R-FT88946: A Fully Accessible SNP Confirmed Across T2T, GRCh38, and GRCh37

Every haplogroup name points to a specific mutation at a specific location on the Y chromosome. Here is exactly where R-FT88946 (G to A) sits across every reference genome. • T2T (CHM13v2.0): chrY:5,879,924, Yp11.2 • GRCh38/HG38: chrY:6,199,934 • GRCh37/HG19: chrY:6,067,975 R-FT88946 sits on the short arm of the Y chromosome in the Yp11.2 region. It is fully accessible to all reference assemblies. Any Big Y test can reach it. Any Whole Genome Sequence can reach it. No special re-alignment is required. This stands in direct contrast to two private candidate SNPs found through T2T re-alignment of this same lineage: R-Y505850 (C to T) at chrY:11,913,409 and R-Y506397 (G to A) at chrY:12,172,010, which sit on the long arm in the Yq11.21 ampliconic palindrome zone with no coordinate in either GRCh37 or GRCh38, and two further private SNPs in Yq12 at the distal tip of the long arm, also invisible to all prior assemblies: R-Y639905 (A to T) at chrY:28,686,034, and R-Y639844 (C to A) at chrY:61,452,124. All four are currently private and not yet named branches on the haplogroup tree. Confirming any of them will require a second, independent tester's T2T-realigned sample to land on the same position. While variants on the short arm remain highly accessible, the distal tip of the long arm demands a different methodological approach. Because both the R-Y639905 and R-Y639844 positions sit in Yq12 and completely lack coordinates in either GRCh37 or GRCh38, they remain entirely invisible to standard alignment and fall outside the target capture range of Big Y testing. R-Y639905 yields a completely clean call with nine fully concordant reads and zero error probability, carrying no H flag. R-Y639844 yields a similarly strong call with eight fully concordant reads and zero error probability, though unlike R-Y639905 it carries an H flag, indicating greater than 95 percent homology with another region, the expected signature of the repetitive satellite sequence that characterizes this part of the chromosome, and not a mark against the call's reliability. Both remain private pending confirmation from a second tester. Ultimately, the only way another tester can detect either variant is by having a high-depth Whole Genome Sequence (WGS) re-aligned to the Telomere-to-Telomere (T2T) reference genome. One lineage. Three regions of the Y chromosome. From the short arm to the very end of the long arm. Each one telling a different story about what current and past reference assemblies can and cannot see, and about how much of that story is confirmed versus still waiting on a second match.