Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > Z46512 > FGC20747 > BY3330 > CTS5329 > BY3331

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
5506028-C-T 5637987-C-T +
13374988-C-A 11219312-C-A +
13670627-C-T 11514951-C-T FGC32582 +
13618743-A-G 11463067-A-G +
13612082-A-G 11456406-A-G +
13501929-A-T 11346253-A-T +
13501921-T-G 11346245-T-G +
13414578-A-G 11258902-A-G +
13375817-C-T 11220141-C-T +
13292081-C-CT 11136405-C-CT +
13936262-AG-A 11815556-AG-A +
13285508-G-T 11129832-G-T +
13138438-C-A 10627924-C-A +
10077460-G-A 10239851-G-A +
10077454-C-T 10239845-C-T +
8504172-C-T 8636131-C-T Y29253 YY+
8478148-C-A 8610107-C-A S11526 YY+
8433210-G-A 8565169-G-A YY+
8088170-AT-A 8220129-AT-A +
7984061-AG-A 8116020-AG-A +
13902238-C-T 11781532-C-T YY+
14255715-C-T 12135009-C-T FT168491 Y+
7117933-C-T 7249892-C-T B312 Y+
19239099-T-TATCA 17127219-T-TATCA +
28769258-T-C 26623111-T-C Y+
23389530-TC-T 21227644-TC-T +
22444447-A-G 20282561-A-G BY30339 DYZ19 +
22205218-A-C 20043332-A-C Y+
21502807-G-T 19340921-G-T M4411 Y+
21384258-C-A 19222372-C-A YY+
21208120-G-A 19046234-G-A Y+
19377446-G-T 17265566-G-T YY+
19239091-T-TATCC 17127211-T-TATCC +
14818519-T-G 12706590-T-G YY+
19239058-C-CTATA 17127178-C-CTATA +
18772861-C-T 16660981-C-T YY+
17895173-TAA-T 15783293-TAA-T +
17453219-A-G 15341339-A-G Y+
16948612-A-C 14836732-A-C YY+
16886743-G-A 14774863-G-A YY+
16587896-A-G 14476016-A-G M12157 YY+
16312083-AG-A 14200203-AG-A +
15047903-C-A 12935994-C-A CTS3586 YY+
7618116-G-C 7750075-G-C YY+
6953200-AATAC-A 7085159-AATAC-A +
13436375-A-C 11280699-A-C +
17553374-G-A 15441494-G-A CTS7597 S4424 YY+
22810574-T-A 20648688-T-A CTS10864 Y+
21924007-T-A 19762121-T-A YY+
21447214-A-G 19285328-A-G S4419 YY+
21318898-G-T 19157012-G-T S4416 YY+
21284890-T-C 19123004-T-C S4420 YY+
21195107-A-G 19033221-A-G S4421 YY+
18770243-C-A 16658363-C-A YY+
17891622-G-A 15779742-G-A CTS8234 S4415 YY+
17366190-G-A 15254310-G-A YY+
3005225-A-G 3137184-A-G +
15792588-C-T 13680708-C-T CTS4741 YY+
15164016-G-C 13052102-G-C YY+
14755452-C-T 12643521-C-T CTS3232 YY+
7839214-C-T 7971173-C-T YY+
7704966-A-C 7836925-A-C Y+
7666444-T-A 7798403-T-A YY+
6962832-C-T 7094791-C-T S4418 CTS700 YY+
6758694-G-C 6890653-G-C CTS450 YY+
17312215-GA-G 15200335-GA-G 10×A+
24409375-C-T 22263228-C-T Y+
3443228-T-C 3575187-T-C +
6507281-A-G 6639240-A-G +
4871465-C-A 5003424-C-A FGC13074 Z19885 +
5527926-T-G 5659885-T-G +
5506479-C-T 5638438-C-T +
5497828-A-G 5629787-A-G +
5395944-C-T 5527903-C-T S9041 +
5381757-T-A 5513716-T-A +
5205744-C-T 5337703-C-T FT136458 +
5177369-T-A 5309328-T-A FT32125 +
5102309-A-G 5234268-A-G +
5062406-T-C 5194365-T-C +
4788761-C-T 4920720-C-T FT39254 +
3603536-C-G 3735495-C-G +
4751661-G-T 4883620-G-T +
4617974-G-A 4749933-G-A Y95947 BY3150FGC1891 +
4588323-T-A 4720282-T-A +
4446671-C-A 4578630-C-A +
4056389-G-A 4188348-G-A +
3964100-T-C 4096059-T-C +
3960385-T-TGG 4092344-T-TGG +
3960384-G-GTA 4092343-G-GTA +
3924392-C-T 4056351-C-T +
27758753-C-T 25612606-C-T BY3330 P1_Y2 *

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:

Manual19736631-T-C17624751-T-C3 reads, not very clean. 1C, 1G, 1 misaligned.
Manual7817005-AG-A7948964-AG-AYFull 3 reads show the deletion.
Manual17937278-A-G15825398-A-GYFull 1G
Manual22275026-A-G20113140-A-GYFull: 3A 5G
Manual27758753-C-T25612606-C-TYFull: 1C 1T
Manual22422681-C-G20260795-C-G2C 2G

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