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Big Y - Private Variants Guide

The Private Variants tab displays your SNP markers that are not on the list of known SNPs. These markers may or may not be unique to you as an individual. Men in related lineages may share some Private Variants. As men from distantly related lineages test, SNP markers may be moved from Private Variants to Named Variants. 

Y-Chromosome Browsing Tool

The Y-Chromosome browsing tool allows you to view forward and reverse strands for any SNPs in your profile.

Private Variants Tab Columns

The Private Variants tab contains the following columns.

Note: You can use the sort arrow located at the upper-right corner of each column to sort the data in ascending or descending order.

Position

The Position column displays the position (location) of your private variant on the Y-chromosome according to the GRCh38 human reference genome, which is maintained by the Genome Reference Consortium.

Reference 

This column displays the nucleotide base indicated by the GRCh38 human reference genome, which is maintained by the Genome Reference Consortium. The following values are possible:

  • A - Adenine
  • C - Cytosine
  • T - Thymine
  • G - Guanine

Genotype

This column displays your nucleotide base determined in your Y chromosome at the given position. The following values are possible:

  • A - Adenine
  • C - Cytosine
  • T - Thymine
  • G - Guanine
  • - Inconclusive. This indicates that we did not get good coverage on the SNP, therefore, we were unable to confirm your base at the given position.

Viewing a SNP with the Browsing Tool

In the Position column, click on the position of the private variant that you want to view. The Y-Chromosome Browsing Tool opens in a new window displaying the location of the SNP.

The position you selected is displayed in pink with a downward arrow pointing to the position of the private variant. The other pink locations display your other nearby private variant locations.

You can click on any of your private variant positions to see more information for that private variant.

Searching for a Specific Position 

To search for a specific by position:

In the Position Search box at the top of the column, enter the position or part of the position of the private variant.

Filtering by Reference Base

To filter private variants by reference base:

At the top of the Reference column, click the drop-down list, and select ACT, or G.

Filtering by Genotype

To filter private variants by genotype:

At the top of the Genotype column, click on the drop-down list, and select ACTG or ?.

 

 

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