BAMsAway

Description

Allows Big Y customers to use FTDNA's Y-Chromosome Browsing Tool to inspect arbitrary SNPs or positions by temporarily adding them to the "Unnamed Variants" list. This makes it possible to review the evidence supporting a negative result in addition to that for positive results.

To use this tool, go to your Big Y results and click on the "Unnamed Variants" tab. Wait for default list to finish loading, then click on the button labelled "Add SNP or position using 'BAMsAway' Chrome Extension". Enter either a SNP name or a Y chromosome position. If correctly formatted, the SNP or position will be added to the list. You can then click on the SNP or position in the list to view it in the browser, just as you would with the default variants.

Note that only the SNP names known to and used by the FTDNA browser will return results. If the SNP is unknown, the window for displaying the SNP will open, but it will not populate with data; no error message will appear.

Multiple SNPs and positions, separated by commas, can be added simultaneously. Any information in single quotes will be treated as a comment to be displayed along with the name or position in the variant list.

Switching away from the "Unnamed Variants" tab to the "Named Variants" table or the "Matching" tab will clear any manually added SNPs or variants since the "Unnamed Variants" tab will reload the default list from FTDNA upon returning to it.

Note that the "Genotype" and "Reference" items will be listed as "undefined" in the browser. These can generally be deduced from the displayed information, keeping in mind that the reference genome (the letters displayed in the browser) is itself not ancestral for all SNP markers (it is derived for U152>L2>L20 and upstream markers, and probably for certain downstream markers).

Due to intrinsic ambiguity in how STRs are counted, the STR repeats listed as the "Reference" alleles for each STR should be considered provisional and subject to change. Starting after version 1.5.5, any such changes will be specifically noted below. It is not necessarily safe to use those allele repeats as a baseline for deriving STR values for direct comparison to Y12, Y37, Y67 or Y111 STR values. However, you can compare STRs derived from two different Big Y kits to one another by counting the differences from the listed reference repeats. Comparison to repeat counts derived by other companies, either from reanalysis of Big Y or from independent Next Generation Sequencing, is not advised until compatible standardization has been verified.

Version 1.5.6: modified DYS578, DYS490, DYS636, DYS577, DYS499; added FTY214
Version 1.5.7: modified DYS538