Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z367/S255 > Z34/S368 > Z33/S212 > BY164497 > BY3604 > Z256 > Z275 > CTS7352 > PH137 > BY31326 > F26162 > CTS5483 > BY202596

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
23110592-C-T 20948706-C-T CTS11432 Y+
8389569-C-CTTT 8521528-C-CTTT 25×T+
22459365-T-G 20297479-T-G BY42025 DYZ19 +
21501086-A-ATT 19339200-A-ATT 37×T+
21251811-C-CT 19089925-C-CT +
17562007-TG-T 15450127-TG-T +
17085721-C-CTTTT 14973841-C-CTTTT 20×T+
16710761-ATG-A 14598881-ATG-A +
16051002-CTT-C 13939122-CTT-C +
15358787-AGCAG-A 13246907-AGCAG-A +
14709282-A-AC 12597349-A-AC +
14695992-C-CAAA 12584058-C-CAAA 30×A+
13346071-C-CAA 11190395-C-CAA 18×A+
13222624-AGG-A 11066948-AGG-A +
13199164-C-CAAA 11043488-C-CAAA 18×A+
6449900-A-C 6581859-A-C +
16051006-CTTTCTT-C 13939126-CTTTCTT-C +
5887226-AC-A 6019185-AC-A +
5493431-C-CTTT 5625390-C-CTTT 24×T+
4834245-T-TAAA 4966204-T-TAAA 23×A+
3930815-C-CAT 4062774-C-CAT +
19547453-C-CAAAA 17435573-C-CAAAA 24×A+
13222618-AGAGG-A 11066942-AGAGG-A +
28676142-G-A 26529995-G-A +
21780204-C-T 19618318-C-T BY195979 YY+
18187828-C-T 16075948-C-T CTS8772 Y+
17295241-C-T 15183361-C-T CTS7110 YY+
14358411-AA-GG 12237706-AA-GG +
27467214-T-G 25321067-T-G FGC7648 P1_Y2 5×TTAG+

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:

Manual21527519-T-TA19365633-T-TA11 reads, all match the hg19 reference sequence.
Manual26286058-C-G24139911-C-G5C 3G
Manual17156147-AT-A15044267-AT-A6 reads cover the INDEL (short STR) and all are positive.
Manual19900643-C-T17788763-C-T3C 5T
Manual22439866-C-T20277980-C-T5T 2C
Manual16099891-G-A13988011-G-A1G 6A
Manual19772088-A-G17660208-A-G6A 12G

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