Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > Z251/S470 > FGC13899 > ~22449881-G-T

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
19448632-C-A 17336752-C-A Y55906 YY+
15464951-CTAAACAA-C 13353071-CTAAACAA-C +
16077683-T-A 13965803-T-A BY35820 Y+
16255754-G-A 14143874-G-A Y51592 YY+
16982437-C-T 14870557-C-T Y52623 YY+
17719301-G-A 15607421-G-A Y53626 YY+
18977386-A-C 16865506-A-C Y55147 YY+
19090491-G-A 16978611-G-A Y55355 YY+
21699903-A-G 19538017-A-G Y57095 YY+
13826290-A-G 11705584-A-G BY90719 +
21959456-T-C 19797570-T-C Y57430 YY+
22462271-A-C 20300385-A-C DYZ19 +
22471959-T-G 20310073-T-G BY39503 DYZ19 +
22484194-C-G 20322308-C-G DYZ19 +
22689569-T-C 20527683-T-C Y58153 YY+
22818275-C-G 20656389-C-G Y58324 YY+
23314534-G-A 21152648-G-A Y59023 YY+
14507324-G-C 12395529-G-C Y49619 YY+
16350719-T-C 14238839-T-C Y51747 YY+
2871994-G-C 3003953-G-C Y44951 YY+
8026687-C-A 8158646-C-A Y46741 YY+
13278696-G-A 11123020-G-A +
6936141-G-A 7068100-G-A Y45490 YY+
6943163-G-T 7075122-G-T Y45500 YY+
7206586-G-T 7338545-G-T Y45764 YY+
2690948-A-G 2822907-A-G Y44741 YY+
7843073-C-G 7975032-C-G Y46496 YY+
7329600-G-A 7461559-G-A Y45911 YY+
8316147-A-C 8448106-A-C Y47096 YY+
8470305-G-A 8602264-G-A FGC68661 YY+
8683129-G-A 8815088-G-A Y47738 YY+
8900076-A-G 9032035-A-G Y48080 Y+
8966548-CA-C 9128939-CA-C +
15740653-C-G 13628773-C-G Y51083 **
5274762-C-T 5406721-C-T **
25222812-A-G 23076665-A-G P2_r1 ***
25861727-A-T 23715580-A-T P1_Y1 ***
25206043-A-G 23059896-A-G g1 ***
25029395-C-T 22883248-C-T g1 ***
24233281-A-G 22087134-A-G P3_b1 ***
24135066-G-T 21988919-G-T P3_b1 ***
24078493-A-G 21932346-A-G P3_b1 ***
24323450-T-C 22177303-T-C BY13993 P3_t1 ***
13709231-G-A 11553555-G-A ***
22254964-G-T 20093078-G-T BY1877 DYZ19 ***
28550174-A-G 26404027-A-G CTS12258 M4953 ***
3717595-T-C 3849554-T-C ***
22340124-T-G 20178238-T-G DYZ19 ***
22333876-C-G 20171990-C-G DYZ19 ***
22291543-C-A 20129657-C-A DYZ19 ***
22252415-C-G 20090529-C-G DYZ19 ***
19931114-A-G 17819234-A-G P5_Prx ***
13713155-AATGGC-A 11557479-AATGGC-A ***
16123692-A-G 14011812-A-G P8_Prx ***
13713139-GACTGGAATCA-G 11557463-GACTGGAATCA-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.

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
168 4053561-C-A 4185520-C-A FGC18232 Uncertain, but assumed positive.
490 6069952-C-T 6201911-C-T FGC18233 Uncertain, but assumed positive.

Age Analysis Information (work in progress)

Kit: 2976271090379079418238020490
Used in age calculations1090379079418238020490
Counts of SNPs2525
Variant counts last updated 2018-07-08 21:01:54.

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