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=3.769e^-2)
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

1255 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	10029474	2L_10029474_INS [dm3] 2L_10029474_INS [dm6]	A	AA	9.974e^-4	0.706	DOWNSTREAM CG13127 INTERGENIC
2L	10054971	2L_10054971_SNP [dm3] 2L_10054971_SNP [dm6]	C	A	9.974e^-4	0.706	NON_SYNONYMOUS_CODING Cpr31A DOWNSTREAM CR44875	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	10062402	2L_10062402_SNP [dm3] 2L_10062402_SNP [dm6]	A	G	9.974e^-4	0.706	INTRON Spn31A
2L	10062459	2L_10062459_SNP [dm3] 2L_10062459_SNP [dm6]	T	A	9.974e^-4	0.706	INTRON Spn31A
2L	10062460	2L_10062460_DEL [dm3] 2L_10062460_DEL [dm6]	ATCAT	A	9.974e^-4	0.706	INTRON Spn31A
2L	10062466	2L_10062466_SNP [dm3] 2L_10062466_SNP [dm6]	C	T	9.974e^-4	0.706	INTRON Spn31A
2L	10062550	2L_10062550_SNP [dm3] 2L_10062550_SNP [dm6]	T	G	9.974e^-4	0.706	INTRON Spn31A
2L	10063954	2L_10063954_SNP [dm3] 2L_10063954_SNP [dm6]	A	C	9.974e^-4	0.706	DOWNSTREAM CG44153 & 1 other INTERGENIC
2L	10075423	2L_10075423_SNP [dm3] 2L_10075423_SNP [dm6]	G	A	9.974e^-4	0.706	INTRON CG44153
2L	10080850	2L_10080850_SNP [dm3] 2L_10080850_SNP [dm6]	A	G	9.974e^-4	0.706	INTRON CG44153
2L	10086847	2L_10086847_SNP [dm3] 2L_10086847_SNP [dm6]	A	T	9.974e^-4	0.706	INTRON CG44153
2L	10092944	2L_10092944_SNP [dm3] 2L_10092944_SNP [dm6]	G	A	9.974e^-4	0.706	UPSTREAM CG13133 INTRON CG44153
2L	10119403	2L_10119403_SNP [dm3] 2L_10119403_SNP [dm6]	G	A	9.974e^-4	0.706	INTRON CG44153 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb mE1_TFBS_HSA
2L	10120687	2L_10120687_SNP [dm3] 2L_10120687_SNP [dm6]	C	A	9.974e^-4	0.706	INTRON CG44153 & 1 other
2L	10120716	2L_10120716_SNP [dm3] 2L_10120716_SNP [dm6]	A	G	9.974e^-4	0.706	SPLICE_SITE_REGION CG34109 INTRON CG44153 & 1 other
2L	10121223	2L_10121223_SNP [dm3] 2L_10121223_SNP [dm6]	A	T	9.974e^-4	0.706	DOWNSTREAM CG13135 INTRON CG44153 & 1 other
2L	10127650	2L_10127650_SNP [dm3] 2L_10127650_SNP [dm6]	C	G	9.974e^-4	0.706	INTRON CG44153
2L	10180185	2L_10180185_DEL [dm3] 2L_10180185_DEL [dm6]	TT	T	9.974e^-4	0.706	UTR_5_PRIME CG44153	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	10180900	2L_10180900_DEL [dm3] 2L_10180900_DEL [dm6]	TT	T	9.974e^-4	0.706	UPSTREAM CG44153 INTERGENIC	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	10347263	2L_10347263_SNP [dm3] 2L_10347263_SNP [dm6]	A	G	9.974e^-4	0.706	SYNONYMOUS_CODING CG5022 DOWNSTREAM CG34367	TF binding site mE1_TFBS_cad
2L	10359977	2L_10359977_SNP [dm3] 2L_10359977_SNP [dm6]	T	C	9.974e^-4	0.706	INTRON Cand1	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	10367257	2L_10367257_SNP [dm3] 2L_10367257_SNP [dm6]	G	A	9.974e^-4	0.706	NON_SYNONYMOUS_CODING CG5056 DOWNSTREAM lft & 1 other	TF binding site BDTNP1_TFBS_hb BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens
