Tree Position

R-P312/S116 > L238/S182 > Z2245 > Z2247 > Y29874

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
HG00157
Manual
Edits
18892323-A-G 16780443-A-G YY+
13568022-C-A 11412346-C-A +
17788200-C-T 15676320-C-T Y+
17561983-G-T 15450103-G-T YY+
17259728-C-T 15147848-C-T Y+
16924250-G-T 14812370-G-T YY+
16460826-C-G 14348946-C-G YY+
16181590-G-A 14069710-G-A PR5722 Y+
15683578-C-T 13571698-C-T Z9212 Y+
14629851-G-A 12517920-G-A Z2103Y4371 Z8128 M12149 YY+
14495604-G-T 12383801-G-T YY+
13543629-C-A 11387953-C-A +
18029869-C-G 15917989-C-G Y+
13518649-T-C 11362973-T-C +
13518645-T-G 11362969-T-G +
13339313-C-A 11183637-C-A +
13294580-T-G 11138904-T-G +
13141961-C-T 10631447-C-T +
9901453-G-C 10063844-G-C Y+
9831939-G-A 9994330-G-A YY+
9794763-A-G 9957154-A-G Y+
8994257-A-G 9156648-A-G Y+
8773674-C-T 8905633-C-T Y6681 Z3979 YY+
17906864-T-G 15794984-T-G YY+
18076003-T-C 15964123-T-C M1960 YY+
7736507-G-A 7868466-G-A YY+
28711259-C-T 26565112-C-T Y+
13302979-ATGGATC-A 11147303-ATGGATC-A +
4571068-AC-A 4703027-AC-A +
3970481-TG-T 4102440-TG-T +
3115733-CG-C 3247692-CG-C +
14399072-T-TG 12278368-T-TG +
9798080-TC-T 9960471-TC-T +
9510731-T-TCC 9673122-T-TCC +
2827907-TTC-T 2959866-TTC-T +
24479285-T-TA 22333138-T-TA 9×A+
22771340-CT-C 20609454-CT-C 10×T+
26834536-G-A 24688389-G-A P1_g2 +
18155990-T-A 16044110-T-A Y+
23998677-G-A 21852530-G-A Y+
23399858-G-T 21237972-G-T Z38482 Y+
23117686-G-C 20955800-G-C YY+
22438807-C-G 20276921-C-G DYZ19 +
22361840-C-T 20199954-C-T DYZ19 +
21136260-T-C 18974374-T-C YY+
19462882-A-C 17351002-A-C CTS10452 Y+
19453426-T-G 17341546-T-G YY+
18539746-G-T 16427866-G-T Y+
18195719-A-T 16083839-A-T YY+
8680838-T-C 8812797-T-C YY+
6891628-G-T 7023587-G-T YY+
13517436-C-A 11361760-C-A +
23538238-G-T 21376352-G-T YY+
58862363-G-C 56728508-C-G +
13504062-A-G 11348386-A-G +
13482989-C-A 11327313-C-A +
3172144-G-C 3304103-G-C +
28759466-T-G 26613319-T-G Y+
5927678-T-G 6059637-T-G +
13339812-G-A 11184136-G-A +
14386294-C-A 12265590-C-A Y+
28496488-T-C 26350341-T-C Y+
23446156-T-A 21284270-T-A YY+
3164640-T-C 3296599-T-C PF26 L412 +
22758481-T-C 20596595-T-C YY+
21825852-G-T 19663966-G-T Z27736 YY+
19118414-T-A 17006534-T-A YY+
18642558-A-T 16530678-A-T YY+
13972306-C-T 11851600-C-T Y+
8578432-T-G 8710391-T-G A1943 YY+
6884419-C-T 7016378-C-T YY+
6716745-T-A 6848704-T-A YY+
22114325-A-G 19952439-A-G Y+
14725963-A-C 12614031-A-C M4183 Y+
2838509-C-A 2970468-C-A YY+
4278793-T-A 4410752-T-A +
6615892-C-T 6747851-C-T FGC24539 +
3067806-G-A 3199765-G-A Z8488 +
6407317-C-T 6539276-C-T FGC22805 Z21103 +
6000625-T-C 6132584-T-C +
5669748-T-C 5801707-T-C +
5634122-T-A 5766081-T-A +
5334178-C-T 5466137-C-T +
5017283-C-T 5149242-C-T +
4302750-T-C 4434709-T-C +
3967953-C-T 4099912-C-T FGC37892 +
3928246-C-T 4060205-C-T Z20989 +
3479835-C-T 3611794-C-T +
22742968-G-A 20581082-G-A YY+
9984482-C-A 10146873-C-A Y+
21044334-G-T 18882448-G-T Y+
15487487-C-T 13375607-C-T Y21172 YY+
13837561-C-A 11716855-C-A +
13716617-G-C 11560941-G-C +
13622662-C-T 11466986-C-T +
13622661-A-G 11466985-A-G +
13602284-T-C 11446608-T-C +
13587406-C-T 11431730-C-T 9×T+
13587405-T-C 11431729-T-C +
13546132-G-A 11390456-G-A +
22767500-TTA-T 20605614-TTA-T +

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
Manual21253443-A-G19091557-A-GAccording to YFull, 3G reads.
Manual3270481-C-A3402440-C-AAccording to YFull, 6A reads.
Manual7071234-C-A7203193-C-AAccording to YFull, 1A read.
Manual22545488-A-G20383602-A-GAccording to YFull, 3G reads.
Manual18741745-A-AT16629865-A-AT2 reads, both positive.
Manual6184170-G-A6316129-G-A2G 1A
Manual15529195-T-C13417315-T-C1T 4C
Manual21683542-G-A19521656-G-A2A
Manual17800118-C-T15688238-C-T1T
Manual8331670-G-T8463629-G-T2T
Manual23151468-A-G20989582-A-G1G
Manual18313822-G-A16201942-G-A1A
Manual16043492-G-A13931612-G-A1A
Manual25929449-A-C23783302-A-C1A 2C
Manual22227292-C-T20065406-C-T5C 4T
Manual19955038-A-G17843158-A-G6A 2G
Manual22225481-C-G20063595-C-G5C 4G
Manual4212715-G-C4344674-G-C2C, 1 misaligned read
Manual19683671-G-A17571791-G-A4A
Manual21149572-AT-A18987686-AT-A4 positive reads, 1 read that doesn't look as if it belongs there.
Manual3761766-C-T3893725-C-T3T
Manual13514668-C-T11358992-C-T1T
Manual4560000-C-A4691959-C-A3A 1C
Manual4478335-T-C4610294-T-C2C
Manual5942123-GTAGT-G6074082-GTAGT-GJust one read, but it is positive.
Manual3914715-T-A4046674-T-A2A
Manual4650484-T-C4782443-T-C1C
Manual22346158-A-G20184272-A-G4A 2G
Manual22346159-C-T20184273-C-T3C 2T



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