Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > L513/S215/DF1 > S6365 > Z16385 > Z16386 > Z16387 > BY50635 > BY50579

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
9881995-A-C 10044386-A-C BY81740 YY+
24412573-T-C 22266426-T-C BY149686 Y+
18386282-T-A 16274402-T-A BY121538 P6_Gap +
17518092-A-C 15406212-A-C BY115424 YY+
7759944-A-G 7891903-A-G FGC57 L1067 SK2079 Z8148 YY+
9399070-G-C 9561461-G-C CLD19 M841 YY+
14820579-C-T 12708646-C-T BY97785 YY+
15020848-T-C 12908937-T-C M248 YY*
6868730-G-A 7000689-G-A Y4781PR534 Y4781 **
27149714-TA-T 25003567-TA-T P1_g3 16×A**
18118057-A-G 16006177-A-G **
17826332-A-G 15714452-A-G CTS8075 **
17644132-T-A 15532252-T-A **
17412308-C-A 15300428-C-A **
16046168-G-A 13934288-G-A CTS5161 **
7461424-C-G 7593383-C-G CTS1530 IR1_L **
24675448-CT-C 22529301-CT-C P3_b2 12×T**
3274923-C-A 3406882-C-A **
22722580-C-T 20560694-C-T **
8110520-A-T 8242479-A-T **
25492335-CT-C 23346188-CT-C P2_r2 11×T**
2762077-C-G 2894036-C-G **
20128497-G-A 18016617-G-A P5_Dst ***
13704416-T-G 11548740-T-G ***
14116679-GATAC-G 11995973-GATAC-G 10×ATAC***
20206644-TA-T 18044758-TA-T P5_Dst 11×A***
25345594-T-C 23199447-T-C P2_r1 ***
25205073-C-T 23058926-C-T g1 ***
23722783-C-T 21560897-C-T ***
22224681-A-T 20062795-A-T DYZ19 ***
13863145-T-C 11742439-T-C ***
18354192-AAG-A 16242312-AAG-A P6_Prx ***
27087610-GCCTTCCTT-G 24941463-GCCTTCCTT-G S190 P1_r4 15×CCTT***
13194862-C-T 11039186-C-T ***
28808133-G-A 26661986-G-A ZZ76_1 BY2561 ***
22489574-A-T 20327688-A-T DYZ19 ***
22489581-A-T 20327695-A-T DYZ19 ***
13674842-C-A 11519166-C-A ***
28799161-G-T 26653014-G-T ***
9774492-T-C 9936883-T-C FT208169 ***
13478497-C-T 11322821-C-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.

Uncertain Mutations

NGS tests don't always cover all of the Y chromosome and, even when they do, the results can be inconclusive. The following mutations don't have clear results and have been assumed to be positive or negative. For those mutations that are assumed to be positive, the assumed SNP/INDEL will likely be found on the tree in some upstream block. It is unclear if it should be placed upstream of your results or parallel to them. The situation is reversed for mutations assumed negative. Those SNPs/INDELs will likely be found on a parallel branch on the tree, and it is unclear if they should be positioned upstream. As more results come in, the ambiguity may resolve itself, or it may be necessary to consult the BAM file for your test (available from FamilyTreeDNA or FullGenomes Corp) or by direct SNP testing (Sanger Sequencing - YSEQ or FamilyTreeDNA).


BlockRegionPOS-REF-ALT (hg19)POS-REF-ALT (hg38)NamesNotes
504 15581048-C-T 13469168-C-T Z16546 FGC11797 Uncertain, but assumed positive.
504 8900973-ATATAT-A 9032932-ATATAT-A Z16544 Uncertain, but assumed positive.
504P1_Y2 27690368-A-G 25544221-A-G Z16399 Uncertain, but assumed positive.
504 7705790-C-T 7837749-C-T FGC11788 Uncertain, but assumed negative.

Age Analysis Information (work in progress)

Kit: 21834962026468367126882800
Used in age calculations962026468367126882800
Counts of SNPs67
Variant counts last updated 2022-07-19 03:21:59.

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