Tree Position

A0-T-YP2191 > P305[A1] > L413/PF1409/V31 > M168/PF1416[CT] > P143[CF] > M89/PF2746[F] > F1329/M3658[GHI > F929[HIJK] > IJK > K > P295[P] > M207[R] > M173[R1] > L146/M420[R1a] > M459 > M198 > M417 > Z645 > Z93 > 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
14906008-T-C 12794075-T-C S3413 CTS3412 Z2475 YY+
21185780-C-T 19023894-C-T S3422 YY+
16876834-T-C 14764954-T-C CTS6407 S3416 YY+
17295658-G-A 15183778-G-A CTS7114 YY+
17324082-AGAAG-A 15212202-AGAAG-A 5×GAAG+
17410423-C-A 15298543-C-A CTS7297 S3418 YY+
17495584-G-C 15383704-G-C S3419 CTS7463 YY+
18033923-G-A 15922043-G-A Z2477 CTS8448 S4520 YY+
18730705-C-T 16618825-C-T Y38013 Y+
18890300-T-C 16778420-T-C CTS9431 S3420 YY+
19220804-C-T 17108924-C-T CTS10041 YY+
19262425-T-C 17150545-T-C F2997 YY+
21795736-C-T 19633850-C-T Y+
16084880-A-T 13973000-A-T Y+
21823286-G-A 19661400-G-A S3424 YY+
21932820-C-T 19770934-C-T Y37899 YY+
22228587-C-A 20066701-C-A BY52101 DYZ19 +
22228588-C-T 20066702-C-T DYZ19 +
22271060-G-A 20109174-G-A BY41471 DYZ19 +
22467279-G-A 20305393-G-A DYZ19 +
22473236-T-C 20311350-T-C DYZ19 +
22827098-C-A 20665212-C-A Y37900 YY+
22973515-A-G 20811629-A-G S3425 CTS11140 YY+
23048199-G-A 20886313-G-A Y37901 Y+
23974205-T-C 21828058-T-C Z2478 S3426 Y+
16574657-A-G 14462777-A-G CTS5959 Y+
15981656-A-C 13869776-A-C Y37898 YY+
2657349-T-C 2789308-T-C Z2469 S3403 CTS6 YY+
9898980-T-C 10061371-T-C Z2473 S3408 Y+
2670160-G-T 2802119-G-T CTS17 S3404 Y+
5123609-G-T 5255568-G-T +
5613782-A-G 5745741-A-G +
6954059-C-T 7086018-C-T Y37895 YY+
7004736-T-G 7136695-T-G M12196 FGC22264 Y+
7074607-G-A 7206566-G-A Z2471 YY+
7376974-T-G 7508933-T-G Y37896 YY+
7976938-C-G 8108897-C-G Y37897 YY+
8529228-C-T 8661187-C-T S3406 YY+
8605676-C-A 8737635-C-A Z2472 FGC99 F1345 YY+
9992450-T-C 10154841-T-C Y+
15771025-A-T 13659145-A-T Y2622 S4575 M12202 YY+
10059252-C-G 10221643-C-G +
13515251-A-G 11359575-A-G +
13625264-T-A 11469588-T-A S3409 +
13693710-A-G 11538034-A-G +
13868295-G-A 11747589-G-A +
13945601-T-C 11824895-T-C Y+
14015086-C-T 11894380-C-T Y+
14236070-T-G 12115364-T-G CTS2253 Z2474 M582 YY+
14579616-G-A 12467816-G-A Y2621 FGC13805 M12201 YY+
15062207-T-C 12950299-T-C Z2476 S3414 CTS3605 YY+
15557420-G-A 13445540-G-A YY+
28790415-G-C 26644268-G-C BY30076 +

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.

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