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=8.817e^-2)
Null hypothesis is not rejected (p>0.05).
Interpretation: 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

8005 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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Search:

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	10046382	2L_10046382_SNP [dm3] 2L_10046382_SNP [dm6]	A	C	2.737e^-4	0.165	INTERGENIC
2L	10152030	2L_10152030_SNP [dm3] 2L_10152030_SNP [dm6]	C	T	2.737e^-4	0.165	INTRON CG44153 & 1 other
2L	10175708	2L_10175708_SNP [dm3] 2L_10175708_SNP [dm6]	G	A	2.737e^-4	0.165	INTRON CG44153
2L	10175782	2L_10175782_SNP [dm3] 2L_10175782_SNP [dm6]	G	A	2.737e^-4	0.165	INTRON CG44153
2L	10558634	2L_10558634_SNP [dm3] 2L_10558634_SNP [dm6]	A	T	2.737e^-4	0.165	INTRON Trim9	TF binding site mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA
2L	10610046	2L_10610046_SNP [dm3] 2L_10610046_SNP [dm6]	C	G	2.737e^-4	0.165	INTRON Trim9	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	10785769	2L_10785769_SNP [dm3] 2L_10785769_SNP [dm6]	A	G	2.737e^-4	0.165	INTRON CG31869 EXON CR44582
2L	10989253	2L_10989253_SNP [dm3] 2L_10989253_SNP [dm6]	G	A	2.737e^-4	0.165	UPSTREAM CG16833 DOWNSTREAM CG12253 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	11955098	2L_11955098_SNP [dm3] 2L_11955098_SNP [dm6]	G	A	2.737e^-4	0.165	EXON CR43314
2L	11985228	2L_11985228_SNP [dm3] 2L_11985228_SNP [dm6]	G	A	2.737e^-4	0.165	SYNONYMOUS_CODING CG6686 UTR_3_PRIME CG6686 DOWNSTREAM CG16965	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	1316778	2L_1316778_SNP [dm3] 2L_1316778_SNP [dm6]	T	A	2.737e^-4	0.165	INTERGENIC
2L	1332603	2L_1332603_SNP [dm3] 2L_1332603_SNP [dm6]	C	T	2.737e^-4	0.165	INTERGENIC
2L	13432570	2L_13432570_SNP [dm3] 2L_13432570_SNP [dm6]	T	C	2.737e^-4	0.165	INTRON CG42784
2L	13730579	2L_13730579_SNP [dm3] 2L_13730579_SNP [dm6]	A	T	2.737e^-4	0.165	INTERGENIC
2L	13735601	2L_13735601_SNP [dm3] 2L_13735601_SNP [dm6]	A	G	2.737e^-4	0.165	UPSTREAM CG31813 INTERGENIC
2L	1388851	2L_1388851_SNP [dm3] 2L_1388851_SNP [dm6]	A	C	2.737e^-4	0.165	INTRON lea
2L	1436172	2L_1436172_SNP [dm3] 2L_1436172_SNP [dm6]	T	C	2.737e^-4	0.165	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	14850605	2L_14850605_SNP [dm3] 2L_14850605_SNP [dm6]	T	A	2.737e^-4	0.165	INTRON CG15279
2L	14892130	2L_14892130_SNP [dm3] 2L_14892130_SNP [dm6]	T	C	2.737e^-4	0.165	INTERGENIC
2L	14909333	2L_14909333_SNP [dm3] 2L_14909333_SNP [dm6]	A	G	2.737e^-4	0.165	INTRON CG42313
2L	15343588	2L_15343588_SNP [dm3] 2L_15343588_SNP [dm6]	T	A	2.737e^-4	0.165	INTERGENIC
2L	15408884	2L_15408884_SNP [dm3] 2L_15408884_SNP [dm6]	A	T	2.737e^-4	0.165	INTERGENIC
2L	15747445	2L_15747445_SNP [dm3] 2L_15747445_SNP [dm6]	A	G	2.737e^-4	0.165	UPSTREAM CycE & 1 other DOWNSTREAM CR44974 INTRON CycE	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
