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The Cohort mutation summary report provides a row in the table for all variant sites, either SNVs or INDELs, identified in the project (Figure 2).   Hovering over a column header will provide a brief description of the column data.  Columns presented in the table include the following information: View provides a link to Chromosome View by selecting the chromosome iconicon , Chr represents chromosome from the reference assembly, Position represents the base position in the chromosome, Mutation type is the category of variant (Substitution for SNVs and Insertion or Deletion for INDELs), Reference allele is the base(s) in the reference assembly sequence, Case genotypes are the genotypes of the samples with a variant at the locus, Variant frequency represents the frequency of the variant site in the sample cohort, Sample count is the fraction of samples in the cohort with the variant, and Samples are the samples that contain the variant .  The Summarize cohort mutations task is not available for variants detected by LoFreq as no genotypes are produced from the caller.   If variant detection was performed on paired samples in Samtools (Figure 3), the Genotype column will be replaced with four columns:  GT Change presents the possible change in zygosity between cases and controls at the variant locus, Control Genotypes are the genotypes of the designated control samples in the pairs, and Case Genotypes are the genotypes of the cases in the pairs.  Additional columns can be added to the Cohort mutation summary report table by selecting Optional columns.  The optional columns are dependent upon the information present in the underlying vcf file and include variant and sample metrics from variant detection and information from the annotation.  Hovering over a term in the list will provide a brief description of the data contained in that column.  Optional columns can also be used to exclude default columns in the table.

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