Tree Position

R-P312/S116 > Z40481 > FGC84729 > DF99/S11987 > Z29643 > FGC847 > FGC846

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
27127501-GCTTC-G 24981354-GCTTC-G P1_g3 10×CTTC+
3902537-T-TTTTA 4034496-T-TTTTA +
6120178-T-C 6252137-T-C +
6710417-A-G 6842376-A-G FT345025 Y+
6877328-A-G 7009287-A-G YY+
7395711-A-G 7527670-A-G ZP78FGC14794 A9658 ZP78 YY+
7672719-A-G 7804678-A-G FT366896 YY+
8148863-G-A 8280822-G-A FT345556 YY+
8417319-G-C 8549278-G-C YY+
14546103-A-G 12434304-A-G Z34373 YY+
14722624-G-T 12610692-G-T YY+
15150921-C-T 13039008-C-T CTS3748 Y+
16252086-G-A 14140206-G-A FT346893 YY+
16440975-T-C 14329095-T-C FT346975 YY+
17458021-T-C 15346141-T-C YY+
17949665-C-G 15837785-C-G FT347579 YY+
18122277-C-T 16010397-C-T FT151330 YY+
18196985-T-C 16085105-T-C FT347693 YY+
18715406-T-A 16603526-T-A FT347791 YY+
18829638-A-G 16717758-A-G FTA6120 YY+
19257269-C-T 17145389-C-T FT227258 YY+
21242943-G-A 19081057-G-A FT348250 Y+
23391436-C-T 21229550-C-T FT348962 YY+
28600944-T-A 26454797-T-A CTS12519 M9416 Y+
28725439-C-A 26579292-C-A FTA9352 +
2774662-TC-T 2906621-TC-T +
2970294-G-A 3102253-G-A FT340883 +
2984994-C-A 3116953-C-A +
3080542-G-T 3212501-G-T +
3110877-C-T 3242836-C-T FT109604 +
3166554-A-T 3298513-A-T +
3369505-C-T 3501464-C-T FT366631 +
3374870-AG-A 3506829-AG-A +
3443847-G-A 3575806-G-A +
3531327-C-T 3663286-C-T FT366646 +
3879311-A-T 4011270-A-T +
4175942-T-G 4307901-T-G +
4285040-T-G 4416999-T-G +
4416549-C-T 4548508-C-T FGC7808 +
4573067-T-C 4705026-T-C FT366716 +
4632597-T-C 4764556-T-C FT366723 +
4895144-A-T 5027103-A-T FT366739 8×T+
5035557-ATT-A 5167516-ATT-A +
5096521-T-C 5228480-T-C FT366752 +
5179557-CAT-C 5311516-CAT-C +
5255347-G-A 5387306-G-A FT323285 +
5270737-G-A 5402696-G-A FT366761 +
5410823-A-G 5542782-A-G +
5634970-C-T 5766929-C-T FT366790 +
5872258-AT-A 6004217-AT-A +
5937276-ATATT-A 6069235-ATATT-A +
5962107-GTC-G 6094066-GTC-G +
6129915-A-T 6261874-A-T +
6468954-AC-A 6600913-AC-A +
6718901-G-C 6850860-G-C FT345031 YY+
6794849-G-A 6926808-G-A FT345058 YY+
7154826-C-A 7286785-C-A Y+
8403305-A-AAAT 8535264-A-AAAT +
8535202-TTG-T 8667161-TTG-T +
13257652-G-A 11101976-G-A +
13313238-G-T 11157562-G-T +
13330327-T-TAA 11174651-T-TAA +
13354858-T-TAAA 11199182-T-TAAA 14×A+
13389196-G-A 11233520-G-A +
14492790-A-C 12380987-A-C YY+
14522619-C-A 12410820-C-A Z29291 YY+
15299959-A-C 13188058-A-C Y+
15840726-T-C 13728846-T-C FT346767 YY+
16095517-A-G 13983637-A-G FT346860 Y+
16533515-CAT-C 14421635-CAT-C +
16828618-C-A 14716738-C-A YY+
17569253-AGC-A 15457373-AGC-A +
19372315-T-TAGAG 17260435-T-TAGAG +
21520230-TAGA-T 19358344-TAGA-T +
22477950-T-C 20316064-T-C FT460042 DYZ19 +
22540565-TATATATAC-T 20378679-TATATATAC-T +
22542506-G-T 20380620-G-T Y+
22696406-A-T 20534520-A-T YY+
23226305-G-A 21064419-G-A Y+
23519048-A-G 21357162-A-G Y+
24481060-G-A 22334913-G-A FT367483 +
24932892-A-AC 22786745-A-AC g1 +
28492019-T-G 26345872-T-G +
28645829-C-A 26499682-C-A +
28711504-T-TG 26565357-T-TG +
58861963-T-G 56728908-A-C +

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:

Manual13840815-C-CGAATG11720109-C-CGAATGThe reference sequence has 9 repeats of GAATG. The data has just one read aligned properly and in a suitable position to cover the whole sequence. It does show the insertion.
Manual4404325-G-A4536284-G-A3 reads, all are A. Two of the reads have mates which overlap a segment allowing these reads to be unambiguously determined to belong to the Y chromosome, rather than the nearly identical X chromosome.
Manual23245493-AT-A21083607-AT-A3 reads show the deletion.
Manual6109515-C-T6241474-C-T3C 3T