Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z367/S255 > L20/S144 > Z46420 > BY5690 > Y45467

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
154861
13449922-C-T 11294246-C-T A*
20954374-A-G 18792488-A-G P4_Dst A*
56836153-T-TTCTGC A*
18371486-T-C 16259606-T-C P6_Prx A*
19593951-G-A 17482071-G-A P5_Prx YA*
6239575-C-A 6371534-C-A IR3_Dst A*
5377909-T-C 5509868-T-C A*
5377938-T-C 5509897-T-C A*
15270869-A-G 13158958-A-G YY+
16596138-C-T 14484258-C-T FT347041 YY+
16435690-T-A 14323810-T-A FT346974 YY+
16263080-T-C 14151200-T-C FT346903 YY+
15581634-G-A 13469754-G-A FT346679 YY+
15455391-T-G 13343511-T-G FT346640 YY+
15308124-GA-G 13196226-GA-G +
14197931-A-G 12077225-A-G FT346213 YY+
10622067-A-T FT275557 +
14098759-C-T 11978053-C-T FT346172 YY+
16883053-G-C 14771173-G-C FT347152 Y+
9028699-T-C 9191090-T-C FT345895 Y+
13925847-A-C 11805141-A-C FT73363 Y+
13828606-G-T 11707900-G-T FT350276 +
13304852-G-C 11149176-G-C FT442496 +
10745547-A-T FT429343 +
10626922-C-G +
16659342-C-T 14547462-C-T FT347069 YY+
8403749-G-A 8535708-G-A S190S308 A71 FGC7853 YY+
16969095-C-A 14857215-C-A FT347185 YY+
21340662-A-G 19178776-A-G FT348306 YY+
28722598-G-A 26576451-G-A FT349297 +
28497584-C-T 26351437-C-T FT349182 Y+
27856287-G-A 25710140-G-A P1_Y2 +
22977631-G-T 20815745-G-T FT460838 YY+
22654140-G-A 20492254-G-A FT348691 YY+
22011659-T-C 19849773-T-C FT348556 Y+
21946067-A-G 19784181-A-G FT348527 YY+
19409112-G-A 17297232-G-A FT348063 YY+
17041934-TCTC-T 14930054-TCTC-T +
19108897-C-T 16997017-C-T FT347949 YY+
19040306-C-A 16928426-C-A FT347911 YY+
19005015-A-C 16893135-A-C FT347897 YY+
18891753-G-C 16779873-G-C FT347854 YY+
18722878-G-A 16610998-G-A FT347794 YY+
18666113-T-G 16554233-T-G FT347781 YY+
8224419-A-G 8356378-A-G FT345577 YY+
17904548-C-T 15792668-C-T FT347550 YY+
8553744-C-T 8685703-C-T FT345716 YY+
10870483-A-G FT144562 +
7401505-C-T 7533464-C-T FT345292 YY+
3835916-C-T 3967875-C-T FT349550 +
21973333-G-A 19811447-G-A FGC40263 YY+
14627170-G-A 12515238-G-A FT73382 YY+
6507013-G-C 6638972-G-C FT350166 +
3416640-TA-T 3548599-TA-T 9×A+
3100833-C-T 3232792-C-T FT349361 +
3366033-T-C 3497992-T-C FT73177 +
3664903-T-C 3796862-T-C FT349498 +
28798525-C-T 26652378-C-T FT462106 +
4824251-G-A 4956210-G-A FT349785 +
5869154-G-A 6001113-G-A FT350056 +
4938294-A-G 5070253-A-G FT349816 +
4013252-G-A 4145211-G-A FT349588 +
10767663-TTCCACTCCAC-T *
5395446-A-T 5527405-A-T *
10971897-T-TATTCC *
22318941-A-G 20157055-A-G DYZ19 *
24425365-A-ATG 22279218-A-ATG 8×TG*
23969674-A-AACACAC 21823527-A-AACACAC 20×AC*
7608436-CCTCTCT-C,CCT 7740395-CCTCTCT-C,CCT 15×CT*
5272101-G-A 5404060-G-A *
16052719-C-A 13940839-C-A Y*
3015575-T-TAC 3147534-T-TAC 17×AC*
26201114-G-T 24054967-G-T P1_Y1 15×T**
23094657-A-T 20932771-A-T FT299208 **
23036414-C-G 20874528-C-G **
6262638-G-A 6394597-G-A IR3_Dst 11×CA**
5114698-A-G 5246657-A-G FGC50536 **
8333593-TCTTCTC-T 8465552-TCTTCTC-T 5×CTTCTC**
16860770-AAAAG-A 14748890-AAAAG-A **
20312773-T-A 18150887-T-A P5_Dst **
28805826-C-T 26659679-C-T **
28819219-G-A 26673072-G-A **
3871509-T-C 4003468-T-C **
18963555-C-T 16851675-C-T **
18797782-C-A 16685902-C-A **
26044660-T-TC 23898513-T-TC P1_Y1 **
3632606-T-C 3764565-T-C **
16800747-G-T 14688867-G-T **
16398329-T-C 14286449-T-C **
5704150-C-T 5836109-C-T **
17162409-TG-T 15050529-TG-T **
17260467-TG-T 15148587-TG-T **
17259377-C-G 15147497-C-G **
5979155-G-GA 6111114-G-GA **
13349016-A-G 11193340-A-G FGC48916 ***
10899992-T-A ***
19013749-A-T 16901869-A-T ***
10899991-G-C ***
56828785-TTTCCA-T ***
19611206-CTT-C 17499326-CTT-C P5_Prx 26×T***
19541452-T-C 17429572-T-C ***
21078582-A-T 18916696-A-T ***
17085721-CTTTT-C 14973841-CTTTT-C 20×T***
15876360-CAAA-C,CAA 13764480-CAAA-C,CAA 21×A***
28619438-G-GT 26473291-G-GT ***
28720132-CTTTTTTTTT-C,CTT 26573985-CTTTTTTTTT-C,CTT 24×T***
13488844-G-C,GGC 11333168-G-C,GGC ***
18565234-CTTATTTATTTATTTATTTAT-C,CTTATTTATTTATTTAT 16453354-CTTATTTATTTATTTATTTAT-C,CTTATTTATTTATTTAT 12×TTAT***

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: 1548611521882695262838362316
Used in age calculations1521882695262838362316
Counts of SNPs3330
Variant counts last updated 2022-10-30 03:25:59.



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