Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF63/S522 > CTS6919 > b38:22282103T>A

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
22250221-T-A 20088335-T-A DYZ19 +
17064178-T-G 14952298-T-G M4837 YY+
15969976-AG-A 13858096-AG-A +
16406824-G-T 14294944-G-T YY+
16583257-C-G 14471377-C-G YY+
16739151-G-C 14627271-G-C Y+
16828612-G-A 14716732-G-A YY+
16890687-A-T 14778807-A-T YY+
17500836-T-G 15388956-T-G M8509 Y+
15358791-G-A 13246911-G-A S17041 YY+
18239758-A-C 16127878-A-C Y+
18756817-T-TTG 16644937-T-TTG +
18767202-TG-T 16655322-TG-T +
19010468-T-A 16898588-T-A Y103365 YY+
19138143-A-T 17026263-A-T FTB37804 Y+
19143142-TG-T 17031262-TG-T +
19472667-G-C 17360787-G-C YY+
15799114-C-T 13687234-C-T M8143 YY14×CCTT+
15299959-A-C 13188058-A-C Y+
21037683-A-C 18875797-A-C Y+
14026940-TTTGA-T 11906234-TTTGA-T +
13620795-T-A 11465119-T-A +
13621477-G-C 11465801-G-C +
13635244-T-C 11479568-T-C +
13657139-C-T 11501463-C-T Z9018 +
13962042-C-CTTT 11841336-C-CTTT 28×T+
14025670-A-G 11904964-A-G A290A290 YY+
14025710-A-G 11905004-A-G YY+
14143424-A-AAC 12022718-A-AAC +
14884737-G-A 12772803-G-A YY+
14334340-G-GT 12213635-G-GT +
14430299-T-G 12309572-T-G Y+
14512657-C-G 12400862-C-G Y+
14532773-A-C 12420974-A-C Y+
14533046-A-C 12421247-A-C HU508 Y+
14612378-T-C 12500584-T-C BY23189 YY+
14884734-G-A 12772800-G-A BY98247 YY+
19575889-T-C 17464009-T-C P5_Prx Y+
21096451-T-C 18934565-T-C Y+
13478859-A-C 11323183-A-C +
58842471-C-T 56748400-G-A +
28597828-A-C 26451681-A-C +
28639078-A-C 26492931-A-C +
28664864-T-G 26518717-T-G +
28664876-T-C 26518729-T-C +
28683725-T-G 26537578-T-G +
58842799-CAAGGG-C 56748066-GCCCTT-G +
28545776-T-G 26399629-T-G +
58855573-A-G 56735298-T-C +
58855577-A-C 56735294-T-G +
58859650-T-C 56731221-A-G +
58863028-C-G 56727843-G-C +
58971884-GTACATATA-G 56825737-GTACATATA-G +
58976191-A-ACTCCC 56830044-A-ACTCCC +
58976196-A-ACTCCC 56830049-A-ACTCCC +
28597821-A-C 26451674-A-C +
21234631-T-G 19072745-T-G YY+
22962202-G-T 20800316-G-T YY+
21464232-G-GAAAC 19302346-G-GAAAC +
21965835-C-A 19803949-C-A Y+
22165238-C-A 20003352-C-A YY+
22463699-A-G 20301813-A-G DYZ19 +
22463704-T-A 20301818-T-A DYZ19 +
22474258-T-C 20312372-T-C ZS1827 DYZ19 +
22950214-TG-T 20788328-TG-T +
22991983-T-G 20830097-T-G FT292382 YY+
24386624-CTA-C 22240477-CTA-C +
23792045-C-T 21630159-C-T Y+
23951422-N-A 21805275-N-A +
23951423-N-T 21805276-N-T +
23951424-N-G 21805277-N-G +
23951425-N-G 21805278-N-G +
23951426-N-C 21805279-N-C +
23962993-A-C 21816846-A-C Y+
13499890-A-G 11344214-A-G +
13462284-T-C 11306608-T-C +
2649675-C-G 2781634-C-G Y+
21196229-T-C 19034343-T-C FT291825 YY+
16853857-G-A 14741977-G-A FT290905 YY+
17707227-A-T 15595347-A-T FT291175 YY+
17812577-C-T 15700697-C-T CTS8050 Y+
18117285-C-G 16005405-C-G FT291323 YY+
18848594-G-T 16736714-G-T FT291494 Y+
21144431-TCT-AAA 18982545-TCT-AAA +