2L	10369573	2L_10369573_SNP [dm3] 2L_10369573_SNP [dm6]	C	T	9.974e^-4	0.706	INTRON rho-5	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	10424144	2L_10424144_SNP [dm3] 2L_10424144_SNP [dm6]	G	T	9.974e^-4	0.706	INTRON CG5168	TF binding site mE1_TFBS_HSA
2L	10452634	2L_10452634_INS [dm3] 2L_10452634_INS [dm6]	T	TT	9.974e^-4	0.706	UPSTREAM ppk10 DOWNSTREAM CG5322 INTERGENIC
2L	10519370	2L_10519370_SNP [dm3] 2L_10519370_SNP [dm6]	C	T	9.974e^-4	0.706	DOWNSTREAM Lrr47 INTERGENIC
2L	10519382	2L_10519382_SNP [dm3] 2L_10519382_SNP [dm6]	G	C	9.974e^-4	0.706	DOWNSTREAM Lrr47 INTERGENIC
2L	10519441	2L_10519441_SNP [dm3] 2L_10519441_SNP [dm6]	A	T	9.974e^-4	0.706	DOWNSTREAM Lrr47 INTERGENIC
2L	10519468	2L_10519468_SNP [dm3] 2L_10519468_SNP [dm6]	A	T	9.974e^-4	0.706	DOWNSTREAM Lrr47 INTERGENIC
2L	10553084	2L_10553084_SNP [dm3] 2L_10553084_SNP [dm6]	T	G	9.974e^-4	0.706	INTRON Trim9	TF binding site mE1_TFBS_HSA
2L	10570308	2L_10570308_SNP [dm3] 2L_10570308_SNP [dm6]	C	T	9.974e^-4	0.706	INTRON Trim9
2L	10574826	2L_10574826_SNP [dm3] 2L_10574826_SNP [dm6]	T	G	9.974e^-4	0.706	INTRON Trim9
2L	10581244	2L_10581244_SNP [dm3] 2L_10581244_SNP [dm6]	T	C	9.974e^-4	0.706	DOWNSTREAM CG34160 INTRON Trim9 & 1 other
2L	10614434	2L_10614434_SNP [dm3] 2L_10614434_SNP [dm6]	A	T	9.974e^-4	0.706	INTRON Trim9	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	10672633	2L_10672633_SNP [dm3] 2L_10672633_SNP [dm6]	T	G	9.974e^-4	0.706	INTERGENIC
2L	10683725	2L_10683725_SNP [dm3] 2L_10683725_SNP [dm6]	T	C	9.974e^-4	0.706	UTR_3_PRIME CG7299 DOWNSTREAM CG7299
2L	10707204	2L_10707204_SNP [dm3] 2L_10707204_SNP [dm6]	A	C	9.974e^-4	0.706	INTRON Lip2	TF binding site mE1_TFBS_inv
2L	10707288	2L_10707288_SNP [dm3] 2L_10707288_SNP [dm6]	A	G	9.974e^-4	0.706	INTRON Lip2	TF binding site mE1_TFBS_inv
2L	10728519	2L_10728519_SNP [dm3] 2L_10728519_SNP [dm6]	A	C	9.974e^-4	0.706	NON_SYNONYMOUS_CODING CG6431 UPSTREAM CG6443	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	10733491	2L_10733491_SNP [dm3] 2L_10733491_SNP [dm6]	C	T	9.974e^-4	0.706	SYNONYMOUS_CODING Nup107 DOWNSTREAM Dpy-30L1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	10771641	2L_10771641_SNP [dm3] 2L_10771641_SNP [dm6]	C	T	9.974e^-4	0.706	DOWNSTREAM CG31869 & 1 other INTERGENIC
2L	10780515	2L_10780515_SNP [dm3] 2L_10780515_SNP [dm6]	C	T	9.974e^-4	0.706	INTRON CG31869
2L	10782134	2L_10782134_SNP [dm3] 2L_10782134_SNP [dm6]	G	A	9.974e^-4	0.706	INTRON CG31869
2L	10792117	2L_10792117_SNP [dm3] 2L_10792117_SNP [dm6]	A	C	9.974e^-4	0.706	DOWNSTREAM CG31870 INTRON CG31869
2L	10793291	2L_10793291_SNP [dm3] 2L_10793291_SNP [dm6]	A	T	9.974e^-4	0.706	INTRON CG31869
2L	10793297	2L_10793297_SNP [dm3] 2L_10793297_SNP [dm6]	T	A	9.974e^-4	0.706	INTRON CG31869
2L	10795325	2L_10795325_SNP [dm3] 2L_10795325_SNP [dm6]	G	T	9.974e^-4	0.706	INTRON CG31869	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
2L	10795731	2L_10795731_SNP [dm3] 2L_10795731_SNP [dm6]	T	A	9.974e^-4	0.706	INTRON CG31869	TF binding site mE1_TFBS_inv