2L	15936911	2L_15936911_SNP [dm3] 2L_15936911_SNP [dm6]	A	T	2.737e^-4	0.165	INTRON beat-Ib
2L	16227606	2L_16227606_SNP [dm3] 2L_16227606_SNP [dm6]	T	A	2.737e^-4	0.165	INTERGENIC
2L	16381965	2L_16381965_SNP [dm3] 2L_16381965_SNP [dm6]	A	C	2.737e^-4	0.165	INTERGENIC
2L	16398612	2L_16398612_SNP [dm3] 2L_16398612_SNP [dm6]	G	A	2.737e^-4	0.165	INTERGENIC	TF binding site BDTNP1_TFBS_da
2L	16495368	2L_16495368_SNP [dm3] 2L_16495368_SNP [dm6]	C	T	2.737e^-4	0.165	INTRON Tpr2	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2L	16495441	2L_16495441_SNP [dm3] 2L_16495441_SNP [dm6]	T	C	2.737e^-4	0.165	INTRON Tpr2	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2L	16541834	2L_16541834_SNP [dm3] 2L_16541834_SNP [dm6]	C	T	2.737e^-4	0.165	UPSTREAM CG31816 INTERGENIC
2L	16552475	2L_16552475_SNP [dm3] 2L_16552475_SNP [dm6]	C	T	2.737e^-4	0.165	INTRON CG42389
2L	16782048	2L_16782048_SNP [dm3] 2L_16782048_SNP [dm6]	A	T	2.737e^-4	0.165	INTRON Mhc	TF binding site mE1_TFBS_chinmo
2L	16931936	2L_16931936_SNP [dm3] 2L_16931936_SNP [dm6]	A	T	2.737e^-4	0.165	INTERGENIC
2L	16936043	2L_16936043_SNP [dm3] 2L_16936043_SNP [dm6]	A	G	2.737e^-4	0.165	INTERGENIC
2L	18214668	2L_18214668_SNP [dm3] 2L_18214668_SNP [dm6]	A	G	2.737e^-4	0.165	INTRON CG42750
2L	19233521	2L_19233521_SNP [dm3] 2L_19233521_SNP [dm6]	C	T	2.737e^-4	0.165	INTERGENIC
2L	19233543	2L_19233543_SNP [dm3] 2L_19233543_SNP [dm6]	A	T	2.737e^-4	0.165	INTERGENIC
2L	19853839	2L_19853839_SNP [dm3] 2L_19853839_SNP [dm6]	A	C	2.737e^-4	0.165	INTRON sick
2L	19915232	2L_19915232_SNP [dm3] 2L_19915232_SNP [dm6]	T	A	2.737e^-4	0.165	INTRON sick	TF binding site mE1_TFBS_bab1
2L	20594789	2L_20594789_SNP [dm3] 2L_20594789_SNP [dm6]	A	G	2.737e^-4	0.165	INTRON CR44909
2L	20665210	2L_20665210_SNP [dm3] 2L_20665210_SNP [dm6]	T	A	2.737e^-4	0.165	UPSTREAM CG31678 INTRON CG31678 EXON CR45004
2L	20934506	2L_20934506_DEL [dm3] 2L_20934506_DEL [dm6]	TTTAT	T	2.737e^-4	0.165	UPSTREAM CG9270 INTERGENIC
2L	2093907	2L_2093907_INS [dm3] 2L_2093907_INS [dm6]	A	AA	2.737e^-4	0.165	INTRON dpr3	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	2097587	2L_2097587_SNP [dm3] 2L_2097587_SNP [dm6]	T	C	2.737e^-4	0.165	INTRON dpr3
2L	21009278	2L_21009278_SNP [dm3] 2L_21009278_SNP [dm6]	T	A	2.737e^-4	0.165	INTRON CG42238	TF binding site BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_HSA
2L	21119254	2L_21119254_SNP [dm3] 2L_21119254_SNP [dm6]	C	G	2.737e^-4	0.165	INTRON Nhe2
2L	21764438	2L_21764438_SNP [dm3] 2L_21764438_SNP [dm6]	C	A	2.737e^-4	0.165	INTRON CG31612
2L	22111021	2L_22111021_SNP [dm3] 2L_22111021_SNP [dm6]	T	G	2.737e^-4	0.165	DOWNSTREAM CG6675 INTERGENIC	transposable element FlyBase
2L	2264980	2L_2264980_SNP [dm3] 2L_2264980_SNP [dm6]	G	A	2.737e^-4	0.165	NON_SYNONYMOUS_CODING CG34049 DOWNSTREAM CG4270
