Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > DF21/S192 > S5488 > Z16294 > BY11121 > Z16281 > Z16282 > Z16291 > BY3829 > V1640

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
94756
56837050-C-G A*
25872999-A-C 23726852-A-C P1_Y1 A*
13451023-C-T 11295347-C-T A*
13448479-C-T 11292803-C-T A*
13489722-C-T 11334046-C-T A*
18316819-G-A 16204939-G-A P6_Prx A*
13450807-A-C 11295131-A-C A*
24342018-G-T 22195871-G-T P3_t1 A*
25919003-C-T 23772856-C-T P1_Y1 A*
13449887-C-T 11294211-C-T A*
25948677-G-A 23802530-G-A P1_Y1 A*
25948679-A-T 23802532-A-T P1_Y1 A*
3107332-A-C 3239291-A-C A*
18492284-C-T 16380404-C-T P6_Dst A*
4714286-A-G 4846245-A-G FT88633 +
13527198-A-C 11371522-A-C +
2851386-T-C 2983345-T-C BY56832 YY+
13938484-T-C 11817778-T-C FT89210 Y+
10825989-TC-T +
15719740-T-C 13607860-T-C BY103571 YY+
16002220-G-A 13890340-G-A FT89380 Y+
17674275-G-T 15562395-G-T BY54976 YY+
17759713-T-C 15647833-T-C BY117193 YY+
18084260-TC-T 15972380-TC-T +
8503878-T-A 8635837-T-A BY73478 YY+
21973303-C-T 19811417-C-T BY136749 YY+
4919323-C-T 5051282-C-T BY58431 +
5646180-C-T 5778139-C-T FT88846 +
24483403-G-C 22337256-G-C BY150302 +
23624074-A-T 21462188-A-T BY146807 YY+
21941985-G-A 19780099-G-A FT89669 Y+
10828826-A-ACCATTCCATT *
56825749-A-G *
20376639-G-A 18214753-G-A P5_Dst *
9493188-A-G 9655579-A-G **
10080063-T-C 10242454-T-C **
13348376-A-G 11192700-A-G **
28644554-G-A 26498407-G-A **
7712098-G-A 7844057-G-A **
18011771-T-TC 15899891-T-TC P7_Dst **
14377947-G-T 12257243-G-T **
14446586-C-T 12325859-C-T **
14501494-GA-G 12389699-GA-G **
14766751-C-T 12654820-C-T **
19330309-A-G 17218429-A-G **
18968183-G-T 16856303-G-T **
17826847-A-G 15714967-A-G **
21940112-G-A 19778226-G-A **
13341427-C-A 11185751-C-A **
5492375-CT-C 5624334-CT-C 9×T**
3451407-T-C 3583366-T-C **
9524354-C-CAA 9686745-C-CAA 13×A**
19425608-G-C 17313728-G-C CTS10373 FGC39 **
5684024-G-C 5815983-G-C **
13460136-C-A 11304460-C-A **
14766746-A-G 12654815-A-G **
26224266-T-C 24078119-T-C BY49382 P1_Y1 **
15566817-GAAA-G 13454937-GAAA-G 22×A***
18340489-TACACAC-T,TAC 16228609-TACACAC-T,TAC P6_Prx 12×AC***
21796018-C-T 19634132-C-T ***
7149485-AT-A 7281444-AT-A ***
3076069-C-CTT 3208028-C-CTT 25×T***
16712985-CTT-C 14601105-CTT-C 11×T***
19226755-A-G 17114875-A-G ***
19204308-C-CT 17092428-C-CT ***
5255069-ATT-A 5387028-ATT-A 15×T***
19510208-C-T 17398328-C-T ***
23121399-G-A 20959513-G-A ***
22584320-T-C 20422434-T-C ***
22723269-C-A 20561383-C-A ***
22938878-A-G 20776992-A-G ***
23121403-T-G 20959517-T-G ***
7149479-C-T 7281438-C-T ***
4023431-C-T 4155390-C-T ***
22914674-CAAAAAAAA-C 20752788-CAAAAAAAA-C 27×A***
23121405-C-T 20959519-C-T ***
17678621-CTTTTTT-C 15566741-CTTTTTT-C 26×T***
8702810-G-GTT 8834769-G-GTT 21×T***
28492645-G-T 26346498-G-T ***
28529232-CAAAAAAAA-C 26383085-CAAAAAAAA-C 23×A***
10079480-A-AT 10241871-A-AT 10×T***
5753522-C-CT 5885481-C-CT 10×T***
3521303-ATT-A 3653262-ATT-A 14×T***
15410503-A-G 13298623-A-G ***
13919208-CA-C,CAAAAA 11798502-CA-C,CAAAAA 17×A***
7015324-CTTTT-C,CT 7147283-CTTTT-C,CT 23×T***
6816713-CAAAA-C,CAAA 6948672-CAAAA-C,CAAA 19×A***
6642664-T-TG 6774623-T-TG ***
4986084-T-TATA 5118043-T-TATA ***
2831929-AAT-A 2963888-AAT-A ***
4814241-G-T 4946200-G-T ***
13438289-G-A 11282613-G-A ***
4654940-TT-T,TA 4786899-TT-T,TA ***
4021930-CTTTT-C,CTT 4153889-CTTTT-C,CTT 15×T***
3374837-G-T 3506796-G-T ***
13670006-G-C 11514330-G-C ***
13669996-CAATGGAATGG-C 11514320-CAATGGAATGG-C 4×AATGG***
13466591-C-T 11310915-C-T ***
19513578-AT-A,ATT 17401698-AT-A,ATT 20×T***
14377944-A-C 12257240-A-C ***
3306207-G-A 3438166-G-A ***
13484110-T-A 11328434-T-A ***
12371950-CAA-C,CAAA ***
15669964-CAAAAAA-C,CAAAAAAA 13558084-CAAAAAA-C,CAAAAAAA 18×A***
9125447-CTT-C,CT ***
15794347-C-T 13682467-C-T ***
13484158-T-A 11328482-T-A ***
16494412-G-T 14382532-G-T ***
17189355-GAAAA-G,GAAAAA 15077475-GAAAA-G,GAAAAA 19×A***
14875592-GTTTTTT-G 12763662-GTTTTTT-G 28×T***
7149493-T-C 7281452-T-C ***
4446635-T-TA 4578594-T-TA 27×A***

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: 947561467136892033288197913
Used in age calculations1467136892033288197913
Counts of SNPs107
Variant counts last updated 2020-03-16 02:56:57.



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