2L	10801325	2L_10801325_SNP [dm3] 2L_10801325_SNP [dm6]	G	A	9.974e^-4	0.706	UPSTREAM CG31869 DOWNSTREAM CR44581 INTERGENIC
2L	10816756	2L_10816756_SNP [dm3] 2L_10816756_SNP [dm6]	C	T	9.974e^-4	0.706	INTRON Nos
2L	10860001	2L_10860001_SNP [dm3] 2L_10860001_SNP [dm6]	G	A	9.974e^-4	0.706	NON_SYNONYMOUS_CODING Stam	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
2L	10860335	2L_10860335_SNP [dm3] 2L_10860335_SNP [dm6]	C	T	9.974e^-4	0.706	NON_SYNONYMOUS_CODING Stam	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	10897997	2L_10897997_SNP [dm3] 2L_10897997_SNP [dm6]	A	T	9.974e^-4	0.706	INTERGENIC
2L	10898036	2L_10898036_SNP [dm3] 2L_10898036_SNP [dm6]	A	T	9.974e^-4	0.706	INTERGENIC
2L	10898281	2L_10898281_SNP [dm3] 2L_10898281_SNP [dm6]	T	A	9.974e^-4	0.706	INTERGENIC
2L	10905150	2L_10905150_SNP [dm3] 2L_10905150_SNP [dm6]	T	C	9.974e^-4	0.706	INTERGENIC
2L	10912877	2L_10912877_SNP [dm3] 2L_10912877_SNP [dm6]	A	G	9.974e^-4	0.706	INTERGENIC
2L	10929110	2L_10929110_SNP [dm3] 2L_10929110_SNP [dm6]	A	T	9.974e^-4	0.706	INTRON dpr2
2L	10929248	2L_10929248_SNP [dm3] 2L_10929248_SNP [dm6]	C	T	9.974e^-4	0.706	INTRON dpr2
2L	1094105	2L_1094105_SNP [dm3] 2L_1094105_SNP [dm6]	T	A	9.974e^-4	0.706	INTRON CG4629
2L	10972807	2L_10972807_SNP [dm3] 2L_10972807_SNP [dm6]	A	T	9.974e^-4	0.706	SYNONYMOUS_CODING CG16743 DOWNSTREAM YL-1 & 1 other
2L	10994129	2L_10994129_INS [dm3] 2L_10994129_INS [dm6]	A	AA	9.974e^-4	0.706	UTR_3_PRIME CG16833 INTRON CG16833
2L	11017608	2L_11017608_SNP [dm3] 2L_11017608_SNP [dm6]	C	T	9.974e^-4	0.706	NON_SYNONYMOUS_CODING CG14913 INTRON Samuel
2L	11017636	2L_11017636_SNP [dm3] 2L_11017636_SNP [dm6]	C	T	9.974e^-4	0.706	SYNONYMOUS_CODING CG14913 INTRON Samuel
2L	11080932	2L_11080932_SNP [dm3] 2L_11080932_SNP [dm6]	C	T	9.974e^-4	0.706	INTRON AstC
2L	11193864	2L_11193864_SNP [dm3] 2L_11193864_SNP [dm6]	A	T	9.974e^-4	0.706	INTRON Ca-beta	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_prd
2L	11231977	2L_11231977_SNP [dm3] 2L_11231977_SNP [dm6]	T	G	9.974e^-4	0.706	INTRON ab
2L	11234129	2L_11234129_SNP [dm3] 2L_11234129_SNP [dm6]	T	C	9.974e^-4	0.706	UPSTREAM snoRNA:Me18S-G642 & 1 other INTRON ab	TF binding site mE1_TFBS_cnc
2L	11267228	2L_11267228_SNP [dm3] 2L_11267228_SNP [dm6]	A	G	9.974e^-4	0.706	SYNONYMOUS_CODING cmet	TF binding site mE1_TFBS_sens
2L	11349845	2L_11349845_SNP [dm3] 2L_11349845_SNP [dm6]	C	G	9.974e^-4	0.706	INTERGENIC	regulatory region REDfly_CRMs
2L	11423716	2L_11423716_SNP [dm3] 2L_11423716_SNP [dm6]	T	C	9.974e^-4	0.706	INTERGENIC
2L	11426949	2L_11426949_SNP [dm3] 2L_11426949_SNP [dm6]	A	G	9.974e^-4	0.706	INTERGENIC
2L	11537002	2L_11537002_SNP [dm3] 2L_11537002_SNP [dm6]	A	T	9.974e^-4	0.706	DOWNSTREAM CG43438 INTERGENIC
2L	11636734	2L_11636734_SNP [dm3] 2L_11636734_SNP [dm6]	A	C	9.974e^-4	0.706	INTERGENIC
2L	11637728	2L_11637728_SNP [dm3] 2L_11637728_SNP [dm6]	C	A	9.974e^-4	0.706	INTERGENIC
