Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > DF21/S192 > Z30233 > FGC3903/S5201 > S5199 > Z246 > DF25 > DF5 > FGC15498 > CTS50

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
24551718-C-CGT 22405571-C-CGT P3_t2 20×GT+
59004463-AAAAGAAAG-A 56858316-AAAAGAAAG-A 15×AAAG+
13743926-G-A 11588250-G-A DYZ17 +
17663116-G-A 15551236-G-A YY+
14624249-G-GAA 12512450-T-A +
17663110-G-A 15551230-G-A YY+
22461631-G-A 20299745-G-A BY24525 DYZ19 +
13143253-T-C 10632739-T-C +
23951427-N-NT 21805280-N-NT +
13545333-AAG-A 11389657-AAG-A +
58845157-C-T 56745714-G-A +
58836907-C-T 56753964-G-A +
24388090-A-ATG 22241943-A-ATG +
28791753-C-T 26645606-C-T +
13139011-C-G 10628497-C-G +
58830844-A-C 56760027-T-G +
9403521-G-GTTT 9565912-G-GTTT 21×T+
13717605-C-G 11561929-C-G F18233 DYZ17 +
5941845-T-C 6073804-T-C +
14866163-A-G 12754233-A-G BY98097 YY+
14866140-C-T 12754206-C-T YY11×GT+
7361449-C-A 7493408-C-A YY17×A+
21620499-A-G 19458613-A-G BY46072 YY+
22995376-G-T 20833490-G-T YY21×T+
22185899-A-C 20024013-A-C S24093 YY+
7622068-T-G 7754027-T-G YY+
7622025-T-C 7753984-T-C YY+
18157115-C-T 16045235-C-T Y22841 Y+
2703900-T-C 2835859-T-C YY+
6676646-T-C 6808605-T-C YY+
7206681-A-C 7338640-A-C YY+
7280942-C-T 7412901-C-T M1950 YY+
8093722-T-C 8225681-T-C FT289582 YY+
8107520-T-C 8239479-T-C Z36912 YY+
8810261-G-A 8942220-G-A Y7348 YY+
14151567-T-C 12030861-T-C S3800 CTS2005 YY+
14987820-C-G 12875886-C-G YY+
15150678-A-G 13038765-A-G S3798 CTS3747 Y+
16059914-C-G 13948034-C-G Y+
16766659-T-C 14654779-T-C CTS6247 YY+
17245186-C-T 15133306-C-T CTS7024 S3795 Y+
17664472-C-T 15552592-C-T CTS7787 S3794 YY+
18157127-T-C 16045247-T-C Z4044 Y+
19016939-C-T 16905059-C-T Y+
22125321-A-G 19963435-A-G FT339622 YY+
22193802-C-T 20031916-C-T S3790 Y+
23313658-A-G 21151772-A-G S25454 YY+
28798958-TGCAG-T 26652811-TGCAG-T +
13433889-T-G 11278213-T-G +
13746532-A-C 11590856-A-C DYZ17 +
2806181-A-C 2938140-A-C YY+
3249547-G-T 3381506-G-T +
3256136-CTAT-C 3388095-CTAT-C +
3653598-T-C 3785557-T-C ZS346 +
3844796-G-A 3976755-G-A +
3845140-T-TGC 3977099-T-TGC 11×G+
4419616-G-A 4551575-G-A FT320578 +
4510382-A-T 4642341-A-T +
4726459-T-C 4858418-T-C FT321568 +
4740620-C-A 4872579-C-A BY37496 +
4740627-AG-A 4872586-AG-A +
4894693-G-T 5026652-G-T +
4894699-C-T 5026658-C-T +
4997166-C-A 5129125-C-A +
5013450-G-T 5145409-G-T +
5023001-G-A 5154960-G-A +
5023055-A-G 5155014-A-G +
5081887-T-G 5213846-T-G FTB54840 +
5082304-C-T 5214263-C-T FTB20021 +
5270689-A-T 5402648-A-T +
5270693-C-T 5402652-C-T 22×T+
5421472-A-C 5553431-A-C 4×TCCC+
5941749-A-T 6073708-A-T ZS49 +
5971660-C-T 6103619-C-T +
6007384-T-C 6139343-T-C +
6007430-T-C 6139389-T-C +
6069884-C-T 6201843-C-T FT136930 +
6413802-G-A 6545761-G-A FT326477 +
6434962-C-T 6566921-C-T +
6517830-C-T 6649789-C-T +
6980106-AT-A 7112065-AT-A +
7160076-T-C 7292035-T-C YY+
7223229-C-T 7355188-C-T Y+
7252603-A-C 7384562-A-C M1945 YY+
7258783-C-A 7390742-C-A Y+
8296263-G-A 8428222-G-A Y17×A+
8555575-G-GTTTTTT 8687534-G-GTTTTTT +
9310573-TAC-T 9472964-TAC-T +
9429693-G-A 9592084-G-A Y+
9429709-C-A 9592100-C-A Y+
9955964-A-C 10118355-A-C Y+
9955981-T-G 10118372-T-G Y+
13140304-C-G 10629790-C-G +
13143331-AT-A 10632817-AT-A +
13143393-G-C 10632879-G-C +
13206798-A-AAG 11051122-A-AAG +
13213819-GCGGA-G 11058143-GCGGA-G +
13252190-A-G 11096514-A-G +
13276019-G-A 11120343-G-A +
13289035-G-A 11133359-G-A +
13289048-C-T 11133372-C-T +
13308969-T-C 11153293-T-C +
13322455-C-CCA 11166779-C-CCA +
13323852-C-CTA 11168176-C-CTA +
13329873-G-A 11174197-G-A +
13374622-C-G 11218946-C-G FGC78503 +
13379763-G-C 11224087-G-C +
