Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > Z193 > Z40483 > CTS2617 > 3079273-C-T

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
16978189-G-A 14866309-G-A CTS6557 Y+
16831229-A-AT 14719349-A-AT 8×T+
13392904-G-A 11237228-G-A +
13392883-G-A 11237207-G-A +
7852987-A-G 7984946-A-G FT334084 YY+
14090854-C-A 11970148-C-A CTS1839 YY+
14199389-A-T 12078683-A-T PH990 YY+
14617067-G-A 12505265-G-A CTS3021 Y+
14891978-T-G 12780044-T-G BY206840 YY+
15009545-C-A 12897630-C-A CTS3557 YY+
16371118-A-T 14259238-A-T BY107309 YY15×T+
16559002-T-A 14447122-T-A CTS5929 YY+
16631864-C-T 14519984-C-T CTS6042 YY+
16991569-T-C 14879689-T-C PH2740 YY+
17140647-G-A 15028767-G-A PH2856 YY+
17220594-C-T 15108714-C-T Y24684 Y+
17455859-C-G 15343979-C-G Z30042 YY+
17526896-G-T 15415016-G-T CTS7545 YY+
17605464-C-T 15493584-C-T CTS7670 YY+
17622855-C-T 15510975-C-T CTS7709 M5494 YY+
18572584-T-A 16460704-T-A Z29231 YY+
18744930-T-G 16633050-T-G FT338220 YY+
18872726-A-C 16760846-A-C FT291502 YY+
18924606-C-T 16812726-C-T Y103059 YY+
19083321-T-A 16971441-T-A Y+
21410243-T-G 19248357-T-G Y24685 YY+
21443267-T-C 19281381-T-C YY+
21846051-GA-G 19684165-GA-G 8×A+
22125769-C-T 19963883-C-T FGC36625FT124356 YY+
22784669-G-T 20622783-G-T ZS1172 YY+
22928321-A-G 20766435-A-G CTS11068 YY+
23524543-G-C 21362657-G-C FT292570 YY+
13510943-T-C 11355267-T-C +
2738780-T-TTTA 2870739-T-TTTA +
2934179-G-A 3066138-G-A +
3192913-T-C 3324872-T-C +
3443861-G-C 3575820-G-C +
4316122-T-C 4448081-T-C K66 +
4331543-C-A 4463502-C-A +
4682420-A-G 4814379-A-G +
4790648-AC-A 4922607-AC-A +
4890657-T-C 5022616-T-C +
5346046-A-G 5478005-A-G +
5691968-T-C 5823927-T-C +
5765927-C-T 5897886-C-T +
6060791-T-C 6192750-T-C +
6402722-A-G 6534681-A-G +
7002523-C-T 7134482-C-T Y+
7002524-A-G 7134483-A-G Y+
7058085-G-T 7190044-G-T FTA51572 YY+
7590696-T-G 7722655-T-G YY+
7683468-A-T 7815427-A-T YY+
8577264-A-G 8709223-A-G YY+
8706660-C-T 8838619-C-T YY+
8782101-T-G 8914060-T-G M1321 YY+
9342738-A-AG 9505129-A-AG +
9654335-GA-G 9816726-GA-G IR3_Prx +
9999304-T-G 10161695-T-G Y+
9999322-A-G 10161713-A-G Y+
10068130-G-A 10230521-G-A +
13256858-G-T 11101182-G-T 18×T+
13354496-T-G 11198820-T-G +
13414248-T-C 11258572-T-C +
13414395-A-G 11258719-A-G +
13414546-C-A 11258870-C-A +
13460979-A-T 11305303-A-T +
13636131-A-G 11480455-A-G +
13846460-G-A 11725754-G-A FT190455 +
14198967-TAC-T 12078261-TAC-T +
14360436-C-A 12239731-C-A YY+
14776923-C-A 12664992-C-A YY15×A+
15065776-G-A 12953868-G-A CTS3610 YY+
15324003-A-G 13212121-A-G MF1491 YY+
15590078-G-A 13478198-G-A YY+
15947950-TC-T 13836070-TC-T +
16088118-G-A 13976238-G-A CTS5253 Y+
16576367-T-C 14464487-T-C PH2375 YY+
16658781-T-C 14546901-T-C Y+
16960667-AAC-A 14848787-AAC-A +
17006421-C-T 14894541-C-T FT290953 YY+
17153148-C-A 15041268-C-A YY+
17175506-G-A 15063626-G-A CTS6892 M4840 YY+
17659929-C-A 15548049-C-A YY+
17668513-T-TTTTTG 15556633-T-TTTTTG 7×TTTG+
17676044-TC-T 15564164-TC-T +
17770024-T-G 15658144-T-G S20182 YY+
19029208-A-T 16917328-A-T Y+
19103898-G-T 16992018-G-T YY+
19475139-C-T 17363259-C-T Y104883 YY+
20810695-TC-T 18648809-TC-T P4_Gap +
21455949-G-T 19294063-G-T YY+
21892364-A-G 19730478-A-G FT348512 YY+
22460669-T-A 20298783-T-A Z21891 DYZ19 +
22520787-T-TAA 20358901-T-TAA +
22530201-A-G 20368315-A-G FT103069 Y+
22587852-G-T 20425966-G-T YY+
22737117-T-G 20575231-T-G YY+
22972501-T-A 20810615-T-A YY+
22972502-T-G 20810616-T-G YY+
22972505-A-C 20810619-A-C YY+
23240598-G-T 21078712-G-T Y29152 Y+
23292150-G-T 21130264-G-T YY+
23322005-T-A 21160119-T-A YY+
23411411-G-C 21249525-G-C CTS11999 YY+
24127009-G-C 21980862-G-C P3_b1 +
24485667-C-CA 22339520-C-CA +
24873794-G-A 22727647-G-A g1 +
26526565-TG-T 24380418-TG-T P1_Y1 +
27484483-C-G 25338336-C-G P1_Y2 +
28604285-T-G 26458138-T-G +
28756605-A-G 26610458-A-G Y+
28785704-G-T 26639557-G-T +
58999442-T-C 56853295-T-C +
59033258-A-AGTT 56887111-A-AGTT 10×GTT+

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:

Manual22425315-C-T20263429-C-T4C 1T
Manual22440651-A-G20278765-A-G2 reads -- 1 A and 1 G.