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• View provides a link to Chromosome View by selecting the chromosome icon .
• 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
• HWE is p-value of Exact test on Hardy-Weinberg Equilibrium[1], small p-value indicates deviation from HWE, which might be the consequence of e.g. genotyping error.
• 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
• Samples are the names of the samples that contain the variant.

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At any point, information in the Cohort mutation summary report table can be saved in text or vcf format by selecting Download at the bottom right corner of the table. If the table is exported in text format, the visible table will be appended with additional columns for all samples in the project. These columns specify the genotype call for each variant locus in the project. In instances where no variant was detected within a sample, the value specified by Minimum coverage for genotype calls in the task dialog will be used to call either a homozygous reference genotype if above the specified threshold or no genotype if below the specified threshold. 

References

1. Janis E, et al. A Note on Exact Tests of Hardy-Weinberg Equilibrium. PMC1199378

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