The InDel variants track (InDel):

The Indel variants track contains a row for each of the called insertions or deletions that fulfills the requirements for being of a 'variant' type (see section 25.12.3 for a description of the variant types "Insertion" and "Deletion"). These are the small to medium sized insertions and deletions (up to 200 bp in length) for which the algorithm was able to identify the allele sequence (that is, the exact inserted sequence, or the exact deleted sequence). For insertions, the full allele sequence is found from the unaligned ends of mapped reads. For some insertions the length and allele sequence cannot be determined and as these do not fulfill the requirements of a 'variant', they do not qualify for representation in the 'InDel variant' track but instead appear in the Structural Variants track (see below). The information provided for each of the indels in the InDel variant track is the 'Chromosome', 'Region', 'Type', 'Reference', 'Allele', 'Reference Allele', 'Length' and 'Zygosity' columns that are provided for all variants (see section 25.12.1). In addition the following information, which is primarily intended to allow the user to assess the degree of evidence supporting each predicted indel, is provided: The 'Zygosity' field is set to 'Homozygous' if the 'Variant ratio' is 0.80 or above, and 'Heterozygous' otherwise.