Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z41150 > Z49 > A21822 > S8183 > 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
B437744
21022869-C-A 18860983-C-A P4_Dst YA+
20621300-G-T 18459414-G-T P4_Prx A+
56834019-A-G A*
25893403-T-C 23747256-T-C P1_Y1 A*
25919442-T-A 23773295-T-A P1_Y1 A*
4401366-A-G 4533325-A-G A*
13450701-T-AA 11295025-T-AA A*
19758105-C-T 17646225-C-T P5_Prx A*
19793707-T-C 17681827-T-C P5_Prx A*
19927683-A-G 17815803-A-G P5_Prx A*
26011183-G-A 23865036-G-A P1_Y1 A*
13449867-C-T 11294191-C-T A*
26254089-T-A 24107942-T-A P1_Y1 A*
22310187-T-C 20148301-T-C DYZ19 A*
13470897-G-A 11315221-G-A A*
56830747-C-T A*
25532564-C-T 23386417-C-T P1_gr1 A*
15205287-T-C 13093373-T-C FT134000 YY+
22513112-G-T 20351226-G-T FT134840 Y+
15389373-A-G 13277493-A-G FT134025 YY+
15746772-A-T 13634892-A-T FT134076 YY+
22600441-AAAT-A 20438555-AAAT-A +
15114333-T-C 13002420-T-C BY187222 YY+
14943959-A-G 12832033-A-G FT133972 YY+
16799401-G-A 14687521-G-A YY+
14279144-G-A 12158438-G-A Y+
14219310-A-G 12098604-A-G FT133848 Y+
13988556-A-T 11867850-A-T FT133795 YY+
13639693-T-C 11484017-T-C +
16445757-G-A 14333877-G-A FT134175 YY+
19255000-A-G 17143120-A-G FT134589 YY+
17382492-G-C 15270612-G-C FT134335 YY+
17803866-A-C 15691986-A-C FT134401 YY+
18385744-A-G 16273864-A-G FT134483 P6_Gap +
18394084-C-T 16282204-C-T BY205319 P6_Gap +
18554778-A-C 16442898-A-C FT134494 YY+
18987443-A-G 16875563-A-G Y+
19022634-C-A 16910754-C-A FT134551 YY+
19401913-A-G 17290033-A-G FT134611 YY+
19429662-T-C 17317782-T-C FT134615 YY+
21831538-C-T 19669652-C-T FT134773 Y+
21076289-T-C 18914403-T-C YY+
21163739-G-T 19001853-G-T FT134651 YY+
21174703-G-C 19012817-G-C FT134652 YY+
21301229-T-C 19139343-T-C FT134678 YY+
13575703-G-A 11420027-G-A +
9868992-C-T 10031383-C-T FT133730 YY+
21521313-A-G 19359427-A-G FT134714 YY+
6921466-C-T 7053425-C-T FT133350 YY+
21875658-G-A 19713772-G-A FGC52935 YY+
6330225-AACAC-A 6462184-AACAC-A IR3_Dst 14×AC+
28800002-G-A 26653855-G-A +
10979387-A-C FT92159 +
23476033-T-G 21314147-T-G BY145552 FGC83084 YY+
6801102-C-T 6933061-C-T FT75646 YY+
3075091-T-G 3207050-T-G FT132366 +
3747770-C-A 3879729-C-A FT132547 +
4864061-G-A 4996020-G-A FT132880 +
5104169-A-T 5236128-A-T FT132933 +
5107776-G-A 5239735-G-A FT132934 +
5865009-T-A 5996968-T-A FT133160 +
23873488-T-A 21711602-T-A FT135016 Y+
23188201-C-T 21026315-C-T FT134949 Y+
6242340-A-G 6374299-A-G FT133250 IR3_Dst +
6936739-C-T 7068698-C-T YY+
8223290-T-A 8355249-T-A FT133529 YY+
21724095-G-C 19562209-G-C FT134753 YY+
9672705-T-C 9835096-T-C FT133708 IR3_Prx +
8722789-A-G 8854748-A-G FT133610 YY+
8672772-A-T 8804731-A-T FT133604 YY+
8496242-C-G 8628201-C-G FT133577 YY+
8463802-G-A 8595761-G-A FT133569 YY+
8260985-C-T 8392944-C-T FT133539 YY+
23405511-C-A 21243625-C-A FT134977 YY+
8221566-C-T 8353525-C-T YY+
7363615-C-T 7495574-C-T FT133418 Y+
7265910-T-C 7397869-T-C FT133404 YY+
6983149-C-T 7115108-C-T YY+
22280678-G-A 20118792-G-A DYZ19 *
22299207-G-C 20137321-G-C DYZ19 *
22317206-T-C 20155320-T-C DYZ19 *
22299223-A-T 20137337-A-T BY51368 DYZ19 *
25030237-T-C 22884090-T-C g1 **
25929270-G-T 23783123-G-T P1_Y1 **
25929293-C-A 23783146-C-A P1_Y1 **
25983815-A-AG 23837668-A-AG P1_Y1 **
27967478-C-CT 25821331-C-CT P1_Y2 **
22983744-T-C 20821858-T-C **
13459176-C-G 11303500-C-G **
19698950-T-C 17587070-T-C P5_Prx **
9887076-C-T 10049467-C-T **
13459077-A-G 11303401-A-G **
16116345-C-A 14004465-C-A P8_Prx **
6330115-CAA-C 6462074-CAA-C IR3_Dst 18×A**
18309163-T-A 16197283-T-A P6_Prx **
28006372-G-GTACA 25860225-G-GTACA P1_Y2 **
9429666-AC-A 9592057-AC-A **
4966201-A-C 5098160-A-C **
7632283-A-G 7764242-A-G **
6201615-T-C 6333574-T-C IR3_Dst **
15146670-C-T 13034757-C-T **
13459171-C-A 11303495-C-A **
15376757-G-A 13264877-G-A **
16323799-T-A 14211919-T-A **
15296757-G-A 13184856-G-A **
13373516-A-C 11217840-A-C ***
12371644-C-A ***
22280161-C-A 20118275-C-A DYZ19 ***
22548086-T-C 20386200-T-C ***
4277201-CTTT-C,CT 4409160-CTTT-C,CT 20×T***
13453202-T-G 11297526-T-G ***
22299231-G-A 20137345-G-A BY177813 DYZ19 ***
22299222-T-C 20137336-T-C DYZ19 ***
16967420-T-C 14855540-T-C ***
22280037-A-T 20118151-A-T BY215917 DYZ19 ***
19290551-A-G 17178671-A-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.

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: B4377441501651494055328324373
Used in age calculations1501651494055328324373
Counts of SNPs4538
Variant counts last updated 2020-04-08 02:34:33.



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