The Named Variants tab displays your Y-DNA SNPs (single nucleotide polymorphisms) that are on the list of 600,000+ known SNPs against which Big Y data is compared
Y-Chromosome Browsing Tool
The Y-Chromosome Browsing Tool allows you to view forward and reverse strands for any SNPs in your profile.
Named Variants Tab Columns
The Named 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.
SNP Name
The SNP Name column displays the names of known SNP markers. Some SNP markers may have multiple names according to different publications and sources.
SNP mutations are assigned names as they are discovered. New private mutations might have reserved names that are not yet added to this list.
Derived?
The values in this column indicate whether or not the called genotype is in the derived state. When a SNP is in the derived state, it means that you are “positive” for this SNP mutation. When the SNP is not in the derived state, it means that the SNP is ancestral. The following values are possible:
- Yes (+) - Indicates that you have the SNP mutation (the SNP is derived).
- No (-) - Indicates that you are not positive for the SNP mutation (the SNP is ancestral not derived).
- ? - Inconclusive. This indicates that we did not get good coverage on the SNP, therefore, we were unable to confirm whether or not the called genotype is derived.
Indicates if you have the SNP mutation. Yes (+) is a positive result, No (-) is a negative result, and ? is a no-call (inconclusive) result.
On Y Tree?
The values in this column indicate whether or not the SNP exists on the Y-DNA Haplotree. Named SNPs that are not placed on the haplotree may not be phylogenetically relevant. The following values are possible in this column:
- Yes - Indicates the SNP exists on the Y-DNA Haplotree.
- No - Indicates the SNP does not exist on the Y-DNA Haplotree.
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 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 SNP Name column, click on the SNP that you want to view. The Y-Chromosome Browsing Tool opens in a new window displaying the location of the SNP.
The SNP you selected is displayed in pink with a downward arrow pointing to the position of the SNP. The other pink locations display your other nearby SNP positions.
You can click on any of your SNP positions to see more information for that SNP.
Searching for a Specific SNP
To search for a specific SNP:
At the top of the SNP Name column, enter the name or partial name of the SNP in the SNP Name Search box at the top of the column.
Filtering Derived SNPs
To filter SNPs by whether or not they are derived, ancestral, or unconfirmed:
At the top of the Derived column, click the drop-down list at the top of the column, and select Yes (+), No (-), or ?.
Note: By default, this column is set to Yes (+).
Filtering Y-DNA Haplotree SNPs
To filter SNPs by whether or not your SNP exists on the Y-DNA haplotree:
At the top of the On Y-Tree column, click the drop-down list, and select Yes or No.
Filtering SNPs by Reference Base
To filter SNPs by reference base:
At the top of the Reference column, click the drop-down list, and select A, C, T, or G.
Filtering SNPs by Genotype
To filter SNPs by genotype:
At the top of the Genotype column, click on the drop-down list, and select A, C, T, G or ?.