Variants table
By default, the Variants table for the Mito Alignment viewer lists each variant call in increasing order of their sequence position, where:
• A major allele is defined as the allele with the highest frequency at a given position.
• All major alleles are reported unless the allele is the same as the reference.
• Minor alleles are any other allele at a given position with a frequency that is greater than the Sequence IT Count (the minimum threshold for a sequence to be flagged as a possible allele).
• Insertions are reported as major alleles if they occur at a frequency that is greater than or equal to 50% and as minor alleles if they occur at a frequency that is less than 50%.
• Because reference alleles can represent a secondary mutation of a major allele, reference alleles are reported as minor alleles if their frequencies occur at a rate that is greater than the minimum threshold for Allele Frequency.
Also by default, the Variants table shows both (major and minor) allele types, but the following options are available:
• You can choose to show only major alleles or only minor alleles.
• The specific alleles and the information that is displayed for the alleles in the Variants table are determined by the filter settings and table settings that were in place at the time that the project was saved, but you can always edit these settings after the project is completed.
Mito Alignment Viewer Filter Settings. • You can click a column header to change the default sort order of the data. An icon in the column header indicates the sort direction. An Up arrow indicates an ascending sort and a Down arrow indicates a descending sort.