Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z41150 > Z49 > Z142/S211 > Z51 > Z50 > Z57 > Y12119 > Z52 > CTS9462 > 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
23976848-TTG-T 21830701-TTG-T 8×TG+
9310538-TCA-T 9472929-TCA-T +
16340146-AG-A 14228266-AG-A +
16197137-T-G 14085257-T-G ZS7970 YY+
16172130-C-T 14060250-C-T FT301330 Y+
15691983-T-A 13580103-T-A CTS4521 YY+
15122158-A-G 13010245-A-G F19569 YY+
15047688-C-T 12935779-C-T YY+
14667694-AT-A 12555759-AT-A +
13272119-A-AAAAT 11116443-A-AAAAT 7×AAAT+
13267473-T-G 11111797-T-G +
13133744-G-T 10623230-G-T +
9994798-A-C 10157189-A-C FT165197 Y+
9030477-A-AG 9192868-A-AG +
17286352-G-A 15174472-G-A CTS7096 YY+
8986649-C-T 9149040-C-T +
8986647-C-T 9149038-C-T +
8649789-C-A 8781748-C-A YY13×A+
8221227-AC-A 8353186-AC-A +
8146079-T-G 8278038-T-G FT300345 YY+
8085515-TC-T 8217474-TC-T +
7414304-AGG-A 7546263-AGG-A +
7165572-C-A 7297531-C-A YY+
7165286-G-T 7297245-G-T FTA7214 YY+
6613151-C-G 6745110-C-G +
6130334-G-A 6262293-G-A +
16898888-ATTAT-A 14787008-ATTAT-A 6×TTAT+
17304733-TACAC-T 15192853-TACAC-T +
6010357-C-A 6142316-C-A +
21482743-C-T 19320857-C-T YY4×TTTCT+
28720126-C-T 26573979-C-T +
24447211-C-G 22301064-C-G Y+
23969673-T-TAA 21823526-T-TAA +
23899401-C-CGT 21737515-C-CGT 17×GT+
22902100-T-A 20740214-T-A YY+
22484671-C-A 20322785-C-A DYZ19 +
22464607-G-T 20302721-G-T DYZ19 +
22269120-G-A 20107234-G-A DYZ19 +
22269114-T-C 20107228-T-C DYZ19 +
22269058-G-C 20107172-G-C DYZ19 +
21504254-TA-T 19342368-TA-T +
21482738-C-T 19320852-C-T YY+
17332772-ATCG-A 15220892-ATCG-A +
21172023-T-G 19010137-T-G YY+
21134911-A-C 18973025-A-C YY+
20557658-TGC-T 18395772-TGC-T P5_Dst +
19187367-G-A 17075487-G-A Y+
19052439-G-A 16940559-G-A YY+
19042178-G-A 16930298-G-A Y+
18982546-T-TCA 16870666-T-TCA +
18889988-G-T 16778108-G-T FT302004 YY+
18130890-A-T 16019010-A-T Z34608 Y+
17952640-C-T 15840760-C-T YY8×T+
17713850-C-CTTT 15601970-C-CTTT 23×T+
17453031-C-A 15341151-C-A Y+
6093307-G-A 6225266-G-A +
5991855-G-A 6123814-G-A FT325745 +
13314034-A-C 11158358-A-C +
2886641-A-G 3018600-A-G FT299939 YY+
16861574-A-C 14749694-A-C FT301494 YY+
16517411-T-C 14405531-T-C YY+
14447009-T-C 12326282-T-C FT300931 Y+
13994574-G-T 11873868-G-T FT76143 Y+
8520792-A-G 8652751-A-G FT300466 YY+
8500996-C-T 8632955-C-T FT300460 YY+
8339643-G-T 8471602-G-T FT300409 YY+
7733520-G-A 7865479-G-A FT300236 YY+
7703673-T-A 7835632-T-A FT300219 YY+
7682803-A-C 7814762-A-C FT300210 YY+
6659092-A-C 6791051-A-C FT299957 YY+
2720508-T-C 2852467-T-C CTS82 YY+
17380184-C-T 15268304-C-T FT301619 YY+
9040197-G-A 9202588-G-A Z17893 Y+
9040207-A-T 9202598-A-T F17669 Y16×T+
22715168-G-A 20553282-G-A YY+
13219525-T-G 11063849-T-G +
21691570-A-T 19529684-A-T M222M2626 S629 YY+
16215720-A-G 14103840-A-G Y+
22017853-T-G 19855967-T-G YY+
14319328-C-T 12198622-C-T CTS2469 YY+
6347733-A-G 6479692-A-G BY29004 +
28794922-A-G 26648775-A-G +
18354240-A-G 16242360-A-G P6_Prx +
17256128-T-C 15144248-T-C FT301591 YY+
17632030-A-C 15520150-A-C FT301684 YY+
5905932-T-G 6037891-T-G +
2950242-TAC-T 3082201-TAC-T +
5047485-T-C 5179444-T-C FT322542 +
4983777-C-T 5115736-C-T 22×T+
4983763-T-A 5115722-T-A +
4834238-A-G 4966197-A-G +
4778009-T-A 4909968-T-A +
4394521-T-G 4526480-T-G FT320510 +
4389744-C-T 4521703-C-T +
4353254-T-C 4485213-T-C FT320367 +
4276649-T-C 4408608-T-C FT320111 +
3922947-A-G 4054906-A-G +
3568153-A-C 3700112-A-C +
2810364-G-T 2942323-G-T YY+
17895057-G-T 15783177-G-T FT301771 YY+
2810322-A-T 2942281-A-T YY+
5400487-TG-T 5532446-TG-T +
7263862-A-C 7395821-A-C YY+
22902573-T-G 20740687-T-G YY+
22651795-T-A 20489909-T-A FT302672 YY+
21809248-C-A 19647362-C-A FT147687 YY+
21561074-A-G 19399188-A-G FT302416 YY+
21508937-G-A 19347051-G-A FT48262 YY+
21254804-C-T 19092918-C-T FT302274 YY+
19002383-G-A 16890503-G-A FT302042 YY+
18701550-T-C 16589670-T-C CTS9125 YY+
18089169-T-C 15977289-T-C CTS8575 Y+
28805074-T-C 26658927-T-C BY151801 +

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:

Manual23718872-G-A21556986-G-A1G 2A
Manual22220675-T-G20058789-T-G3G 2T
Manual6286531-A-G6418490-A-G3G 2A

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