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=9.822e^-10)
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

1635 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	7061433	2L_7061433_SNP [dm3] 2L_7061433_SNP [dm6]	C	A	3.335e^-7	0.438	SYNONYMOUS_CODING Mnn1 UPSTREAM CG31907
2R	13906362	2R_13906362_SNP [dm3] 2R_18018857_SNP [dm6]	A	G	4.669e^-7	0.438	INTRON CG5084
2R	13906501	2R_13906501_SNP [dm3] 2R_18018996_SNP [dm6]	A	C	1.288e^-6	0.624	INTRON CG5084
3L	18882728	3L_18882728_SNP [dm3] 3L_18889628_SNP [dm6]	T	G	1.347e^-6	0.624	INTRON CG3961	TF binding site BDTNP1_TFBS_dl
2R	13905904	2R_13905904_SNP [dm3] 2R_18018399_SNP [dm6]	C	T	1.664e^-6	0.624	UPSTREAM CG5084 INTERGENIC
3L	5915266	3L_5915266_SNP [dm3] 3L_5922166_SNP [dm6]	T	A	2.013e^-6	0.629	UTR_5_PRIME CG32407 UPSTREAM CG10483 & 1 other	TF binding site BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
2L	1477042	2L_1477042_SNP [dm3] 2L_1477042_SNP [dm6]	C	T	2.698e^-6	0.722	INTERGENIC	TF binding site mE1_TFBS_sens
2R	7510120	2R_7510120_SNP [dm3] 2R_11622615_SNP [dm6]	A	G	3.213e^-6	0.753	SYNONYMOUS_CODING CG9005	TF binding site mE1_TFBS_cad mE1_TFBS_sens
X	12056885	X_12056885_SNP [dm3] X_12162852_SNP [dm6]	A	T	3.814e^-6	0.754	INTRON Ten-a
3L	10006039	3L_10006039_SNP [dm3] 3L_10012939_SNP [dm6]	T	G	4.235e^-6	0.754	INTRON dpr6	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	8796971	3L_8796971_SNP [dm3] 3L_8803871_SNP [dm6]	A	T	4.427e^-6	0.754	SYNONYMOUS_CODING CG32023 UPSTREAM CG34427 DOWNSTREAM CG34426
2R	13905903	2R_13905903_SNP [dm3] 2R_18018398_SNP [dm6]	T	C	5.083e^-6	0.794	UPSTREAM CG5084 INTERGENIC
2R	13906509	2R_13906509_INS [dm3] 2R_18019004_INS [dm6]	A	AGCTATGCCAGAA...	5.757e^-6	0.83	INTRON CG5084
3L	8778099	3L_8778099_SNP [dm3] 3L_8784999_SNP [dm6]	C	T	7.381e^-6	0.979	SPLICE_SITE_REGION Fhos SYNONYMOUS_CODING Fhos UTR_5_PRIME Fhos	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_inv
2R	18162249	2R_18162249_SNP [dm3] 2R_22274744_SNP [dm6]	T	C	7.981e^-6	0.979	INTRON dve
3L	340943	3L_340943_INS [dm3] 3L_340943_INS [dm6]	C	CCAGCT	8.627e^-6	0.979	UTR_5_PRIME mthl10 INTRON Ptpmeg & 1 other
X	17449540	X_17449540_SNP [dm3] X_17555507_SNP [dm6]	C	T	8.881e^-6	0.979	INTRON CG43658
2R	7687410	2R_7687410_SNP [dm3] 2R_11799905_SNP [dm6]	A	C	1.102e^-5	1	INTRON ths	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad
3L	340811	3L_340811_SNP [dm3] 3L_340811_SNP [dm6]	G	A	1.141e^-5	1	UTR_5_PRIME mthl10 INTRON Ptpmeg & 1 other
3L	1513633	3L_1513633_SNP [dm3] 3L_1513633_SNP [dm6]	T	A	1.144e^-5	1	INTRON Psa & 1 other
X	12084934	X_12084934_SNP [dm3] X_12190901_SNP [dm6]	C	T	1.152e^-5	1	INTRON Ten-a
2R	14185456	2R_14185456_SNP [dm3] 2R_18297951_SNP [dm6]	C	T	1.193e^-5	1	UPSTREAM CG18539 DOWNSTREAM CG18538 INTRON sbb & 1 other
3L	340826	3L_340826_SNP [dm3] 3L_340826_SNP [dm6]	C	T	1.265e^-5	1	UTR_5_PRIME mthl10 INTRON Ptpmeg & 1 other
