T	1.405e^-5	0.489	SYNONYMOUS_CODING Cyp6g2 UPSTREAM Cyp6t3	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	3791539	X_3791539_SNP [dm3] X_3897506_SNP [dm6]	G	T	1.409e^-5	0.489	INTRON CG42541
X	11844826	X_11844826_SNP [dm3] X_11950793_SNP [dm6]	G	C	1.474e^-5	0.503	INTRON cac
X	14154141	X_14154141_SNP [dm3] X_14260108_SNP [dm6]	T	G	1.661e^-5	0.527	INTERGENIC
2R	6792245	2R_6792245_SNP [dm3] 2R_10904740_SNP [dm6]	C	T	1.664e^-5	0.527	SYNONYMOUS_CODING CG12943 UTR_3_PRIME CG12943
2L	14628324	2L_14628324_SNP [dm3] 2L_14628324_SNP [dm6]	C	A	1.700e^-5	0.527	INTRON osp	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2L	12831910	2L_12831910_SNP [dm3] 2L_12831910_SNP [dm6]	A	T	1.721e^-5	0.527	INTERGENIC
2R	8082493	2R_8082493_SNP [dm3] 2R_12194988_SNP [dm6]	T	A	1.727e^-5	0.527	SYNONYMOUS_CODING CG8858	TF binding site mE1_TFBS_cad
2R	8087114	2R_8087114_SNP [dm3] 2R_12199609_SNP [dm6]	A	G	1.727e^-5	0.527	UPSTREAM CG8858 & 1 other DOWNSTREAM snoRNA:Me28S-C3420a INTRON RpS11	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med
2L	11772626	2L_11772626_SNP [dm3] 2L_11772626_SNP [dm6]	G	C	1.810e^-5	0.527	INTERGENIC
3R	16821132	3R_16821132_SNP [dm3] 3R_20995410_SNP [dm6]	C	G	1.825e^-5	0.527	INTRON Calx	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	6334848	2L_6334848_SNP [dm3] 2L_6334848_SNP [dm6]	A	C	1.831e^-5	0.527	SYNONYMOUS_CODING Pez	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	7153581	2L_7153581_SNP [dm3] 2L_7153581_SNP [dm6]	G	C	1.855e^-5	0.527	INTRON Pvf3
2R	8079175	2R_8079175_SNP [dm3] 2R_12191670_SNP [dm6]	T	G	1.855e^-5	0.527	NON_SYNONYMOUS_CODING Cyp6t3 DOWNSTREAM CG8858
2L	5907343	2L_5907343_SNP [dm3] 2L_5907343_SNP [dm6]	T	C	1.931e^-5	0.534	INTRON bchs	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
2L	12831011	2L_12831011_SNP [dm3] 2L_12831011_SNP [dm6]	A	T	1.937e^-5	0.534	INTERGENIC
3R	22879684	3R_22879684_SNP [dm3] 3R_27053962_SNP [dm6]	T	C	2.057e^-5	0.543	INTRON RYa-R
3L	12357421	3L_12357421_SNP [dm3] 3L_12364321_SNP [dm6]	G	A	2.070e^-5	0.543	INTERGENIC
3L	12357296	3L_12357296_DEL [dm3] 3L_12364196_DEL [dm6]	GGACAC	G	2.073e^-5	0.543	INTERGENIC
2R	8078006	2R_8078006_INS [dm3] 2R_12190501_INS [dm6]	G	GG	2.106e^-5	0.543	UPSTREAM Cyp6t3 & 1 other INTERGENIC
2R	17345220	2R_17345220_SNP [dm3] 2R_21457715_SNP [dm6]	G	A	2.113e^-5	0.543	INTRON Sdc
2R	10083055	2R_10083055_SNP [dm3] 2R_14195550_SNP [dm6]	G	T	2.249e^-5	0.567	SYNONYMOUS_CODING CG30069	TF binding site BDTNP1_TFBS_twi
2R	8090749	2R_8090749_SNP [dm3] 2R_12203244_SNP [dm6]	T	A	2.267e^-5	0.567	INTERGENIC
2L	13941122	2L_13941122_SNP [dm3] 2L_13941122_SNP [dm6]	G	A	2.381e^-5	0.58	INTRON Ance-3
3L	12357247	3L_12357247_SNP [dm3] 3L_12364147_SNP [dm6]	T	A	2.389e^-5	0.58	INTERGENIC
