Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > ZZ10 > Z253 > BY4086 > FGC17436 > Z17693 > FGC73657 > S7897 > A495 > S7898 > S15280 > ~18618565-G-A

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
28691900-T-TA 26545753-T-TA 13×AA*
6032961-G-A 6164920-G-A A*
25868696-A-C 23722549-A-C P1_Y1 A*
7462955-G-A 7594914-G-A IR1_L A*
56833561-T-C A*
20613457-C-T 18451571-C-T P4_Prx A*
13450057-C-A 11294381-C-A A*
19771510-C-A 17659630-C-A P5_Prx A*
6097382-A-G 6229341-A-G FT133243 +
13850670-T-C 11729964-T-C FT133748 +
14180037-G-A 12059331-G-A FT133842 Y+
7887227-C-T 8019186-C-T FT133484 YY+
15719331-G-T 13607451-G-T FT134067 YY+
16462157-T-C 14350277-T-C FT134179 YY+
14902967-T-C 12791034-T-C FT133968 YY+
4233987-T-G 4365946-T-G FT132690 +
4087493-A-G 4219452-A-G FT132652 +
3893933-C-T 4025892-C-T FT132595 +
22610296-C-T 20448410-C-T YY+
23119548-A-G 20957662-A-G FT134936 YY+
19749309-CT-C 17637429-CT-C P5_Prx 22×T+
3830810-C-T 3962769-C-T FT48881 +
8244238-T-C 8376197-T-C FT133533 YY+
6076854-C-T 6208813-C-T *
6167025-CTGTG-C 6298984-CTGTG-C IR3_Dst 12×TG*
5273768-C-T 5405727-C-T *
10982191-CTCCATTCCAT-C *
13338429-G-T 11182753-G-T **
10081212-A-G 10243603-A-G **
9524123-A-C 9686514-A-C **
13470709-T-G 11315033-T-G **
21950107-T-A 19788221-T-A **
16097032-T-G 13985152-T-G **
17432247-T-C 15320367-T-C **
19706389-T-C 17594509-T-C P5_Prx **
20689840-A-T 18527954-A-T P4_Prx **
21823716-T-C 19661830-T-C **
22478076-A-T 20316190-A-T DYZ19 **
26482446-CA-C 24336299-CA-C P1_Y1 **
3662620-T-C 3794579-T-C **
16148507-CT-C 14036627-CT-C P8_Dst 22×T**
22208987-C-A 20047101-C-A **
20574944-GTTTT-G 18413058-GTTTT-G P5_Dst 19×T**
5784599-A-T 5916558-A-T FT2673 **
21950104-T-A 19788218-T-A BY136628 **
5784601-A-T 5916560-A-T FT2674 **
17061107-A-G 14949227-A-G **
13453226-A-C 11297550-A-C 10×TCCAT**
19706383-A-C 17594503-A-C P5_Prx **
19720709-A-ATT 17608829-A-ATT P5_Prx 23×T**
5784602-A-AT 5916561-A-AT 9×AT**
13962042-CTTT-C,CTT 11841336-CTTT-C,CTT 28×T***
20816924-CAAAA-C 18655038-CAAAA-C P4_Gap 22×A***
2651883-CTTTTTTT-C 2783842-CTTTTTTT-C 19×T***
18465469-GAAAAAAA-G 16353589-GAAAAAAA-G P6_Dst 26×A***
2960062-CA-C,CAA 3092021-CA-C,CAA 17×A***
4537586-CTTTTT-C 4669545-CTTTTT-C 21×T***
13476980-A-C 11321304-A-C ***
13448836-C-G 11293160-C-G ***
4414167-CTTT-C 4546126-CTTT-C 18×T***
10825274-G-GCATTC ***
13365795-AT-A 11210119-AT-A 16×T***
8650012-AAG-A 8781971-AAG-A ***
20804004-T-TTG 18642118-T-TTG P4_Gap 19×TG***
16340147-G-GAAA 14228267-G-GAAA 22×A***
15963828-A-T 13851948-A-T ***
7269610-CTT-C,CT 7401569-CTT-C,CT 22×T***
14464165-ATT-A,AT 12343438-ATT-A,AT 18×T***
15593274-CAAA-C,CAA 13481394-CAAA-C,CAA 23×A***
22537275-CAA-C,CAAA 20375389-CAA-C,CAAA 15×A***
5777882-A-C 5909841-A-C ***
3370477-GT-G 3502436-GT-G ***
4983174-ATTT-A,AT 5115133-ATTT-A,AT 28×T***
4511188-AAG-A 4643147-AAG-A ***
7591201-A-G 7723160-A-G ***
13470445-C-A 11314769-C-A ***
13470410-T-A 11314734-T-A ***
9211374-C-A 9373765-C-A ***
10776302-C-G ***
11008984-C-T ***
4573079-C-CT 4705038-C-CT 9×T***
13364145-TC-T 11208469-TC-T ***
20958967-CTT-C 18797081-CTT-C P4_Dst 13×T***
7723048-T-A 7855007-T-A ***
28602249-G-A 26456102-G-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)

Kit: B4412791490218193390288299339
Used in age calculations1490218193390288299339
Counts of SNPs87
Variant counts last updated 2020-07-15 02:47:23.

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