Q: What are SNPs "currently defining" a subclade and subclade "formed" age, "TMRCA" and confidence intervals?
A: The following definitions and methodologies relate to the subclades in the YTree:
Subclade name: Each subclade name is highlighted in green.
SNPs "defining" a subclade: These are listed to the right of the subclade name (by SNP name, with additional SNP names in the grey-shaded pop-up: "X (a number) SNPs"). The SNP list for a subclade may change in the future as more samples are added to the YFull database and new branches are added. These SNPs are also listed in one of the tabs of the "info" pop-up table, as are subclade defining derived STR values. For a subclade quite close to the present, "defining" SNPs and STRs may be considered as a "family signature."
Subclade "formed" age: The TMRCA (time to most recent common ancestor) of a subclade is used as the "formed" age of each branch of the subclade. Stated otherwise, the formed age of a branch is the same as the TMRCA of the "parent" subclade of that branch.
Determination of TMRCA for a subclade: The general rule is that the TMRCA of a subclade is equal to the average age (after rounding) shown in the yellow bar of the YTree "info" pop-up table for the subclade. In the situations where the general rule is not followed YFull will add an explanatory note at the bottom of the pop-up table. Rounding rules: An age of less than 500 ybp is rounded to the nearest "25" (e.g., 267 becomes 275); an age of 500 to 1999 is rounded to the nearest "50" (e.g., 1267 becomes 1250); and an age of 2000 or more is rounded to the nearest "100" (e.g., 2267 becomes 2300).
Formed CI xx% yyyy <-> zzzz ybp, TMRCA CI aa% bbbb <-> cccc ybp: CI means "Confidence Interval". A confidence interval is an indicator of the precision of the YFull "formed" age and "TMRCA" data in the YTree. YFull developed its own statistical analysis computer script in order to calculate its confidence intervals.
Yellow Bar in "info" pop-up table: The "ybp" (years before the present) for the subclade is the average of the ages of the branches and samples (if any) highlighted in green in the Branch ID column, as shown in the yellow bar "Formula".
Number of SNPs column in "info" pop-up table: For a branch, the number in this column is the average of the numbers reported for the samples in the branch. For a sample, the number in this column is the total of the Known SNPs and Novel SNPs located between the subclade and the present.
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Q: What are SNPs "currently defining" a subclade and subclade "formed" age, "TMRCA" and confidence intervals?
A: The following definitions and methodologies relate to the subclades in the YTree:
Subclade name: Each subclade name is highlighted in green.
SNPs "defining" a subclade: These are listed to the right of the subclade name (by SNP name, with additional SNP names in the grey-shaded pop-up: "X (a number) SNPs"). The SNP list for a subclade may change in the future as more samples are added to the YFull database and new branches are added. These SNPs are also listed in one of the tabs of the "info" pop-up table, as are subclade defining derived STR values. For a subclade quite close to the present, "defining" SNPs and STRs may be considered as a "family signature."
Subclade "formed" age: The TMRCA (time to most recent common ancestor) of a subclade is used as the "formed" age of each branch of the subclade. Stated otherwise, the formed age of a branch is the same as the TMRCA of the "parent" subclade of that branch.
Determination of TMRCA for a subclade: The general rule is that the TMRCA of a subclade is equal to the average age (after rounding) shown in the yellow bar of the YTree "info" pop-up table for the subclade. In the situations where the general rule is not followed YFull will add an explanatory note at the bottom of the pop-up table. Rounding rules: An age of less than 500 ybp is rounded to the nearest "25" (e.g., 267 becomes 275); an age of 500 to 1999 is rounded to the nearest "50" (e.g., 1267 becomes 1250); and an age of 2000 or more is rounded to the nearest "100" (e.g., 2267 becomes 2300).
Formed CI xx% yyyy <-> zzzz ybp, TMRCA CI aa% bbbb <-> cccc ybp: CI means "Confidence Interval". A confidence interval is an indicator of the precision of the YFull "formed" age and "TMRCA" data in the YTree. YFull developed its own statistical analysis computer script in order to calculate its confidence intervals.
Yellow Bar in "info" pop-up table: The "ybp" (years before the present) for the subclade is the average of the ages of the branches and samples (if any) highlighted in green in the Branch ID column, as shown in the yellow bar "Formula".
Number of SNPs column in "info" pop-up table: For a branch, the number in this column is the average of the numbers reported for the samples in the branch. For a sample, the number in this column is the total of the Known SNPs and Novel SNPs located between the subclade and the present.
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