2R	10072916	2R_10072916_SNP [dm3] 2R_14185411_SNP [dm6]	C	G	2.413e^-5	0.58	UTR_5_PRIME CG30069	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	15273574	X_15273574_SNP [dm3] X_15379541_SNP [dm6]	A	G	2.559e^-5	0.607	UPSTREAM acj6 DOWNSTREAM CG9164 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_chinmo mE1_TFBS_HSA
2R	14880380	2R_14880380_SNP [dm3] 2R_18992875_SNP [dm6]	A	G	2.612e^-5	0.612	INTRON tn
2R	8078014	2R_8078014_SNP [dm3] 2R_12190509_SNP [dm6]	T	C	2.695e^-5	0.617	UPSTREAM Cyp6t3 & 1 other INTERGENIC
2R	8085156	2R_8085156_SNP [dm3] 2R_12197651_SNP [dm6]	A	G	2.706e^-5	0.617	SYNONYMOUS_CODING CG8858	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	22983234	3R_22983234_SNP [dm3] 3R_27157512_SNP [dm6]	A	T	2.738e^-5	0.617	UTR_3_PRIME Men-b UPSTREAM grass	TF binding site mE1_TFBS_Trl
2R	8097749	2R_8097749_SNP [dm3] 2R_12210244_SNP [dm6]	T	C	2.821e^-5	0.617	INTRON Sr-CII	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
3L	12357338	3L_12357338_SNP [dm3] 3L_12364238_SNP [dm6]	A	T	2.889e^-5	0.617	INTERGENIC
X	14154236	X_14154236_SNP [dm3] X_14260203_SNP [dm6]	C	T	2.927e^-5	0.617	INTERGENIC
3L	12357323	3L_12357323_SNP [dm3] 3L_12364223_SNP [dm6]	G	T	2.940e^-5	0.617	INTERGENIC
3L	10780345	3L_10780345_SNP [dm3] 3L_10787245_SNP [dm6]	C	T	2.947e^-5	0.617	INTERGENIC
3R	25256581	3R_25256581_SNP [dm3] 3R_29430859_SNP [dm6]	G	A	2.971e^-5	0.617	INTRON Ptp99A
3R	8988291	3R_8988291_INS [dm3] 3R_13162569_INS [dm6]	G	TGGA	2.982e^-5	0.617
2L	9058129	2L_9058129_SNP [dm3] 2L_9058129_SNP [dm6]	T	C	3.007e^-5	0.617	INTRON CG31708
2R	14883274	2R_14883274_SNP [dm3] 2R_18995769_SNP [dm6]	T	G	3.040e^-5	0.617	DOWNSTREAM snoRNA:abba-a INTRON tn
2L	1548815	2L_1548815_SNP [dm3] 2L_1548815_SNP [dm6]	C	T	3.062e^-5	0.617	INTERGENIC
2R	8079569	2R_8079569_SNP [dm3] 2R_12192064_SNP [dm6]	A	T	3.099e^-5	0.618	SYNONYMOUS_CODING Cyp6t3 DOWNSTREAM CG8858
3R	9078765	3R_9078765_SNP [dm3] 3R_13253043_SNP [dm6]	C	T	3.218e^-5	0.632	INTRON Ace
3R	26581271	3R_26581271_SNP [dm3] 3R_30755549_SNP [dm6]	T	A	3.238e^-5	0.632	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2R	14142166	2R_14142166_SNP [dm3] 2R_18254661_SNP [dm6]	C	T	3.271e^-5	0.632	INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	7449682	2L_7449682_SNP [dm3] 2L_7449682_SNP [dm6]	A	T	3.359e^-5	0.643	UTR_5_PRIME santa-maria INTRON santa-maria
2R	7995313	2R_7995313_SNP [dm3] 2R_12107808_SNP [dm6]	G	T	3.397e^-5	0.644	INTRON jeb
3R	9031423	3R_9031423_SNP [dm3] 3R_13205701_SNP [dm6]	G	T	3.443e^-5	0.646	INTERGENIC

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By genomic position
Variant impact
Gene name

LD50_Azinphos_Methyl phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results