Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z198 > CTS4188 > S14445 > S11121 > BY27671 > S11475 > BY3274 > PH4190 > Z29707 > BY35592

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
17007092-CTA-C 14895212-CTA-C +
13254019-TC-T 11098343-TC-T +
16635267-A-G 14523387-A-G M8505 S18585 YY+
16242388-G-T 14130508-G-T YY+
15673254-T-A 13561374-T-A Y+
14373438-A-C 12252734-A-C YY+
13618226-T-G 11462550-T-G +
13389990-A-G 11234314-A-G +
13389962-A-G 11234286-A-G 13×TG+
13276504-G-A 11120828-G-A +
13222768-A-T 11067092-A-T +
17304010-T-G 15192130-T-G YY+
13222616-GGAGA-G 11066940-GGAGA-G +
9516725-T-C 9679116-T-C +
8702763-A-C 8834722-A-C YY+
8377942-A-ACG 8509901-A-ACG +
8377941-C-CAA 8509900-C-CAA +
7730431-G-GC 7862390-G-GC +
7643729-G-T 7775688-G-T YY+
7569382-G-T 7701341-G-T YY+
7536337-C-CAAA 7668296-C-CAAA 28×A+
17160359-G-A 15048479-G-A Y+
17769212-T-C 15657332-T-C YY+
7401154-TG-T 7533113-TG-T +
22577950-TG-T 20416064-TG-T +
58834218-G-T 56756653-C-A +
58823348-A-G 56767523-T-C +
28747705-A-ATTT 26601558-A-ATTT 27×T+
28642807-CAG-C 26496660-CAG-C +
28539167-T-A 26393020-T-A M4647 +
28539156-A-T 26393009-A-T +
24387918-C-A 22241771-C-A +
23899701-G-A 21737815-G-A +
22446621-G-A 20284735-G-A BY52709 DYZ19 +
18612749-ATG-A 16500869-ATG-A +
22440322-G-C 20278436-G-C DYZ19 +
22270000-G-T 20108114-G-T DYZ19 +
22269999-A-C 20108113-A-C DYZ19 +
22262982-G-A 20101096-G-A FT165128 DYZ19 +
22228512-G-C 20066626-G-C FGC28388 DYZ19 +
22228465-G-C 20066579-G-C DYZ19 +
21353282-C-T 19191396-C-T FT13805 YY+
19305554-C-CG 17193674-C-CG +
19305551-G-GC 17193671-G-GC +
7438252-G-C 7570211-G-C Y+
7311382-A-C 7443341-A-C YY+
16679088-C-T 14567208-C-T YY+
9426725-C-T 9589116-C-T YY+
28549587-C-A 26403440-C-A +
21984256-C-T 19822370-C-T YY+
21116406-G-A 18954520-G-A BY154950 YY+
19520501-A-G 17408621-A-G YY+
19037316-T-A 16925436-T-A BY125685 YY+
18079753-C-T 15967873-C-T Y+
17877478-T-A 15765598-T-A YY+
15687681-T-C 13575801-T-C FT13211 YY+
2866167-T-C 2998126-T-C Y+
13618164-C-A 11462488-C-A +
2694457-G-A 2826416-G-A Y23409 YY+
21881055-C-A 19719169-C-A YY13×A+
4351388-T-A 4483347-T-A +
19442403-C-A 17330523-C-A YY+
4351403-A-C 4483362-A-C FT129806 +
58917657-N-A 56673214-N-T +
13389554-G-A 11233878-G-A +
7211965-A-C 7343924-A-C YY+
18612747-GTA-G 16500867-GTA-G +
14532749-G-C 12420950-G-C Y+
2685623-C-T 2817582-C-T M5575 YY+
7310721-C-A 7442680-C-A YY+
4982349-C-T 5114308-C-T +
7258780-AG-A 7390739-AG-A +
7216349-A-C 7348308-A-C YY+
6998009-T-C 7129968-T-C YY+
6406214-T-C 6538173-T-C +
6388513-G-GA 6520472-G-GA +
6149867-GTT-G 6281826-GTT-G IR3_Dst +
5937660-A-ACC 6069619-A-ACC +
5178082-AG-A 5310041-AG-A +
5165948-G-A 5297907-G-A +
4932973-G-T 5064932-G-T Z22399 +
2871378-C-A 3003337-C-A YY+
4932745-C-T 5064704-C-T +
4403580-T-C 4535539-T-C +
3902263-G-GTAAACA 4034222-G-GTAAACA +
3726883-G-C 3858842-G-C FT11678 +
3557391-TTC-T 3689350-TTC-T +
3557390-GTTC-G 3689349-GTTC-G +
3138819-G-A 3270778-G-A +
3032464-G-T 3164423-G-T +
3004917-A-G 3136876-A-G +
59019549-CACAA-C 56873402-CACAA-C FGC80623 +

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:

Manual19942076-T-C17830196-T-C3T, but 1A 1G at the opposite position, 20237701.
Manual22474912-G-C20313026-G-C6C 1G
Manual25893780-G-A23747633-G-A4A 3G
Manual22285505-T-A20123619-T-A8T 1A
Manual22362063-G-C20200177-G-C2G 2C
Manual27022001-A-C24875854-A-C1A 4C
Manual25935747-T-C23789600-T-C3T 1C
Manual18027435-TAA-T15915555-TAA-T3 reads cover this deletion and all are positive.
Manual22444525-T-A20282639-T-A5A 1G 2T
Manual22281020-G-A20119134-G-A8G 4A
Manual22275699-A-G20113813-A-G10A 4G
Manual22275680-G-T20113794-G-T12G 4T

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