Tree Position

R-P312/S116 > A9063 > BY67350

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 STRBigY3
28808763-C-T 26662616-C-T BY23330 A*
6219302-T-A 6351261-T-A IR3_Dst A*
18285238-A-G 16173358-A-G P6_Prx A*
18378914-G-A 16267034-G-A P6_Prx A*
18523870-T-C 16411990-T-C P6_Dst A*
19763827-C-G 17651947-C-G P5_Prx A*
26004284-T-G 23858137-T-G P1_Y1 6×TTTTGA*
26063506-T-C 23917359-T-C P1_Y1 A*
26102721-T-G 23956574-T-G P1_Y1 A*
26130173-C-T 23984026-C-T P1_Y1 A*
4134485-A-C 4266444-A-C FT289 +
3033726-C-T 3165685-C-T Y9463 Z8485 +
13852277-G-A 11731571-G-A FT20696 +
9847372-C-T 10009763-C-T FT20571 YY+
15114736-C-A 13002823-C-A FT21832 YY+
21464829-C-G 19302943-C-G FT452957 YY+
3621500-G-C 3753459-G-C FT15495 +
3917870-A-G 4049829-A-G FT15856 +
4023973-CAA-C 4155932-CAA-C +
4349426-T-C 4481385-T-C FT16371 +
4625905-G-A 4757864-G-A FT16688 +
5125295-A-T 5257254-A-T FT17223 +
5507399-G-A 5639358-G-A FT17646 +
6970590-A-C 7102549-A-C FT18856 YY+
7034041-A-G 7166000-A-G FT18896 YY+
7694805-C-T 7826764-C-T FT19366 YY+
7694815-C-A 7826774-C-A FT19367 YY+
7880102-A-G 8012061-A-G FT19497 YY+
8449445-C-T 8581404-C-T BY176577 YY+
8622874-G-A 8754833-G-A FT20024 YY+
8640610-A-G 8772569-A-G FT20039 YY+
8734611-C-T 8866570-C-T BY193752 YY+
9419805-G-C 9582196-G-C FT20392 YY+
10843576-C-A FT433727 +
10988396-C-T FT439352 +
13600646-C-T 11444970-C-T FT44692 +
13812127-G-A 11691421-G-A FT20618 +
13858275-G-A 11737569-G-A FT20714 +
13973486-C-T 11852780-C-T FT20905 YY+
14050962-A-G 11930256-A-G FT20997 YY+
14193766-A-C 12073060-A-C FT21132 YY+
14194687-C-A 12073981-C-A FT21135 YY+
14229683-A-C 12108977-A-C FT21168 YY+
14923726-T-C 12811791-T-C FT21707 YY+
15584558-T-C 13472678-T-C FT22135 YY+
16454269-A-G 14342389-A-G FT22732 YY+
16468729-G-A 14356849-G-A FT22746 Y+
16512057-C-T 14400177-C-T FT22770 YY+
17107615-G-A 14995735-G-A FT23230 YY+
17428068-T-C 15316188-T-C FT23470 YY+
18159095-T-G 16047215-T-G FT24120 Y+
18383224-T-G 16271344-T-G FT24235 P6_Gap +
18394640-T-A 16282760-T-A FT24251 P6_Gap +
18673652-A-C 16561772-A-C FT24378 YY+
21334800-G-T 19172914-G-T FT25284 YY+
21455705-G-A 19293819-G-A FT25379 Y+
22465706-G-A 20303820-G-A BY221583 DYZ19 +
23162697-G-A 21000811-G-A FT26460 Y+
27903144-T-TC 25756997-T-TC P1_Y2 **
13457742-A-T 11302066-A-T **
14695992-CAAAAA-C 12584058-CAAAAA-C 30×A**
13453324-C-A 11297648-C-A **
25995050-TATATAC-T 23848903-TATATAC-T P1_Y1 **
13453364-C-A 11297688-C-A **
6339129-A-ACG 6471088-A-ACG IR3_Dst **
13338972-A-T 11183296-A-T **
3152293-A-G 3284252-A-G **
6457724-T-C 6589683-T-C **
13325040-GTTT-G 11169364-GTTT-G **
13338993-T-C 11183317-T-C **
13339002-C-G 11183326-C-G **
13339004-C-A 11183328-C-A **
13339007-G-A 11183331-G-A **
13339015-C-G 11183339-C-G **
13453331-T-TTCTAC 11297655-T-TTCTAC **
13457735-C-CCGTAT 11302059-C-CCGTAT **
13459357-A-T 11303681-A-T **
13713053-G-T 11557377-G-T **
19675898-A-C 17564018-A-C P5_Prx **
19930406-G-T 17818526-G-T P5_Prx **
22419830-C-A 20257944-C-A BY52468 DYZ19 **
13470649-T-A 11314973-T-A ***
4583115-C-A 4715074-C-A 22×T***
3910070-TAA-T 4042029-TAA-T 12×A***
21384763-GAT-G 19222877-GAT-G ***
13530079-CAAAAAAA-C,CAA 11374403-CAAAAAAA-C,CAA 24×A***
14795622-A-C 12683693-A-C ***
15562703-GAAAAA-G,GAAAA 13450823-GAAAAA-G,GAAAA 17×A***
15893678-T-C 13781798-T-C ***
16999405-C-A 14887525-C-A ***
23969674-AACACACAC-A 21823527-AACACACAC-A 20×AC***

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.