Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z367/S255 > L20/S144

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 STRFTDNA
B59826
14000809-A-G 11880103-A-G Y89972 YY+
8445646-A-T 8577605-A-T Y86886 YY+
22976878-G-A 20814992-G-A Y110274 YY+
16183641-A-T 14071761-A-T BY105799 Y+
15925788-C-G 13813908-C-G Y95148 YY+
15383968-A-T 13272088-A-T BY3586 YY+
15020950-T-G 12909039-T-G Y92799 YY+
14838762-AT-A 12726829-AT-A +
14608524-T-C 12496726-T-C Y91821 YY+
14342287-T-C 12221582-T-C Y91155 YY+
17995585-T-C 15883705-T-C Y100899 P7_Gap Y+
23030846-G-A 20868960-G-A FGC27790 YP3662 YY+
8518489-T-A 8650448-T-A Y87154 YY+
8482070-C-G 8614029-C-G Y87036 YY+
8480964-C-G 8612923-C-G Y87029 YY+
8394001-C-T 8525960-C-T Y86708 YY+
17509995-A-G 15398115-A-G Y99373 YY+
8050800-G-A 8182759-G-A Y85711 YY+
7865453-C-T 7997412-C-T Y85194 YY+
7808181-T-G 7940140-T-G Y85027 YY+
7620745-G-A 7752704-G-A BY66343 YY+
18382436-A-T 16270556-A-T Y101820 P6_Gap +
5601410-C-T 5733369-C-T BY58750 +
18427272-T-C 16315392-T-C Y102012 P6_Gap +
22683123-C-T 20521237-C-T BY140033 YY+
22483741-T-C 20321855-T-C DYZ19 +
21521896-G-A 19360010-G-A Y106780 YY+
6932171-G-C 7064130-G-C L817 YY+
21784003-G-T 19622117-G-T BY135448 YY+
16486837-T-C 14374957-T-C BY3589 YY+
22218673-T-A 20056787-T-A DYZ19 **
22477260-G-A 20315374-G-A BY223767 DYZ19 **
16305696-C-A 14193816-C-A FT180639 **
4271023-C-T 4402982-C-T Y81969 **
22365597-T-C 20203711-T-C DYZ19 ***
23716541-C-T 21554655-C-T ***
24118843-C-T 21972696-C-T P3_b1 ***
24126629-C-T 21980482-C-T P3_b1 ***
24837606-A-C 22691459-A-C P3_b2 ***
25106815-C-A 22960668-C-A g1 ***
25848399-C-G 23702252-C-G P1_b3 ***
26093425-A-C 23947278-A-C P1_Y1 ***
22452395-G-C 20290509-G-C DYZ19 ***
22366756-G-C 20204870-G-C DYZ19 ***
13845463-A-T 11724757-A-T ***
22264791-G-T 20102905-G-T DYZ19 ***
22256053-C-T 20094167-C-T FT14176 DYZ19 ***
22227355-C-A 20065469-C-A DYZ19 ***
22220860-T-A 20058974-T-A DYZ19 ***
19884563-GA-G 17772683-GA-G P5_Prx ***
19657366-A-AGT 17545486-A-AGT P5_Prx ***
22481483-G-T 20319597-G-T DYZ19 ***
13452315-G-A 11296639-G-A ***
6147406-A-G 6279365-A-G IR3_Dst ***
22437346-G-C 20275460-G-C CLD64 DYZ19 ***
13468149-T-A,G 11312473-T-A,G ***
7460174-G-C 7592133-G-C PH663 IR1_L ***
14768679-A-T 12656748-A-T PF1650 M5456 CTS3250 ***
10031688-C-T 10194079-C-T ***
26272584-C-T 24126437-C-T P1_Y1 ***
26120993-T-C 23974846-T-C P1_Y1 ***

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.

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: B598261071408377760497861804
Used in age calculations1071408377760497861804
Counts of SNPs2523
Variant counts last updated 2020-03-15 02:43:57.



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