The SNP Checker page is an advanced tool that allows you to view the raw data for a specific variant. It provides a visual representation of the DNA sequences, known as reads that cover the position of the variant. This page is a powerful tool for confirming your haplogroup and exploring new or private variants. It can be difficult to interperet without a fammiliarity with Y-DNA SNPs and the Big Y test. You can read more about those topics here:
The SNP Checker page contains information about reads and nucleotide values throughout the Y chromosome covered by the Big Y-700 test. You can learn more about reads in the sections below.
The SNP Checker contains the following information:
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SNP Name - This is the name of the variant you have searched for.
Note: If you have searched by position, this will display the selected position. - Ancestral - The Ancestral value represents the non-mutated state. Testers with this value are negative for this SNP.
- Derived - The Derived value represents the mutated state of this specific SNP. Testers with a value that differs from the ancestral value are positive for this SNP.
- Position - The location of the variant on the Y chromosome. This position corresponds to the GRCh38 human reference genome.
- Forward Read - Indicates the position values were obtained from the forward strand of DNA.
- Reverse Read - Indicates the position values were obtained from the reverse strand of DNA.
- Read Quality - Indicates the reliability of each read.
- Ancestral Value - Displays the nucleotide base indicated by the GRCh38 human reference genome for each position.
- Position - The location of the stretch of the Y chromosome you are currently viewing as defined by the GRCh38 human reference genome.
- Variant Position - This line indicates the exact location of the variant or SNP you have selected
- DNA Reads - Each of these rows represents a read. You will notice that some rows start or stop at different locations. You can read more about reads below.
- Variant Nucleotide - Any letter in pink represents a call for a variant call differing from the GRCh38 human reference genome.
- Grey X - Close the SNP Checker.
What is a Read?
DNA is so long that we cannot sequence the entire genome all at once. When scientists sequence a person's DNA, they must first break it down into many small fragments. These fragments are then sequenced, and the resulting data from each small fragment is called a read. The reads are then put back together by stitching together overlapping reads.
The Big Y Test is designed to focus on a specific area of the Y chromosome. Each read covers as much of this area as possible. To ensure that we get maximum coverage for the area, we run a minimum of seventy (70) reads on the targeted area.
What are Forward and Reverse Reads?
DNA is made of two strands, or chains, connected like rungs on a ladder by nucleotide pairs. Each pair has a nucleotide connected to each strand. For example, you could have an AT nucleotide pair at position 12345. DNA strands have a natural direction, so we differentiate the two by calling them the Forward Strand and the reverse strand.
Nucleotides only pair in specific ways. A always pairs with T, and C always pairs with G. That means we can look at only one half and know what the whole pair is. If we see a C on position 12345 on the forward strand, we know that the reverse strand must have a G at that position. For simplicity's sake, the standard reported value for each nucleotide is the value found on the forward strand.
Forward Reads and Reverse Reads simply mean that the read focused on either the Forward Strand or the Reverse Strand. For simplicity's sake, the standard reporting for each nucleotide is the value found on the Forward Strand.
What is Read Quality?
Each read covers only a portion of the larger DNA sequence. We stitch together each read by looking at the overlapping regions that two reads have. Some edges can look similar to other though, like a puzzle that has similarly shaped pieces.
Read Quality indicates the probability that the read belongs to the indicated region of the reference genome. Think of it like checking the puzzle for all the places your piece might fit into the larger whole.
What do the Pink Squares on the reads mean?
Reads with a pink background represent a non-reference allele, i.e. an A/C/G/T value identified in your DNA which is different from the reference allele
It is important that we report accurate data, so in order to call a SNP as positive, it must meet a minimum number of positive reads to be reported. Very few positive calls, especially in a well-covered area, may indicate false positives.