2L	2387522	2L_2387522_SNP [dm3] 2L_2387522_SNP [dm6]	A	G	2.737e^-4	0.165	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	2585061	2L_2585061_SNP [dm3] 2L_2585061_SNP [dm6]	C	A	2.737e^-4	0.165	INTRON Drp1	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA
2L	2796422	2L_2796422_SNP [dm3] 2L_2796422_SNP [dm6]	A	T	2.737e^-4	0.165	UPSTREAM Syt1 INTRON Syt1
2L	3409785	2L_3409785_DEL [dm3] 2L_3409785_DEL [dm6]	CC	C	2.737e^-4	0.165	UPSTREAM CG8840 INTRON pgant2
2L	3943760	2L_3943760_SNP [dm3] 2L_3943760_SNP [dm6]	A	G	2.737e^-4	0.165	INTRON fred
2L	3957794	2L_3957794_SNP [dm3] 2L_3957794_SNP [dm6]	T	C	2.737e^-4	0.165	INTRON fred
2L	4169688	2L_4169688_SNP [dm3] 2L_4169688_SNP [dm6]	G	A	2.737e^-4	0.165	INTERGENIC
2L	4227104	2L_4227104_SNP [dm3] 2L_4227104_SNP [dm6]	C	G	2.737e^-4	0.165	UPSTREAM RpL40 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Kr
2L	4331908	2L_4331908_SNP [dm3] 2L_4331908_SNP [dm6]	A	T	2.737e^-4	0.165	DOWNSTREAM CG16857 INTERGENIC	TF binding site BDTNP1_TFBS_da mE1_TFBS_Trl
2L	4427843	2L_4427843_SNP [dm3] 2L_4427843_SNP [dm6]	G	A	2.737e^-4	0.165	INTRON CG15431
2L	4427850	2L_4427850_SNP [dm3] 2L_4427850_SNP [dm6]	A	G	2.737e^-4	0.165	INTRON CG15431
2L	4896875	2L_4896875_SNP [dm3] 2L_4896875_SNP [dm6]	A	G	2.737e^-4	0.165	INTRON CG3036
2L	5337047	2L_5337047_SNP [dm3] 2L_5337047_SNP [dm6]	C	G	2.737e^-4	0.165	UPSTREAM fusl INTRON fusl
2L	5408274	2L_5408274_SNP [dm3] 2L_5408274_SNP [dm6]	T	A	2.737e^-4	0.165	INTRON H15	TF binding site mE1_TFBS_cad
2L	5447080	2L_5447080_SNP [dm3] 2L_5447080_SNP [dm6]	T	C	2.737e^-4	0.165	INTERGENIC
2L	5958205	2L_5958205_SNP [dm3] 2L_5958205_SNP [dm6]	A	T	2.737e^-4	0.165	SYNONYMOUS_CODING Vm26Ac DOWNSTREAM Vm26Ab	TF binding site mE1_TFBS_cad
2L	6106395	2L_6106395_SNP [dm3] 2L_6106395_SNP [dm6]	T	A	2.737e^-4	0.165	INTRON stai
2L	6193583	2L_6193583_SNP [dm3] 2L_6193583_SNP [dm6]	A	C	2.737e^-4	0.165	INTRON CG34380	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	6279844	2L_6279844_DEL [dm3] 2L_6279844_DEL [dm6]	CTATAA	C	2.737e^-4	0.165	INTRON Ddr
2L	6523236	2L_6523236_SNP [dm3] 2L_6523236_SNP [dm6]	T	G	2.737e^-4	0.165	INTRON CG31637	TF binding site mE1_TFBS_inv
2L	6533500	2L_6533500_SNP [dm3] 2L_6533500_SNP [dm6]	G	A	2.737e^-4	0.165	INTRON eya
2L	7173278	2L_7173278_SNP [dm3] 2L_7173278_SNP [dm6]	C	A	2.737e^-4	0.165	INTERGENIC
2L	7177949	2L_7177949_SNP [dm3] 2L_7177949_SNP [dm6]	G	A	2.737e^-4	0.165	EXON CR44613
2L	7189365	2L_7189365_SNP [dm3] 2L_7189365_SNP [dm6]	A	T	2.737e^-4	0.165	INTRON CG4496	TF binding site BDTNP1_TFBS_dl
2L	7254336	2L_7254336_SNP [dm3] 2L_7254336_SNP [dm6]	G	T	2.737e^-4	0.165	INTERGENIC
2L	7467865	2L_7467865_SNP [dm3] 2L_7467865_SNP [dm6]	G	A	2.737e^-4	0.165	INTRON CG6055	TF binding site mE1_TFBS_inv
2L	7578458	2L_7578458_SNP [dm3] 2L_7578458_SNP [dm6]	G	T	2.737e^-4	0.165	SYNONYMOUS_CODING RapGAP1
2L	7579121	2L_7579121_SNP [dm3] 2L_7579121_SNP [dm6]	T	A	2.737e^-4	0.165	UPSTREAM RapGAP1 INTERGENIC
2L	7973482	2L_7973482_SNP [dm3] 2L_7973482_SNP [dm6]	T	C	2.737e^-4	0.165	INTRON Snoo
