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Circadian_Per_ChiSq phenotype

GWAS results were precomputed for all phenotypes using PLINK2 [v2.00a3LM (1 Jul 2021)] and corrected for the 6 main covariates defined in Huang et al., 2014. These covariates are the same than the ones used in the DGRP2 website.
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=3.691e-20)
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
Covariateχ2p-valueSignificance
In_3R_Mo7.64410.0219
PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

GWAS results

1952 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