Tree Position

R-U106/S21 > Z2265 > Z381/S263 > Z301/S499 > L48 > Z9 > Z30/S271 > Z349 > Z2 > Z7 > Z8 > FGC5259 > FGC5254 > Exact position not yet finalized.

Unique Mutations

The mutations unique to this man are summarized in the table below. Those with a '+' or '*' confidence level are considered by FamilyTreeDNA or FullGenomesCorp to be high quality SNPs/INDELs. For completeness, all other mutations of lesser confidence are included as well. These additional mutations may be useful for distinguishing between very closely related men.

Occasionally, some of the mutations listed here will be thought to be shared with other men in which case they might appear in upstream blocks on the tree. When this happens, the 'Blocks' field will indicate what block they appear in. Such a situation might arise with BigY men if the BED data suggests another man may be positive for a SNP, even though it doesn't appear in his VCF data. It might also happen if Chromo2 testing or Sanger sequencing of other men not on the tree show the SNP to be shared.

POS-REF-ALT (hg19) POS-REF-ALT (hg38) Blocks Names Region McDonald BED combBED STRFTDNA
121604
15810964-T-G 13699084-T-G FGC35903L159 S169 YY+
21285190-A-T 19123304-A-T Y910 ZS9483 YY4×AAAT+
2818896-C-T 2950855-C-T BY56630 YY+
6629991-T-C 6761950-T-C BY60408 YY+
6862819-G-A 6994778-G-A BY61810 YY+
6975121-A-G 7107080-A-G BY62674 YY+
8473733-T-G 8605692-T-G BY73136 YY+
8777629-C-T 8909588-C-T BY75824 YY+
14884049-G-T 12772115-G-T BY98241 YY+
15728536-TTTC-T 13616656-TTTC-T +
15784228-G-A 13672348-G-A BY104100 YY+
16358030-A-T 14246150-A-T BY107166 YY+
16671686-C-A 14559806-C-A BY109361 YY+
17015017-G-A 14903137-G-A BY111744 YY+
18109714-G-A 15997834-G-A BY120109 YY+
18981082-G-A 16869202-G-A BY125230 YY+
19079595-C-T 16967715-C-T BY126092 YY+
21340894-C-G 19179008-C-G BY52031 YY+
21642866-G-T 19480980-G-T BY134395 YY+
22192161-G-A 20030275-G-A BY138364 YY+
22470011-C-G 20308125-C-G DYZ19 +
22470246-C-G 20308360-C-G BY222382 DYZ19 +
22472175-A-C 20310289-A-C BY53041 DYZ19 +
22472180-G-C 20310294-G-C BY222725 DYZ19 +
22832720-G-T 20670834-G-T BY141134 YY+
22866963-G-T 20705077-G-T BY141347 YY+
23151935-G-T 20990049-G-T BY143405 YY+
19125434-G-A 17013554-G-A Z17259S936 Z2199 **
22472189-T-G 20310303-T-G BY42690 DYZ19 **
18019974-C-T 15908094-C-T BY119156 **
22472188-T-G 20310302-T-G DYZ19 **
13406124-A-AT 11250448-A-AT ***
13139239-T-TCATTCCATTC 10628725-T-TCATTCCATTC 10×CATTC***
13430155-C-T 11274479-C-T ***
22231540-C-G 20069654-C-G DYZ19 ***
19580917-G-A 17469037-G-A P5_Prx ***
20027098-A-G 17915218-A-G P5_Prx ***
20649768-TTCTG-T 18487882-TTCTG-T P4_Prx ***
22237386-C-A 20075500-C-A DYZ19 ***
22254768-T-C 20092882-T-C DYZ19 ***
22294719-A-T 20132833-A-T DYZ19 ***
22294943-C-T 20133057-C-T DYZ19 ***
22294944-G-C 20133058-G-C DYZ19 ***
22294949-C-G 20133063-C-G DYZ19 ***
22317689-G-C 20155803-G-C DYZ19 ***
22318315-A-T 20156429-A-T DYZ19 ***
22357984-A-C 20196098-A-C DYZ19 ***
22430356-G-T 20268470-G-T DYZ19 ***
24252738-T-C 22106591-T-C P3_b1 ***
24826772-A-T 22680625-A-T P3_b2 ***
24972235-T-C 22826088-T-C g1 ***
25023907-G-GA 22877760-G-GA g1 ***
25239585-C-T 23093438-C-T P2_r1 ***
28794005-A-T 26647858-A-T ***

In the table above, the meaning of the confidence field depends on whether the data comes from an FTDNA kit or an FGC kit. For FTDNA kits, + implies a "PASS" result with just one possible variant, * indicates a "PASS" but with multiple variants, ** indicates "REJECTED" with just a single variant, and *** indicates "REJECTED" with multiple possible variants. 'A*' are heterozygous variants not called by FTDNA, but still pulled from the VCF file. For FGC kits, + indicates over 99% likely genuine (95% for INDELs); * over 95% likely genuine (90% for INDELs); ** about 40% likely genuine; *** about 10% likely genuine. Manual entries read directly from a BAM file will be either + indicating positive, or * indicating that the data show a mixture of possible variants.

For the FTDNA kits, the BED data is encoded in the background color of the cells. Those cells with a white background have coverage, those with a grey background indicate no coverage in the BED file, and those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the vcf file.

The combBED column indicates whether or not the mutation is a SNP and falls in the combBED region defined in Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data by Dmitry Adamov, Vladimir Guryanov, Sergey Karzhavin, Vladimir Tagankin, Vadim Urasin.

The McDonald BED column indicates whether or not the mutation is a SNP and falls in the BED region used by Dr. Iain McDonald in the age analysis he does for R-U106 men.