13379781-G-A 11224105-G-A +
13390795-C-A 11235119-C-A +
13390797-G-A 11235121-G-A +
13392439-A-C 11236763-A-C +
13392504-T-A 11236828-T-A +
13403436-G-A 11247760-G-A +
13413035-C-A 11257359-C-A +
13433866-C-T 11278190-C-T +
13500604-A-T 11344928-A-T +
13509295-A-G 11353619-A-G +
13509296-G-C 11353620-G-C +
13545334-AGG-A 11389658-AGG-A +
13566972-TAC-T 11411296-TAC-T +
13588222-ATAT-A 11432546-ATAT-A +
13608745-C-A 11453069-C-A FGC23625 Z18683 +
13611422-G-GA 11455746-G-GA +
13611436-C-T 11455760-C-T +
13616462-A-T 11460786-A-T +
13620868-T-A 11465192-T-A +
13624344-A-ATG 11468668-A-ATG +
13686909-ACACG-A 11531233-ACACG-A DYZ17 +
13747192-T-C 11591516-T-C DYZ17 +
13888692-T-TTG 11767986-T-TTG 9×TG+
13902906-T-C 11782200-T-C M4509 YY+
13906194-A-C 11785488-A-C Y+
13950945-TTC-T 11830239-TTC-T +
14680809-AG-A 12568875-AG-A +
14930890-G-A 12818955-G-A Z12623 YY+
15035409-G-T 12923497-G-T YY+
15200250-A-C 13088336-A-C M5673 YY+
15234909-T-C 13122995-T-C FT336015 Y+
15557123-TAATATA-T 13445243-TAATATA-T +
15557157-ATATATT-A 13445277-ATATATT-A +
15557158-TATA-T 13445278-TATA-T +
15557159-ATATT-A 13445279-ATATT-A +
15557160-TATTC-T 13445280-TATTC-T +
15557161-ATT-A 13445281-ATT-A +
15780341-A-G 13668461-A-G S264/Z156S264 Z156 YY+
16063227-C-T 13951347-C-T Y+
16237238-G-T 14125358-G-T YY+
16340147-G-A 14228267-G-A YY22×A+
16410142-G-T 14298262-G-T YY+
16572312-A-T 14460432-A-T YY+
16828625-C-A 14716745-C-A YY+
16868437-G-A 14756557-G-A YY+
17203293-A-C 15091413-A-C YY+
17203327-C-T 15091447-C-T FTB11579 YY21×T+
17383033-CAT-C 15271153-CAT-C FT8753 +
17616966-C-CAAAA 15505086-C-CAAAA 35×A+
17662047-TGTGTG-T 15550167-TGTGTG-T +
17662049-TGTG-T 15550169-TGTG-T +
17770024-T-G 15658144-T-G S20182 YY+
18109406-A-T 15997526-A-T YY+
18296619-T-A 16184739-T-A P6_Prx +
18565278-TTTA-T 16453398-TTTA-T +
18565281-A-AT 16453401-A-AT +
18588201-G-A 16476321-G-A Z25333 YY+
18718724-T-TATCC 16606844-T-TATCC +
18830304-TAC-T 16718424-TAC-T +
19189430-C-CTTTT 17077550-C-CTTTT 35×T+
19210905-C-A 17099025-C-A Y+
19293851-C-T 17181971-C-T FT24852 YY+
21227374-TC-T 19065488-TC-T +
21251812-CA-C 19089926-CA-C +
21464179-A-AGAAGGAAG 19302293-A-AGAAGGAAG +
21477809-GAAAA-G 19315923-GAAAA-G +
21700595-G-A 19538709-G-A YY17×A+
21720375-T-G 19558489-T-G YY+
22167919-T-C 20006033-T-C YY+
22319024-TAAGA-T 20157138-TAAGA-T DYZ19 +
22476631-T-A 20314745-T-A BY191964 DYZ19 +
22476643-T-G 20314757-T-G BY45509 DYZ19 +
22962008-G-GTTT 20800122-G-GTTT 27×T+
22996966-TGG-T 20835080-TGG-T +
23098852-G-A 20936966-G-A YY+
23293521-C-T 21131635-C-T YY+
23311196-T-C 21149310-T-C M9384 YY+
23316060-A-ATTTT 21154174-A-ATTTT +
23899718-G-A 21737832-G-A +
23899726-C-A 21737840-C-A +
24782770-T-G 22636623-T-G ZS5698 P3_b2 +
25173627-C-T 23027480-C-T g1 +
25173629-T-C 23027482-T-C g1 +
28534999-C-T 26388852-C-T +
28545696-C-CAAA 26399549-C-CAAA 26×A+
58887928-C-A 56702943-G-T +
58971884-GTACATATA-G 56825737-GTACATATA-G +
58971885-T-TAC 56825738-T-TAC +
59019545-CACACACAA-C 56873398-CACACACAA-C +
59019546-ACACACAAG-A 56873399-ACACACAAG-A +
59019547-CACACAA-C 56873400-CACACAA-C +
59019551-CAA-C 56873404-CAA-C +
59021932-T-TTC 56875785-T-TTC +
59030171-A-AG 56884024-A-AG +

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:

HG0024218393814-A-G16281934-A-GChecked BAM File.
HG0024216342413-A-T14230533-A-TChecked BAM File.
HG0024222221771-G-T20059885-G-TChecked BAM File. The two reads with the ancestral value don't necessarily look like they belong there.
HG0024225324200-T-G23178053-T-GChecked BAM File. There are just two reads, and both are G.