Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z41150 > Z49 > Z142/S211 > Z150 > CTS9490 > S7404 > 14429916-T-A > 7356566-A-G > Exact position not yet finalized.

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.

POSITION-REF-ALT (hg19) Blocks Names Region McDonald BED combBED STR1kG
HG00244
Manual
Edits
25312295-G-AP2_r1+
13336689-C-T+
14098194-G-TZ25311YY+
14082373-C-TCTS1817YY+
13446468-G-T+
13411750-G-T+
13407450-G-T+
13399660-G-A+
13313428-A-G+
14518572-C-AYY+
13295642-T-G+
13289048-C-T+
13289035-G-A+
13259580-G-A+
13143194-GC-G+
9949138-G-AY+
14133969-A-GY+
14532778-A-CY+
9524011-GTA-G+
21254405-C-AYY+
28645367-G-TFGC46206+
24387384-C-T+
23415339-TATA-T+
23018375-C-TCTS11217Y+
21839029-T-AY+
21827597-C-AYY+
19127741-C-AZS2728YY+
14897861-C-TYY+
18672382-T-TG+
18636631-A-TYY+
18064213-A-GYY+
15374439-GA-G+
15226091-G-TY+
15084500-C-AYY+
15010314-T-CYY+
9640887-GTT-GIR3_Prx+
9375924-G-CY+
5776576-G-A13×A+
18211447-A-GY+
2919260-A-G+
28768954-G-CY+
23036406-T-CY+
22874026-A-CY+
21589231-C-TY+
21375671-C-TY20356 FGC46214YY+
17832495-T-CY20352 FGC46209YY+
3166904-T-C+
17470857-C-TCTS7417YY+
14423724-A-GYY+
14154137-G-APF654 M9715Y+
8631871-CAAAC-AAAAA+
8193263-G-CYY+
13810889-C-CAATGG9×AATGG+
3009028-C-T+
4326031-G-CFGC46205+
9162651-T-G+
6434962-C-T+
8660550-C-AYFS032934YY18×A+
8509444-T-GYP4583YY+
8200046-C-AYY+
8007007-G-AY+
7108963-G-TY+
6558802-C-G+
6099383-T-A+
4529219-T-C+
5888482-G-A+
5850288-T-CY672+
5418148-G-A14×A+
5336698-A-TMZ127+
4778009-TA-T+
4778008-AT-A+
4735034-G-AZ4790+
28690110-T-GCTS12747+

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. 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) Note
Manual8207161-G-A1A
Manual14429916-T-A1A
Manual15442163-ACC-A9 reads show the deletion.
Manual17491162-A-T2T
Manual18760721-T-C3C
Manual20809109-A-C1C
Manual21817522-G-GT2 reads show the insertion.
Manual22253872-G-T3G 3T
Manual22276153-G-A2A
Manual22362929-C-A2C 2A
Manual22469473-C-A1A
Manual22469474-C-G1G
Manual23380162-TTATTTATTTATG-T3 reads show the deletion.
Manual23404604-G-A1A
Manual24220899-A-T1T
Manual25080546-T-C1C
Manual25093236-G-A3G 1A
Manual25111744-G-A1A
Manual26594842-C-T1T



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