Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > ZZ51 > DF83 > Z2563 > Z2564 > S4240 > 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 STR1kG
28565702-A-G 26419555-A-G CTS12290 +
16855400-T-G 14743520-T-G YY+
6779491-G-A 6911450-G-A FT289200 YY+
6904110-G-A 7036069-G-A FT289239 YY+
6924792-C-T 7056751-C-T MF1030 YY+
13936474-G-T 11815768-G-T FT290008 Y+
14043724-C-T 11923018-C-T YY+
14150578-C-G 12029872-C-G FT290088 YY+
15094910-T-A 12982998-T-A S4242 CTS3653 YY+
15373681-C-T 13261801-C-T FT290465 YY+
15378567-C-T 13266687-C-T CTS4078 Y+
16020914-A-T 13909034-A-T FT290657 YY+
16062479-G-C 13950599-G-C S4241 CTS5196 Y+
16224002-C-A 14112122-C-A YY+
16368824-C-T 14256944-C-T BY107285 YY+
16599596-C-T 14487716-C-T FT290811 YY+
17433163-A-G 15321283-A-G CTS7348 Y+
17815297-T-C 15703417-T-C FT291220 YY+
17826848-G-C 15714968-G-C CTS8076 Y+
18779452-G-C 16667572-G-C CTS9252 S4245 YY+
21103997-T-A 18942111-T-A S4243 YY+
21429323-C-T 19267437-C-T YY+
21612223-T-C 19450337-T-C BY134188 YY+
22189569-C-T 20027683-C-T FT292230 YY+
22607560-T-C 20445674-T-C S4244 YY+
23009765-T-G 20847879-T-G FT292392 YY+
24471141-G-A 22324994-G-A FT292694 Y+
28642790-T-C 26496643-T-C +
28668186-G-T 26522039-G-T +
2810389-T-TTTG 2942348-T-TTTG +
2812741-C-T 2944700-C-T CTS211 M3227 PF2783 V1095 YY+
3047420-T-C 3179379-T-C +
3072721-C-T 3204680-C-T +
3407835-T-A 3539794-T-A +
3432769-A-G 3564728-A-G +
3963856-G-A 4095815-G-A +
4502969-T-C 4634928-T-C Y2119 FGC1759 Z24180 +
4502972-C-T 4634931-C-T BY29023 +
4502976-A-C 4634935-A-C FGC79452 +
4538697-G-T 4670656-G-T +
4545430-A-G 4677389-A-G +
4936083-A-T 5068042-A-T +
5204866-T-G 5336825-T-G +
5225290-ACG-A 5357249-ACG-A +
5554527-C-T 5686486-C-T +
5658609-AAAAC-A 5790568-AAAAC-A 6×AAAC+
6586559-G-A 6718518-G-A +
6863815-CA-C 6995774-CA-C +
6985098-A-AGG 7117057-A-AGG +
7195534-TGA-T 7327493-TGA-T +
7383887-G-A 7515846-G-A YY+
7660048-T-G 7792007-T-G YY+
8023672-A-G 8155631-A-G FT289550 YY+
8468102-G-A 8600061-G-A YY+
9143977-C-T 9306368-C-T Y+
9725259-TCA-T 9887650-TCA-T IR3_Prx 10×CA+
9955707-G-A 10118098-G-A FT399510 Y+
13214660-A-G 11058984-A-G +
13236355-G-A 11080679-G-A FT414792 +
13275723-T-C 11120047-T-C +
13429055-C-A 11273379-C-A +
13501803-A-C 11346127-A-C +
13706680-A-G 11551004-A-G +
13711732-T-TGGAAA 11556056-T-TGGAAA +
13870425-C-T 11749719-C-T FT328893 +
14119458-G-T 11998752-G-T Y+
14680809-AG-A 12568875-AG-A +
14858685-T-TTTG 12746751-T-TTTG +
15507493-T-G 13395613-T-G FT290502 YY+
16435990-T-G 14324110-T-G YY+
16648091-G-T 14536211-G-T YY+
16729166-C-T 14617286-C-T YY+
16908472-AG-A 14796592-AG-A +
17047896-TG-T 14936016-TG-T +
18035643-A-C 15923763-A-C FTB72278 YY+
18390117-T-G 16278237-T-G P6_Gap +
18390123-T-G 16278243-T-G P6_Gap +
18608588-AC-A 16496708-AC-A +
19112216-AAC-A 17000336-AAC-A +
19293486-A-AT 17181606-A-AT +
19332402-T-G 17220522-T-G YY+
21139347-C-T 18977461-C-T Z34524 YY+
21172007-T-G 19010121-T-G YY+
21172012-T-G 19010126-T-G YY+
21547360-C-G 19385474-C-G FT291989 YY+
22322768-A-C 20160882-A-C DYZ19 +
22437040-C-G 20275154-C-G FT456108 DYZ19 +
22464354-A-C 20302468-A-C DYZ19 +
22488011-C-G 20326125-C-G DYZ19 +
22876990-T-A 20715104-T-A Y+
22876992-C-A 20715106-C-A Y+
22877007-G-A 20715121-G-A Y+
23439877-A-C 21277991-A-C YY+
24127500-C-A 21981353-C-A P3_b1 +
24518972-A-G 22372825-A-G FT332935 +
26526566-G-T 24380419-G-T P1_Y1 16×T+
28556398-T-G 26410251-T-G +
28565749-G-A 26419602-G-A +
28644107-A-G 26497960-A-G +
28680982-T-A 26534835-T-A +
58895590-C-T 56695281-G-A +

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.

Mutation Notes:

Manual6321384-G-GCA6453343-G-GCA4 sufficient reads - 2 with the insertion and 2 without.
Manual7783679-GA-G7915638-GA-GJust one read, but it does show the deletion.
Manual18956466-T-C16844586-T-C4 reads, all are C.
Manual19577629-G-GA17465749-G-GA1 read, and it looks to have the insertion. This location known to have a similar region.
Manual22303212-G-C20141326-G-C7 reads, 2C and 5G.
Manual24936290-A-T22790143-A-T3 reads - 2A and 1T.
Manual22259673-T-A20097787-T-A7 reads - 2T and 5A.