2L	7991923	2L_7991923_SNP [dm3] 2L_7991923_SNP [dm6]	G	C	2.737e^-4	0.165	UPSTREAM pes INTRON pes	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2L	8002560	2L_8002560_SNP [dm3] 2L_8002560_SNP [dm6]	T	G	2.737e^-4	0.165	INTRON Wwox
2L	8351003	2L_8351003_SNP [dm3] 2L_8351003_SNP [dm6]	A	T	2.737e^-4	0.165	UTR_3_PRIME CG7778 DOWNSTREAM CG7778	TF binding site mE1_TFBS_zfh1
2L	8363493	2L_8363493_SNP [dm3] 2L_8363493_SNP [dm6]	C	A	2.737e^-4	0.165	UTR_3_PRIME RpS13 DOWNSTREAM RpS13	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi BDTNP1_TFBS_z mE1_TFBS_sens
2L	8390381	2L_8390381_SNP [dm3] 2L_8390381_SNP [dm6]	C	T	2.737e^-4	0.165	NON_SYNONYMOUS_CODING CG42820 DOWNSTREAM snRNA:U6atac:29B	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	8634006	2L_8634006_SNP [dm3] 2L_8634006_SNP [dm6]	A	T	2.737e^-4	0.165	INTRON Sema-1a	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	8657178	2L_8657178_SNP [dm3] 2L_8657178_SNP [dm6]	G	A	2.737e^-4	0.165	INTRON Sema-1a
2L	8747199	2L_8747199_SNP [dm3] 2L_8747199_SNP [dm6]	A	T	2.737e^-4	0.165	INTERGENIC
2L	8762348	2L_8762348_SNP [dm3] 2L_8762348_SNP [dm6]	C	T	2.737e^-4	0.165	INTERGENIC	TF binding site mE1_TFBS_cad
2L	9188558	2L_9188558_SNP [dm3] 2L_9188558_SNP [dm6]	C	T	2.737e^-4	0.165	INTRON tai
2L	9232950	2L_9232950_SNP [dm3] 2L_9232950_SNP [dm6]	A	T	2.737e^-4	0.165	INTRON tai
2L	9257411	2L_9257411_MNP [dm3] 2L_9257411_MNP [dm6]	CTG	TAA	2.737e^-4	0.165	INTRON Ggamma30A	TF binding site BDTNP1_TFBS_z
2L	9257422	2L_9257422_SNP [dm3] 2L_9257422_SNP [dm6]	A	C	2.737e^-4	0.165	INTRON Ggamma30A	TF binding site BDTNP1_TFBS_z
2L	9257423	2L_9257423_DEL [dm3] 2L_9257423_DEL [dm6]	ATAATCT	A	2.737e^-4	0.165	INTRON Ggamma30A	TF binding site BDTNP1_TFBS_z
2L	9257444	2L_9257444_SNP [dm3] 2L_9257444_SNP [dm6]	T	G	2.737e^-4	0.165	INTRON Ggamma30A	TF binding site BDTNP1_TFBS_z
2L	9257445	2L_9257445_SNP [dm3] 2L_9257445_SNP [dm6]	C	G	2.737e^-4	0.165	INTRON Ggamma30A	TF binding site BDTNP1_TFBS_z
2L	9257454	2L_9257454_SNP [dm3] 2L_9257454_SNP [dm6]	T	G	2.737e^-4	0.165	INTRON Ggamma30A	TF binding site BDTNP1_TFBS_z
2L	9257466	2L_9257466_SNP [dm3] 2L_9257466_SNP [dm6]	G	A	2.737e^-4	0.165	INTRON Ggamma30A	TF binding site BDTNP1_TFBS_z
2L	9257475	2L_9257475_DEL [dm3] 2L_9257475_DEL [dm6]	ATGA	A	2.737e^-4	0.165	INTRON Ggamma30A	TF binding site BDTNP1_TFBS_z
2L	9304036	2L_9304036_SNP [dm3] 2L_9304036_SNP [dm6]	C	T	2.737e^-4	0.165	DOWNSTREAM CR42844 INTERGENIC
2R	10311636	2R_10311636_SNP [dm3] 2R_14424131_SNP [dm6]	C	A	2.737e^-4	0.165	UTR_3_PRIME CG17386
2R	10341606	2R_10341606_SNP [dm3] 2R_14454101_SNP [dm6]	C	T	2.737e^-4	0.165	INTRON Oaz	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens

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By genomic position
Variant impact
Gene name

Sex_Estimate_M phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results