23860637-C-A 21698751-C-A FT292646 Y+
14313866-A-T 12193160-A-T Y+
23866623-G-A 21704737-G-A FT97306 Y+
6895044-AG-A 7027003-AG-A +
22970326-A-T 20808440-A-T YY+
23315713-C-CTTT 21153827-C-CTTT 20×T+
16059314-C-A 13947434-C-A Y+
28600408-T-C 26454261-T-C FTA47319 +
16505988-C-CTTT 14394108-C-CTTT 31×T+
14668000-C-T 12556066-C-T FT168666 YY+
14120018-A-G 11999312-A-G S3687 CTS1912 Y+
3171935-C-T 3303894-C-T +
14213757-G-A 12093051-G-A M10638 YY13×AGAA+
19201339-A-C 17089459-A-C YY+
58828807-C-T 56762064-G-A +
22238401-A-C 20076515-A-C DYZ19 +
58845443-G-C 56745428-C-G +
6918566-AG-A 7050525-AG-A +
9403521-G-GTTT 9565912-G-GTTT 21×T+
6648613-C-T 6780572-C-T YY27×T+
22995376-G-T 20833490-G-T YY21×T+
13910493-C-A 11789787-C-A FT289991 Y+
22674121-C-A 20512235-C-A YY14×A+
18146391-G-A 16034511-G-A CTS8681 YY+
22766548-T-A 20604662-T-A YY10×A+
7370029-C-A 7501988-C-A FT289374 Y+
7428231-A-C 7560190-A-C YY+
8307446-T-C 8439405-T-C FT289643 YY+
13909599-C-A 11788893-C-A YY14×A+
2949499-T-C 3081458-T-C FT315524 +
3247284-C-T 3379243-C-T +
13462276-T-C 11306600-T-C +
13245759-C-T 11090083-C-T +
8901990-TC-T 9033949-TC-T +
9162651-T-G 9325042-T-G +
9428966-T-C 9591357-T-C Y+
9839582-T-G 10001973-T-G YY+
9906675-A-G 10069066-A-G FT328386 Y+
10004866-TGC-T 10167257-TGC-T +
10031595-G-C 10193986-G-C Y+
13254019-TC-T 11098343-TC-T +
8498354-AG-A 8630313-AG-A +
13255133-G-T 11099457-G-T +
13256619-G-C 11100943-G-C +
13258092-T-C 11102416-T-C +
13285518-A-G 11129842-A-G +
13309804-C-T 11154128-C-T +
13338637-T-C 11182961-T-C +
13354496-T-G 11198820-T-G +
8555545-T-TG 8687504-T-TG 5×TTTTTG+
8125049-A-AAAGC 8257008-A-AAAGC +
3275738-G-GC 3407697-G-GC +
4973687-AG-A 5105646-AG-A +
3443608-C-T 3575567-C-T +
3603491-A-T 3735450-A-T 24×T+
3833761-GAT-G 3965720-GAT-G +
3909144-A-T 4041103-A-T +
3970985-C-T 4102944-C-T 17×T+
4583114-TC-T 4715073-TC-T +
4708443-T-G 4840402-T-G +
5178060-TGC-T 5310019-TGC-T +
8110404-C-T 8242363-C-T F1101 YY+
5573583-C-A 5705542-C-A +
5716882-G-A 5848841-G-A +
5904069-G-C 6036028-G-C +
6171494-T-G 6303453-T-G IR3_Dst +
6584737-C-G 6716696-C-G FT326903 +
7258780-AG-A 7390739-AG-A +
7985128-G-A 8117087-G-A Y+
58976214-C-CCATTG 56830067-C-CCATTG +

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:

HG002432818621-G-A2950580-G-AChecked BAM File.
HG0024316107330-A-G13995450-A-GChecked BAM File.
HG0024322223807-C-T20061921-C-TChecked BAM File.
HG0024322226951-A-G20065065-A-GChecked BAM File.
HG0024322239044-A-G20077158-A-GChecked BAM File.
HG0024322453906-T-A20292020-T-AChecked BAM File.
HG0024322478814-C-A20316928-C-AChecked BAM File.
HG0024322297447-T-C20135561-T-CChecked BAM File, and it looks like it probably has mixed reads.
HG002433279698-AAAAT-A3411657-AAAAT-AChecked BAM File.
Manual16107330-A-G13995450-A-G5A 3G

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