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Overview
Experiment overview
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Brief Summary
Experiment Type:
Genome-wide Association Study
Species:
Pristionchus pacificus
Dataset:
Linking genotype and phenotype in P. pacificus (McGaughran et. al.)
Phenotype:
pH 20 5 (ID: PP5P0)
Algorithm:
EMMAX
Parameters:
MAF:
0.1
SNP Encoding:
Additive
Transformation:
SQRT
Manhattan Plots
QQ-Plots
SNP Annotations
Summary/Downloads
GWAS Annotation Options
Multiple Correction Method
Bonferroni (FWER)
Storey & Tibishirani q-value (FDR)
Benjamini & Hochberg (FDR)
Benjamini, Hochberg & Yekutieli (FDR)
Significance level α
0.1
0.05
0.01
Number of SNPs per chromosome
10
25
50
100
200
500
Search Window around SNP
Within Gene
Within Gene + 1kb around Gene
Within Gene + 10kb around Gene
Within Gene + 100kb around Gene
Within Gene + 1000kb around Gene
Use only unique SNPs for Bonferroni threshold:
Top 10 SNP annotations for Chromosome I
Top 10 SNP annotations for Chromosome II
Top 10 SNP annotations for Chromosome III
Top 10 SNP annotations for Chromosome IV
Top 10 SNP annotations for Chromosome Un
Top 10 SNP annotations for Chromosome V
Top 10 SNP annotations for Chromosome X