3L	340824	3L_340824_SNP [dm3] 3L_340824_SNP [dm6]	G	A	1.331e^-5	1	UTR_5_PRIME mthl10 INTRON Ptpmeg & 1 other
2R	7510192	2R_7510192_SNP [dm3] 2R_11622687_SNP [dm6]	G	C	1.396e^-5	1	SYNONYMOUS_CODING CG9005	TF binding site mE1_TFBS_cad mE1_TFBS_sens
2L	9361169	2L_9361169_SNP [dm3] 2L_9361169_SNP [dm6]	G	A	1.422e^-5	1	INTERGENIC
2L	1476915	2L_1476915_SNP [dm3] 2L_1476915_SNP [dm6]	T	G	1.531e^-5	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	10005952	3L_10005952_SNP [dm3] 3L_10012852_SNP [dm6]	T	C	1.618e^-5	1	INTRON dpr6	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2R	11886430	2R_11886430_DEL [dm3] 2R_15998925_DEL [dm6]	ACTAAGACTAAGTATAG...	A	1.668e^-5	1	INTRON ATPCL
3R	18793180	3R_18793180_SNP [dm3] 3R_22967458_SNP [dm6]	T	C	1.808e^-5	1	UTR_3_PRIME Tpl94D	TF binding site mE1_TFBS_cad
2R	13905822	2R_13905822_SNP [dm3] 2R_18018317_SNP [dm6]	G	T	1.825e^-5	1	UPSTREAM CG5084 INTERGENIC
3L	10572035	3L_10572035_SNP [dm3] 3L_10578935_SNP [dm6]	T	C	1.878e^-5	1	INTRON A2bp1	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	18474022	2L_18474022_SNP [dm3] 2L_18474022_SNP [dm6]	G	A	1.897e^-5	1	DOWNSTREAM let-7-C INTRON CG10283
2R	10789346	2R_10789346_SNP [dm3] 2R_14901841_SNP [dm6]	G	A	2.000e^-5	1	UTR_3_PRIME Cyp317a1 & 1 other DOWNSTREAM Cyp317a1
2L	18473805	2L_18473805_SNP [dm3] 2L_18473805_SNP [dm6]	A	T	2.115e^-5	1	DOWNSTREAM let-7-C INTRON CG10283
3L	10005910	3L_10005910_SNP [dm3] 3L_10012810_SNP [dm6]	G	A	2.117e^-5	1	INTRON dpr6	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	7051183	2L_7051183_SNP [dm3] 2L_7051183_SNP [dm6]	A	C	2.208e^-5	1	INTRON milt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	17448837	X_17448837_SNP [dm3] X_17554804_SNP [dm6]	G	C	2.309e^-5	1	INTRON CG43658
2R	14185451	2R_14185451_INS [dm3] 2R_18297946_INS [dm6]	A	CCC	2.450e^-5	1	UPSTREAM CG18539 DOWNSTREAM CG18538 INTRON sbb & 1 other
2L	7050484	2L_7050484_SNP [dm3] 2L_7050484_SNP [dm6]	T	C	2.508e^-5	1	UTR_5_PRIME milt INTRON milt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2R	12489807	2R_12489807_SNP [dm3] 2R_16602302_SNP [dm6]	A	G	2.745e^-5	1	INTRON CG8303
2L	11406488	2L_11406488_SNP [dm3] 2L_11406488_SNP [dm6]	G	T	2.765e^-5	1	INTERGENIC	regulatory region REDfly_CRMs
3L	8798320	3L_8798320_SNP [dm3] 3L_8805220_SNP [dm6]	T	A	2.853e^-5	1	SYNONYMOUS_CODING CG34427 DOWNSTREAM CG13312
3L	10006120	3L_10006120_SNP [dm3] 3L_10013020_SNP [dm6]	T	C	2.900e^-5	1	INTRON dpr6	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	14012277	2L_14012277_SNP [dm3] 2L_14012277_SNP [dm6]	G	A	2.916e^-5	1	UPSTREAM bgm INTERGENIC	TF binding site mE1_TFBS_inv
2R	10268483	2R_10268483_SNP [dm3] 2R_14380978_SNP [dm6]	T	C	2.950e^-5	1	INTRON Dh44-R1
2L	13845361	2L_13845361_SNP [dm3] 2L_13845361_SNP [dm6]	A	G	3.138e^-5	1	UPSTREAM CG8997 INTRON CenG1A	TF binding site mE1_TFBS_cad
2L	18166041	2L_18166041_SNP [dm3] 2L_18166041_SNP [dm6]	T	C	3.315e^-5	1	INTRON CG42750
