Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > FGC78762 > ZZ19 > Z31644 > A2146 > BY1246 > BY19308 > 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
B402690
28804661-G-A 26658514-G-A A+
3377052-G-A 3509011-G-A A+
22243707-T-C 20081821-T-C DYZ19 A+
58978779-C-A 56832632-C-A A*
19801432-A-C 17689552-A-C P5_Prx A*
19896737-T-C 17784857-T-C P5_Prx A*
19866108-G-A 17754228-G-A P5_Prx A*
19865098-G-T 17753218-G-T P5_Prx A*
19623240-C-A 17511360-C-A P5_Prx A*
19704272-T-C 17592392-T-C P5_Prx A*
20765654-C-T 18603768-C-T P4_Prx A*
6201516-C-T 6333475-C-T IR3_Dst A*
6296100-A-G 6428059-A-G IR3_Dst A*
18453825-G-GT 16341945-G-GT P6_Dst 8×TA*
16121157-T-G 14009277-T-G P8_Prx A*
9574280-T-C 9736671-T-C IR3_Prx A*
19931784-G-C 17819904-G-C P5_Prx A*
19784035-G-A 17672155-G-A P5_Prx A*
24262536-C-T 22116389-C-T P3_b1 A*
20878520-G-A 18716634-G-A P4_Dst A*
56851255-C-A A*
22265518-G-T 20103632-G-T BY15521 DYZ19 A*
20841234-A-G 18679348-A-G P4_Gap +
14408558-G-A 12287856-G-A YY+
14810139-T-C 12698210-T-C FT121841 YY+
28797221-G-C 26651074-G-C +
15340266-T-G 13228384-T-G FT121909 YY+
16223369-T-A 14111489-T-A FT122016 YY+
16267525-T-C 14155645-T-C FT122030 YY+
16731778-T-G 14619898-T-G FT122107 YY+
16948319-C-G 14836439-C-G FT122137 YY+
16955460-G-A 14843580-G-A FT122141 YY+
18209745-C-T 16097865-C-T FT122338 YY+
18241798-T-C 16129918-T-C FT122343 Y+
18570122-C-T 16458242-C-T FT122364 YY+
23260536-CCAA-C 21098650-CCAA-C +
23127004-C-G 20965118-C-G FT122822 YY+
18708958-A-G 16597078-A-G FT122388 YY+
18721385-TATAATTTAA-T 16609505-TATAATTTAA-T +
18820281-A-T 16708401-A-T FT122403 YY+
19078021-A-G 16966141-A-G FT122446 YY+
19103945-C-T 16992065-C-T FT122452 YY+
22878101-T-C 20716215-T-C FT122787 Y+
13862870-G-C 11742164-G-C FT121668 +
22771296-G-A 20609410-G-A FT122765 YY+
22270605-G-C 20108719-G-C DYZ19 +
22028502-T-C 19866616-T-C FT122699 YY+
21405664-G-A 19243778-G-A FT122598 YY+
21086339-T-C 18924453-T-C FT122539 YY+
14293717-C-A 12173011-C-A FT121759 YY+
13671704-T-G 11516028-T-G +
5138241-G-T 5270200-G-T FT120889 +
4824023-A-G 4955982-A-G FT120800 +
5689290-A-C 5821249-A-C FT121047 +
5983123-T-C 6115082-T-C FT121129 +
6040765-A-G 6172724-A-G FT32225 +
4299342-T-C 4431301-T-C FT120634 +
3913869-T-C 4045828-T-C FT120524 +
3210431-T-C 3342390-T-C FT120320 +
7011032-G-A 7142991-G-A FT121283 YY+
7584843-G-A 7716802-G-A YY+
3210342-T-A 3342301-T-A FT120319 +
17571993-G-A 15460113-G-A FT122245 YY+
7842871-C-G 7974830-C-G FT121418 YY+
8860061-A-C 8992020-A-C FT121551 YY+
9170844-C-A 9333235-C-A Y+
9400278-G-C 9562669-G-C FT121594 YY+
9410860-T-C 9573251-T-C FT121595 Y+
9422940-C-T 9585331-C-T FT121597 YY+
9454500-T-C 9616891-T-C FT121603 YY+
9964033-G-C 10126424-G-C Y+
9983730-C-T 10146121-C-T Y+
10004306-T-C 10166697-T-C Y+
8419917-A-T 8551876-A-T BY18205Y86801 YY+
8356284-C-T 8488243-C-T BY46946 YY+
22517412-A-AC 20355526-A-AC +
4583115-CTTTTTTTTTTTTT-C 4715074-CTTTTTTTTTTTTT-C 22×T+
20984748-TTATCTATCTATC-T,TTATCTATC 18822862-TTATCTATCTATC-T,TTATCTATC P4_Dst 12×TATC*
16059028-CTTTT-C 13947148-CTTTT-C 19×T*
10864035-G-GCCATT *
6225905-A-T 6357864-A-T IR3_Dst *
13643251-C-G 11487575-C-G **
10065309-T-C 10227700-T-C **
17449786-C-G 15337906-C-G **
13884474-G-C 11763768-G-C **
5264491-T-G 5396450-T-G **
23825738-A-G 21663852-A-G **
17626946-C-T 15515066-C-T **
19706287-T-A 17594407-T-A P5_Prx **
20292450-A-AGT 18130564-A-AGT P5_Dst 12×GT**
17795475-T-A 15683595-T-A **
20678172-A-T 18516286-A-T P4_Prx **
3424220-A-T 3556179-A-T **
6124053-T-A 6256012-T-A **
4421884-A-G 4553843-A-G **
13841847-CGAATGGAATG-C 11721141-CGAATGGAATG-C 6×GAATG***
15690010-T-A 13578130-T-A ***
18195999-G-GTA 16084119-G-GTA ***
21096803-G-A 18934917-G-A ***
10904175-A-G ***
22255308-G-T 20093422-G-T DYZ19 ***
2930319-G-GT 3062278-G-GT 26×T***
5752261-C-A 5884220-C-A ***
3970985-CTTT-C 4102944-CTTT-C 17×T***
21754457-GAA-G,GA ***
6953202-TACACACACAC-T 7085161-TACACACACAC-T 17×AC***
56838589-G-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: B4026901504382394216688340172
Used in age calculations1504382394216688340172
Counts of SNPs1511
Variant counts last updated 2019-10-20 02:34:01.



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