2L	11639483	2L_11639483_SNP [dm3] 2L_11639483_SNP [dm6]	T	C	9.974e^-4	0.706	INTERGENIC
2L	11655692	2L_11655692_SNP [dm3] 2L_11655692_SNP [dm6]	A	C	9.974e^-4	0.706	INTERGENIC
2L	11657723	2L_11657723_SNP [dm3] 2L_11657723_SNP [dm6]	C	T	9.974e^-4	0.706	SYNONYMOUS_CODING CG43167
2L	11858634	2L_11858634_DEL [dm3] 2L_11858634_DEL [dm6]	CC	T	9.974e^-4	0.706	INTRON Pde1c
2L	11858695	2L_11858695_SNP [dm3] 2L_11858695_SNP [dm6]	A	G	9.974e^-4	0.706	INTRON Pde1c
2L	11858730	2L_11858730_SNP [dm3] 2L_11858730_SNP [dm6]	G	C	9.974e^-4	0.706	INTRON Pde1c
2L	11858754	2L_11858754_SNP [dm3] 2L_11858754_SNP [dm6]	T	G	9.974e^-4	0.706	INTRON Pde1c
2L	11858973	2L_11858973_SNP [dm3] 2L_11858973_SNP [dm6]	G	A	9.974e^-4	0.706	SYNONYMOUS_CODING Pde1c INTRON Pde1c
2L	11860258	2L_11860258_SNP [dm3] 2L_11860258_SNP [dm6]	T	C	9.974e^-4	0.706	INTRON Pde1c
2L	11860261	2L_11860261_SNP [dm3] 2L_11860261_SNP [dm6]	A	G	9.974e^-4	0.706	INTRON Pde1c
2L	11863342	2L_11863342_SNP [dm3] 2L_11863342_SNP [dm6]	A	G	9.974e^-4	0.706	INTRON Pde1c
2L	11863473	2L_11863473_SNP [dm3] 2L_11863473_SNP [dm6]	G	A	9.974e^-4	0.706	INTRON Pde1c
2L	11863599	2L_11863599_SNP [dm3] 2L_11863599_SNP [dm6]	T	C	9.974e^-4	0.706	INTRON Pde1c
2L	11863954	2L_11863954_SNP [dm3] 2L_11863954_SNP [dm6]	G	T	9.974e^-4	0.706	INTRON Pde1c
2L	11915746	2L_11915746_SNP [dm3] 2L_11915746_SNP [dm6]	A	G	9.974e^-4	0.706	INTRON Pde1c
2L	11915823	2L_11915823_DEL [dm3] 2L_11915823_DEL [dm6]	ATA	A	9.974e^-4	0.706	INTRON Pde1c
2L	11934072	2L_11934072_SNP [dm3] 2L_11934072_SNP [dm6]	T	C	9.974e^-4	0.706	UPSTREAM Or33a INTERGENIC
2L	11934079	2L_11934079_SNP [dm3] 2L_11934079_SNP [dm6]	G	A	9.974e^-4	0.706	UPSTREAM Or33a INTERGENIC
2L	12024921	2L_12024921_SNP [dm3] 2L_12024921_SNP [dm6]	C	G	9.974e^-4	0.706	INTRON CR44587
2L	12050603	2L_12050603_SNP [dm3] 2L_12050603_SNP [dm6]	G	A	9.974e^-4	0.706	NON_SYNONYMOUS_CODING CG14945	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
2L	12056931	2L_12056931_SNP [dm3] 2L_12056931_SNP [dm6]	A	G	9.974e^-4	0.706	SYNONYMOUS_CODING RpL7-like UTR_5_PRIME CG34164 UPSTREAM JhI-21 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	12057051	2L_12057051_SNP [dm3] 2L_12057051_SNP [dm6]	C	T	9.974e^-4	0.706	SYNONYMOUS_CODING RpL7-like UTR_5_PRIME CG34164 UPSTREAM CG34164	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_sens
2L	12060077	2L_12060077_SNP [dm3] 2L_12060077_SNP [dm6]	A	G	9.974e^-4	0.706	SYNONYMOUS_CODING Rab3-GAP
2L	12060095	2L_12060095_SNP [dm3] 2L_12060095_SNP [dm6]	G	C	9.974e^-4	0.706	NON_SYNONYMOUS_CODING Rab3-GAP
2L	12060105	2L_12060105_SNP [dm3] 2L_12060105_SNP [dm6]	A	G	9.974e^-4	0.706	NON_SYNONYMOUS_CODING Rab3-GAP

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Variant impact
Gene name

HscC phenotype

Phenotype distribution and association to known covariates

QQplot

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GWAS results