3R	24040344	3R_24040344_SNP [dm3] 3R_28214622_SNP [dm6]	A	G	3.423e^-5	1	INTRON CG34354	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi
3R	13420800	3R_13420800_SNP [dm3] 3R_17595078_SNP [dm6]	T	C	3.556e^-5	1	UPSTREAM Sgs5 DOWNSTREAM CG7587 INTERGENIC
3L	5065269	3L_5065269_SNP [dm3] 3L_5065269_SNP [dm6]	C	T	3.623e^-5	1	INTRON Con
2L	19907919	2L_19907919_DEL [dm3] 2L_19907919_DEL [dm6]	AA	A	3.733e^-5	1	INTRON sick
2R	20868370	2R_20868370_SNP [dm3] 2R_24980847_SNP [dm6]	A	G	4.058e^-5	1	INTRON emp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_twi mE1_TFBS_cad
3R	11739979	3R_11739979_SNP [dm3] 3R_15914257_SNP [dm6]	T	A	4.081e^-5	1	INTRON CG45105	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad
2R	6287673	2R_6287673_SNP [dm3] 2R_10400168_SNP [dm6]	T	A	4.095e^-5	1	INTRON CG42732
2R	12489759	2R_12489759_SNP [dm3] 2R_16602254_SNP [dm6]	A	T	4.128e^-5	1	INTRON CG8303
3R	13296893	3R_13296893_SNP [dm3] 3R_17471171_SNP [dm6]	C	T	4.279e^-5	1	INTERGENIC
X	20464472	X_20464472_SNP [dm3] X_20593445_SNP [dm6]	A	C	4.281e^-5	1	SYNONYMOUS_CODING RunxA
3L	18884024	3L_18884024_SNP [dm3] 3L_18890924_SNP [dm6]	C	T	4.288e^-5	1	UPSTREAM CG3961 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
3L	18884048	3L_18884048_SNP [dm3] 3L_18890948_SNP [dm6]	A	T	4.288e^-5	1	UPSTREAM CG3961 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
X	17141942	X_17141942_SNP [dm3] X_17247909_SNP [dm6]	C	T	4.454e^-5	1	UPSTREAM CG42854 DOWNSTREAM CG8675 INTRON f
3L	8778738	3L_8778738_SNP [dm3] 3L_8785638_SNP [dm6]	C	T	4.480e^-5	1	INTRON Fhos	TF binding site mE1_TFBS_inv
3L	14026522	3L_14026522_SNP [dm3] 3L_14033422_SNP [dm6]	A	T	4.616e^-5	1	SYNONYMOUS_CODING CG6650	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
X	17142136	X_17142136_SNP [dm3] X_17248103_SNP [dm6]	G	A	4.761e^-5	1	DOWNSTREAM CG8675 INTRON f
X	17142148	X_17142148_SNP [dm3] X_17248115_SNP [dm6]	T	A	4.761e^-5	1	DOWNSTREAM CG8675 INTRON f
2L	1438468	2L_1438468_SNP [dm3] 2L_1438468_SNP [dm6]	T	C	4.796e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Kr
2L	16934284	2L_16934284_SNP [dm3] 2L_16934284_SNP [dm6]	G	A	4.831e^-5	1	INTERGENIC
2L	12233535	2L_12233535_DEL [dm3] 2L_12233535_DEL [dm6]	AAGCGA	A	4.924e^-5	1	INTRON aret
2R	11074387	2R_11074387_INS [dm3] 2R_15186882_INS [dm6]	C	CATGC	4.992e^-5	1	DOWNSTREAM CG43068 INTRON igl
3L	8817299	3L_8817299_SNP [dm3] 3L_8824199_SNP [dm6]	T	C	5.181e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad
2R	18163969	2R_18163969_SNP [dm3] 2R_22276464_SNP [dm6]	T	G	5.190e^-5	1	INTRON dve
3R	16509975	3R_16509975_INS [dm3] 3R_20684253_INS [dm6]	A	ACTTATA	5.257e^-5	1	INTERGENIC
3R	14149213	3R_14149213_INS [dm3] 3R_18323491_INS [dm6]	G	GTCCACTGGGCATGTGTTTT...	5.293e^-5	1	INTRON CG31235
3L	5914886	3L_5914886_SNP [dm3] 3L_5921786_SNP [dm6]	T	A	5.305e^-5	1	UPSTREAM CG32407 & 1 other INTERGENIC
3R	24546547	3R_24546547_SNP [dm3] 3R_28720825_SNP [dm6]	A	G	5.386e^-5	1	INTRON htt	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	18793257	3R_18793257_SNP [dm3] 3R_22967535_SNP [dm6]	C	A	5.412e^-5	1	UTR_3_PRIME Tpl94D	TF binding site mE1_TFBS_cad
