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=8.347e^-1)
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

38 significant hits at p-value < 0.001.

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

Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	10181713	2L_10181713_SNP [dm3] 2L_10181713_SNP [dm6]	T	G	5.307e^-4	0.443	DOWNSTREAM Sur INTERGENIC	TF binding site mE1_TFBS_inv
2L	10675466	2L_10675466_SNP [dm3] 2L_10675466_SNP [dm6]	G	A	5.307e^-4	0.443	INTERGENIC
2L	11913583	2L_11913583_SNP [dm3] 2L_11913583_SNP [dm6]	T	G	5.307e^-4	0.443	INTRON Pde1c
2L	12910419	2L_12910419_DEL [dm3] 2L_12910419_DEL [dm6]	CCCACCGTCT	C	5.307e^-4	0.443	INTERGENIC
2L	13124290	2L_13124290_SNP [dm3] 2L_13124290_SNP [dm6]	G	A	5.307e^-4	0.443	INTERGENIC
2L	13739990	2L_13739990_SNP [dm3] 2L_13739990_SNP [dm6]	T	C	5.307e^-4	0.443	INTERGENIC
2L	13886149	2L_13886149_SNP [dm3] 2L_13886149_SNP [dm6]	C	A	5.307e^-4	0.443	INTRON CenG1A	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	16568141	2L_16568141_SNP [dm3] 2L_16568141_SNP [dm6]	G	A	5.307e^-4	0.443	INTRON CG42389
2L	17348005	2L_17348005_SNP [dm3] 2L_17348005_SNP [dm6]	A	T	5.307e^-4	0.443	INTERGENIC
2L	17348006	2L_17348006_SNP [dm3] 2L_17348006_SNP [dm6]	C	T	5.307e^-4	0.443	INTERGENIC
2L	21909898	2L_21909898_DEL [dm3] 2L_21909898_DEL [dm6]	CATAATAGGG	C	5.307e^-4	0.443	INTERGENIC	TF binding site BDTNP1_TFBS_prd mE1_TFBS_cad mE1_TFBS_HSA
2L	3388021	2L_3388021_SNP [dm3] 2L_3388021_SNP [dm6]	C	T	5.307e^-4	0.443	UTR_3_PRIME CG42460 UPSTREAM CR45301 & 1 other DOWNSTREAM CG42460
2L	3657139	2L_3657139_SNP [dm3] 2L_3657139_SNP [dm6]	A	G	5.307e^-4	0.443	UPSTREAM for INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_ttk mE1_TFBS_zfh1
2L	3657140	2L_3657140_SNP [dm3] 2L_3657140_SNP [dm6]	C	A	5.307e^-4	0.443	UPSTREAM for INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_HSA mE1_TFBS_kn mE1_TFBS_Trl mE1_TFBS_ttk mE1_TFBS_zfh1
2L	4346565	2L_4346565_SNP [dm3] 2L_4346565_SNP [dm6]	A	G	5.307e^-4	0.443	UPSTREAM CR44697 DOWNSTREAM Atet INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
2L	4346572	2L_4346572_SNP [dm3] 2L_4346572_SNP [dm6]	A	G	5.307e^-4	0.443	UPSTREAM CR44697 DOWNSTREAM Atet INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA mE1_TFBS_Trl
2L	4365702	2L_4365702_SNP [dm3] 2L_4365702_SNP [dm6]	A	G	5.307e^-4	0.443	INTRON Traf4	TF binding site BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_Kr
2L	4422323	2L_4422323_SNP [dm3] 2L_4422323_SNP [dm6]	T	G	5.307e^-4	0.443	INTRON CG15431
2L	4596637	2L_4596637_SNP [dm3] 2L_4596637_SNP [dm6]	C	T	5.307e^-4	0.443	INTRON dp	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_slp1
2L	4804647	2L_4804647_DEL [dm3] 2L_4804647_DEL [dm6]	AA	A	5.307e^-4	0.443	INTERGENIC
2L	5555745	2L_5555745_SNP [dm3] 2L_5555745_SNP [dm6]	A	C	5.307e^-4	0.443	SPLICE_SITE_REGION GluRIIA DOWNSTREAM CG14017 INTRON GluRIIA
2L	6555138	2L_6555138_SNP [dm3] 2L_6555138_SNP [dm6]	T	C	5.307e^-4	0.443	DOWNSTREAM Osm6 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	7361573	2L_7361573_SNP [dm3] 2L_7361573_SNP [dm6]	T	C	5.307e^-4	0.443	INTERGENIC
2L	7641886	2L_7641886_SNP [dm3] 2L_7641886_SNP [dm6]	T	G	5.307e^-4	0.443	DOWNSTREAM Slob INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_prd BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_run mE1_TFBS_zfh1
2L	8648377	2L_8648377_SNP [dm3] 2L_8648377_SNP [dm6]	T	C	5.307e^-4	0.443	INTRON Sema-1a
2L	9485838	2L_9485838_SNP [dm3] 2L_9485838_SNP [dm6]	T	C	5.307e^-4	0.443	INTERGENIC
2L	9800260	2L_9800260_SNP [dm3] 2L_9800260_SNP [dm6]	T	C	5.307e^-4	0.443	INTRON nAChRalpha6
2R	10594754	2R_10594754_SNP [dm3] 2R_14707249_SNP [dm6]	A	C	5.307e^-4	0.443	INTRON mspo
2R	10820271	2R_10820271_SNP [dm3] 2R_14932766_SNP [dm6]	A	G	5.307e^-4	0.443	UPSTREAM CG12853 INTRON CG10253
2R	1764750	2R_1764750_SNP [dm3] 2R_5877245_SNP [dm6]	C	A	5.307e^-4	0.443	INTERGENIC
2R	851779	2R_851779_INS [dm3] 2R_4964274_INS [dm6]	T	TTTTCTGCCTCTAACAATT...	5.307e^-4	0.443	INTRON Ir41a	transposable element FlyBase
2R	958758	2R_958758_SNP [dm3] 2R_5071253_SNP [dm6]	G	A	5.307e^-4	0.443	INTERGENIC	transposable element FlyBase
3L	11249584	3L_11249584_SNP [dm3] 3L_11256484_SNP [dm6]	C	G	5.307e^-4	0.443	DOWNSTREAM scyl INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	13190122	3L_13190122_SNP [dm3] 3L_13197022_SNP [dm6]	T	G	5.307e^-4	0.443	INTERGENIC	TF binding site mE1_TFBS_cad
3L	2058644	3L_2058644_SNP [dm3] 3L_2058644_SNP [dm6]	G	A	5.307e^-4	0.443	SYNONYMOUS_CODING sls INTRON sls
3R	23205716	3R_23205716_SNP [dm3] 3R_27379994_SNP [dm6]	T	G	5.307e^-4	0.443	UTR_3_PRIME side INTRON side
X	14736762	X_14736762_SNP [dm3] X_14842729_SNP [dm6]	A	T	5.307e^-4	0.443	UTR_3_PRIME CG12539 INTRON Flo2	TF binding site BDTNP1_TFBS_sna mE1_TFBS_HSA
X	16044743	X_16044743_DEL [dm3] X_16150710_DEL [dm6]	TCTCTCTCT	T	5.307e^-4	0.443	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl

By genomic position
Variant impact
Gene name

cpoP phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results