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easyGWAS
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Overview
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Brief Summary
Experiment Type:
Genome-wide Association Study
Species:
Arabidopsis thaliana
Dataset:
1001 Genomes Data
Phenotype:
DTF2 (ID: AT1P5947)
Algorithm:
FaSTLMM
Parameters:
MAF:
0.05
SNP Encoding:
Additive
Transformation:
BoxCox
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 1
Top 10 SNP annotations for Chromosome 2
Top 10 SNP annotations for Chromosome 3
Top 10 SNP annotations for Chromosome 4
Top 10 SNP annotations for Chromosome 5