Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z198 > ZS312 > Z262 > M167 > Z264 > Z205 > CTS606 > 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.

POS-REF-ALT (hg19) POS-REF-ALT (hg38) Blocks Names Region McDonald BED combBED STRBigY3
68440
5182531-A-G 5314490-A-G FT17278 +
13397785-C-A 11242109-C-A +
15602168-G-A 13490288-G-A FT22148 YY+
15523992-TAACAGTGA-T 13412112-TAACAGTGA-T +
15336115-T-C 13224233-T-C FT21950 YY+
10954612-A-G +
15050875-T-C 12938966-T-C FT21780 YY+
14137495-A-G 12016789-A-G FT21081 YY+
10654573-C-T +
13842563-C-T 11721857-C-T FT20680 +
13799117-A-G 11678411-A-G +
13653253-C-A 11497577-C-A +
13490793-G-T 11335117-G-T +
13202618-A-G 11046942-A-G +
17418545-G-T 15306665-G-T YY+
10917643-G-A +
3275685-G-C 3407644-G-C FT15103 +
3456855-T-C 3588814-T-C FT15302 +
9079465-C-G 9241856-C-G FT20302 +
8816256-T-C 8948215-T-C FT20153 Y+
8624085-A-G 8756044-A-G FT20025 YY+
8180314-C-G 8312273-C-G FT19690 YY+
5897040-A-G 6028999-A-G FT18134 +
6105255-A-C 6237214-A-C +
6440224-A-C 6572183-A-C FT18484 +
6746050-C-A 6878009-C-A FT18726 YY+
6799140-A-T 6931099-A-T FT18768 YY+
7355074-AC-A 7487033-AC-A +
16692460-A-G 14580580-A-G FT22930 YY+
17529473-A-G 15417593-A-G FT23580 YY+
14547054-G-A 12435255-G-A FGC43114FGC17889 YY+
28663299-T-C 26517152-T-C FT27234 +
4960249-T-C 5092208-T-C Y8761 FGC22564 +
22116219-G-A 19954333-G-A FT25900 YY+
17622767-C-A 15510887-C-A YY+
21141013-C-T 18979127-C-T Y29349 YY+
21881363-A-G 19719477-A-G FT25742 YY+
21238078-A-G 19076192-A-G FT25183 YY+
17876675-T-G 15764795-T-G FT23842 YY+
7160012-G-A 7291971-G-A FT19007 YY+
9081378-G-T 9243769-G-T FT20304 +
19024550-G-T 16912670-G-T FT24616 YY+
18674939-G-A 16563059-G-A FT24381 YY+
19306955-C-A 17195075-C-A FT24872 YY+
18683384-AG-A 16571504-AG-A +
13463262-G-A 11307586-G-A *
4189157-C-T 4321116-C-T *
56861427-G-T *
13964460-C-CTG 11843754-C-CTG 13×TG*
12499082-GATAC-G 10×ATAC*
3800092-A-AAC 3932051-A-AAC 17×AC*
4156847-A-G 4288806-A-G *
14632836-G-C 12520905-G-C **
15380911-T-A 13269031-T-A **
20637643-TG-T 18475757-TG-T P4_Prx **
22429212-G-T 20267326-G-T DYZ19 **
25520334-G-T 23374187-G-T P1_gr1 **
13455780-A-T 11300104-A-T **
19325795-G-T 17213915-G-T **
28795321-AT-A 26649174-AT-A **
19663729-T-A 17551849-T-A P5_Prx **
16216-G-T **
19924654-T-G 17812774-T-G P5_Prx **
3663312-C-T 3795271-C-T **
7016147-CAA-C 7148106-CAA-C 16×A**
22113185-C-A 19951299-C-A **
21575561-T-C 19413675-T-C **
24290749-G-GCACA 22144602-G-GCACA P3_t1 20×CA**
5147441-CAAAAAAAAAAA-C 5279400-CAAAAAAAAAAA-C 30×A**
28812452-C-G 26666305-C-G **
28812398-T-C 26666251-T-C **
19839664-T-A 17727784-T-A P5_Prx **
21575565-T-C 19413679-T-C **
28812498-C-T 26666351-C-T **
23802082-CA-C 21640196-CA-C 24×A**
28812384-A-G 26666237-A-G **
28812430-ATCCAATGGAG-A 26666283-ATCCAATGGAG-A **
27538104-CTTTT-C 25391957-CTTTT-C P1_Y2 23×T**
28812489-C-A 26666342-C-A **
28812394-A-G 26666247-A-G **
28812458-A-G 26666311-A-G **
13468498-C-T 11312822-C-T ***
22264191-T-A 20102305-T-A DYZ19 ***
3889019-CT-C 4020978-CT-C 15×T***
21130591-T-TAAAA 18968705-T-TAAAA ***
5275954-CAAAAAAAA-C 5407913-CAAAAAAAA-C 27×A***
3663316-T-C 3795275-T-C ***
6040608-CA-C 6172567-CA-C 10×A***
4328695-G-A 4460654-G-A ***
14210430-A-AT 12089724-A-AT 9×T***
13481280-A-C 11325604-A-C ***
7643541-AGGAAGGGAAG-A 7775500-AGGAAGGGAAG-A 16×GGAAG***
13481383-T-C 11325707-T-C ***
27699976-T-A 25553829-T-A P1_Y2 ***
16000874-A-G 13888994-A-G ***
15116746-A-G 13004833-A-G ***
13468495-G-T 11312819-G-T ***
14745420-C-CT,CTT 12633489-C-CT,CTT 12×T***
14926462-CAAA-C 12814527-CAAA-C 26×A***
14457387-C-CAA 12336660-C-CAA 18×A***
13481366-G-A 11325690-G-A ***
13884529-CAAA-C 11763823-CAAA-C 17×A***
13540253-AACACAC-A,AAC 11384577-AACACAC-A,AAC 23×AC***
13463303-G-A 11307627-G-A ***
5308797-TAT-T,TAG 5440756-TAT-T,TAG ***
9678221-T-C 9840612-T-C IR3_Prx ***
3978697-C-T 4110656-C-T ***
4026240-G-T 4158199-G-T ***
22924455-A-AT 20762569-A-AT 15×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.

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: 684401518414895092408375943
Used in age calculations1518414895092408375943
Counts of SNPs2322
Variant counts last updated 2019-08-26 23:04:07.



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