X	11812520	X_11812520_SNP [dm3] X_11918487_SNP [dm6]	A	C	5.439e^-5	1	DOWNSTREAM CR43157 EXON CR32661
2L	19915638	2L_19915638_SNP [dm3] 2L_19915638_SNP [dm6]	G	A	5.501e^-5	1	INTRON sick	TF binding site mE1_TFBS_bab1 mE1_TFBS_HSA
3R	13420789	3R_13420789_SNP [dm3] 3R_17595067_SNP [dm6]	T	C	5.726e^-5	1	UPSTREAM Sgs5 DOWNSTREAM CG7587 INTERGENIC
2R	16924278	2R_16924278_SNP [dm3] 2R_21036773_SNP [dm6]	C	T	5.886e^-5	1	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
2R	19901293	2R_19901293_SNP [dm3] 2R_24013770_SNP [dm6]	T	C	5.941e^-5	1	INTRON Unc-89
2L	18473979	2L_18473979_SNP [dm3] 2L_18473979_SNP [dm6]	T	C	5.997e^-5	1	DOWNSTREAM let-7-C INTRON CG10283
2L	6347695	2L_6347695_SNP [dm3] 2L_6347695_SNP [dm6]	C	T	6.005e^-5	1	INTRON CG9497
3L	12926313	3L_12926313_SNP [dm3] 3L_12933213_SNP [dm6]	G	T	6.165e^-5	1	INTERGENIC
X	5333926	X_5333926_SNP [dm3] X_5439893_SNP [dm6]	A	C	6.187e^-5	1	INTERGENIC
2L	7051187	2L_7051187_DEL [dm3] 2L_7051187_DEL [dm6]	ATTTGTGTAGAAGATTCTCA...	A	6.443e^-5	1	INTRON milt	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	18473974	2L_18473974_SNP [dm3] 2L_18473974_SNP [dm6]	T	A	6.474e^-5	1	DOWNSTREAM let-7-C INTRON CG10283
3L	9637111	3L_9637111_SNP [dm3] 3L_9644011_SNP [dm6]	C	A	6.564e^-5	1	UPSTREAM CG33696 INTRON fry
3R	4986665	3R_4986665_SNP [dm3] 3R_9160943_SNP [dm6]	C	T	6.652e^-5	1	INTRON pum	TF binding site mE1_TFBS_Trl
3R	21953730	3R_21953730_SNP [dm3] 3R_26128008_SNP [dm6]	C	T	6.676e^-5	1	UPSTREAM CG31324 DOWNSTREAM CG14556 INTRON CG31324
3L	20908314	3L_20908314_SNP [dm3] 3L_20915214_SNP [dm6]	T	C	6.764e^-5	1	INTERGENIC
2R	14185337	2R_14185337_SNP [dm3] 2R_18297832_SNP [dm6]	T	A	6.767e^-5	1	UTR_5_PRIME CG18539 UPSTREAM CG18539 DOWNSTREAM CG18538 INTRON sbb
3L	12824229	3L_12824229_SNP [dm3] 3L_12831129_SNP [dm6]	A	T	6.874e^-5	1	INTRON CG10960	TF binding site mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_zfh1
2R	18658862	2R_18658862_DEL [dm3] 2R_22771357_DEL [dm6]	GC	T	6.982e^-5	1	INTRON CG42260	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
2R	7622192	2R_7622192_SNP [dm3] 2R_11734687_SNP [dm6]	A	T	7.072e^-5	1	INTERGENIC	TF binding site mE1_TFBS_cad
2L	8092564	2L_8092564_SNP [dm3] 2L_8092564_SNP [dm6]	T	A	7.089e^-5	1	INTRON Bsg	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	17638092	2R_17638092_SNP [dm3] 2R_21750587_SNP [dm6]	T	C	7.131e^-5	1	INTERGENIC
2L	5939808	2L_5939808_SNP [dm3] 2L_5939808_SNP [dm6]	G	A	7.236e^-5	1	UPSTREAM CR45288 DOWNSTREAM dsf INTERGENIC
2R	14230255	2R_14230255_DEL [dm3] 2R_18342750_DEL [dm6]	GCTGCG	G	7.355e^-5	1	INTRON sbb
2L	9112154	2L_9112154_SNP [dm3] 2L_9112154_SNP [dm6]	G	A	7.356e^-5	1	INTRON Or30a

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By genomic position
Variant impact
Gene name

nAcRalpha_34E_CT phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results