Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z198 > CTS4188 > BY178297 > BY178203

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
26991333-T-TAA 24845186-T-TAA P1_r4 33×A+
7124387-TC-T 7256346-TC-T +
3763797-A-G 3895756-A-G FT318397 +
3781044-A-G 3913003-A-G FT318470 +
4012042-C-A 4144001-C-A FT319238 +
4036398-C-G 4168357-C-G FT319302 +
4168487-C-G 4300446-C-G FT319750 +
4226664-C-T 4358623-C-T +
4460957-CA-C 4592916-CA-C +
4460963-CG-C 4592922-CG-C +
4502036-G-T 4633995-G-T FT320840 +
4693285-C-T 4825244-C-T FGC31192 +
5996859-C-T 6128818-C-T FT325773 +
6948092-G-GTT 7080051-G-GTT 31×T+
7077186-T-A 7209145-T-A FT294759 YY+
3498713-A-G 3630672-A-G +
9754531-C-T 9916922-C-T FT328226 +
9754532-C-T 9916923-C-T FT328227 +
9880136-T-TTGTG 10042527-T-TTGTG 14×TG+
9905948-C-A 10068339-C-A FT328380 Y+
13213824-TGGA-T 11058148-TGGA-T +
13222724-T-G 11067048-T-G +
13323494-C-CAA 11167818-C-CAA 24×A+
14612506-TA-T 12500704-TA-T +
14664252-GATC-G 12552317-GATTC-G +
22253017-C-A 20091131-C-A DYZ19 +
22479601-A-G 20317715-A-G BY25220 DYZ19 +
28461869-G-C 26315722-G-C +
28622571-TA-T 26476424-TA-T +
3524948-GTTC-G 3656907-GTTC-G +
14600814-T-TAC 12489014-T-TAC +
27967355-TAG-T 25821208-TAG-T P1_Y2 14×AG+
14923339-T-C 12811404-T-C CTS3437 YY+
14266305-G-GTA 12145599-G-GTA 14×TA+
28680422-C-CATTT 26534275-C-CATTT 11×ATTT+
2661269-G-A 2793228-G-A FT294523 YY+
2704234-G-A 2836193-G-A FT294539 YY+
7656587-T-C 7788546-T-C FT294963 YY+
8139888-C-T 8271847-C-T FT295203 YY+
8408026-C-T 8539985-C-T FT295340 YY+
8497781-C-T 8629740-C-T BY31178 Y47432 YY+
8643261-C-G 8775220-C-G FT295466 YY+
13902319-G-A 11781613-G-A BY91889 YY+
14107886-C-A 11987180-C-A BY178593 YY+
14422858-A-G 12302133-A-G FT296151 YY+
14488349-C-A 12367618-C-A FT296175 YY+
15086499-G-T 12974589-G-T BY178780 YY+
23582858-T-G 21420972-T-G BY180044 YY+
15607643-G-A 13495763-G-A FT296544 YY+
16828313-A-G 14716433-A-G CTS6335 YY+
17062534-T-G 14950654-T-G CTS6695 Y+
18155146-A-T 16043266-A-T CTS8698 YY+
18948127-G-A 16836247-G-A CTS9522 YY+
19479679-A-G 17367799-A-G FT298115 Y+
21246901-T-G 19085015-T-G FT298298 Y+
21561257-C-T 19399371-C-T FT298525 YY+
22208453-A-G 20046567-A-G FT298923 YY+
22576137-G-C 20414251-G-C BY179851 YY+
22580280-G-T 20418394-G-T YY+
23096732-G-A 20934846-G-A CTS11405 Y+
23324174-G-A 21162288-G-A CTS11868 YY+
58866776-G-C 56724095-C-G +

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:

Manual20791774-A-G18629888-A-G2A 7G 1T
Manual6418343-G-A6550302-G-A11A 1G
Manual4516489-TC-T4648448-TC-TAll 6 reads show the deletion.

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