Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > DF79 > Y21423 > 9425685-T-C > Exact position not yet finalized.

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
HG01341
Manual
Edits
2776606-C-T 2908565-C-T YY+
8826677-T-TAA 8958636-T-TAA +
3778798-G-A 3910757-G-A +
4456446-G-T 4588405-G-T +
4471646-A-C 4603605-A-C +
4610865-G-C 4742824-G-C +
5013492-T-C 5145451-T-C +
5363095-G-A 5495054-G-A 12×A+
5490703-C-T 5622662-C-T +
5588610-T-A 5720569-T-A +
5692743-C-T 5824702-C-T +
5875595-C-T 6007554-C-T +
6403512-G-T 6535471-G-T +
6939109-G-T 7071068-G-T M8149 YY+
8269116-C-A 8401075-C-A YY+
9872414-G-A 10034805-G-A YY+
2892540-T-C 3024499-T-C YY+
10017102-AGG-A 10179493-AGG-A +
10019263-G-C 10181654-G-C Y+
13132135-G-A 10621621-G-A +
13305172-C-T 11149496-C-T +
13489597-C-T 11333921-C-T +
13578018-G-T 11422342-G-T +
19333250-T-TTTG 17221370-T-TTTG +
19339985-TC-T 17228105-TC-T +
21362541-AG-A 19200655-AG-A +
22483752-T-C 20321866-T-C DYZ19 +
22768231-G-A 20606345-G-A YY+
22768232-A-G 20606346-A-G YY+
22849472-G-A 20687586-G-A YY+
28739118-C-A 26592971-C-A +
3679168-C-T 3811127-C-T +
28631948-A-G 26485801-A-G Y+
6720022-A-G 6851981-A-G YY+
16769019-C-A 14657139-C-A YY+
6815964-G-C 6947923-G-C YY+
6932828-T-A 7064787-T-A ZS7628 YY+
8054133-T-C 8186092-T-C FGC17136 ZS1601 YY+
8192402-G-A 8324361-G-A YY+
8277343-G-A 8409302-G-A Y+
14015506-G-A 11894800-G-A Y+
14035944-A-G 11915238-A-G YY+
14066478-G-C 11945772-G-C YY+
14259812-C-G 12139106-C-G Y+
15111338-G-C 12999425-G-C YY+
15209482-C-T 13097568-C-T YY+
15378928-T-C 13267048-T-C Y+
15719740-T-G 13607860-T-G YY+
17401679-G-A 15289799-G-A FGC63211 YY+
28544927-G-A 26398780-G-A +
17411064-A-C 15299184-A-C YY+
17738057-C-T 15626177-C-T YY+
17760806-G-C 15648926-G-C YY+
17891410-C-T 15779530-C-T YY+
17908503-A-C 15796623-A-C YY+
18663035-A-T 16551155-A-T YY+
18782209-C-T 16670329-C-T YY+
19188202-T-A 17076322-T-A YY+
21081950-G-T 18920064-G-T YY+
21331757-G-A 19169871-G-A YY+
21445497-A-T 19283611-A-T YY13×T+
21557902-C-T 19396016-C-T YY+
21925567-T-G 19763681-T-G YY+
22829482-A-T 20667596-A-T Y78733 YY+
28803438-G-A 26657291-G-A +

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:

Kit POSITION-REF-ALT (hg19) POSITION-REF-ALT (hg38) Note
Manual19736631-T-C17624751-T-C2 reads. 1C and 1T.
Manual22317532-A-G20155646-A-G7 A reads, 6 G reads, and 1 T read which looks like it doesn't belong there.
Manual9425685-T-C9588076-T-C1C
Manual22240646-G-C20078760-G-C4G 2C

Uncertain Mutations

NGS tests don't always cover all of the Y chromosome and, even when they do, the results can be inconclusive. The following mutations don't have clear results and have been assumed to be positive or negative. For those mutations that are assumed to be positive, the assumed SNP/INDEL will likely be found on the tree in some upstream block. It is unclear if it should be placed upstream of your results or parallel to them. The situation is reversed for mutations assumed negative. Those SNPs/INDELs will likely be found on a parallel branch on the tree, and it is unclear if they should be positioned upstream. As more results come in, the ambiguity may resolve itself, or it may be necessary to consult the BAM file for your test (available from FamilyTreeDNA or FullGenomes Corp) or by direct SNP testing (Sanger Sequencing - YSEQ or FamilyTreeDNA).

SNPs/INDELs:

BlockRegionPOS-REF-ALT (hg19)POS-REF-ALT (hg38)NamesNotes
638 10037161-C-T 10199552-C-T BY28826 Uncertain, but assumed positive.
3160 14610369-C-G 12498571-C-G Y14471 Uncertain, but assumed positive.



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