Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12

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 STRFTDNA
9065498-TC-T 9227889-TC-T +
22239237-G-A 20077351-G-A BY51326 DYZ19 +
21953862-A-G 19791976-A-G Y57428 YY+
21365360-C-T 19203474-C-T Y56577 YY+
22631162-G-A 20469276-G-A Y58072 Y+
15164608-A-T 13052694-A-T A14596 YY12×AT+
19549395-C-T 17437515-C-T Y56057 YY+
19343998-C-G 17232118-C-G Y55744 YY+
18992651-A-G 16880771-A-G Y55175 YY+
18255129-C-A 16143249-C-A Y54474 Y+
18114030-G-A 16002150-G-A Y54265 YY+
16828112-A-C 14716232-A-C Y52393 YY+
16747464-T-G 14635584-T-G Y52279 YY+
16543548-G-A 14431668-G-A Y52013 YY+
15727470-C-T 13615590-C-T Y51059 YY+
15721871-A-G 13609991-A-G Y51049 YY+
15420846-C-A 13308966-C-A Y50629 YY+
14998586-T-A 12886671-T-A Y50155 YY+
6668292-C-A 6800251-C-A Y45173 YY+
17223343-G-GT 15111463-G-GT 9×T+
22465643-A-T 20303757-A-T BY52929 DYZ19 +
28802346-C-T 26656199-C-T BY31277 +
2809698-C-T 2941657-C-T Y44878 YY+
26400932-A-T 24254785-A-T P1_Y1 +
6895786-A-G 7027745-A-G Y45424 YY+
23375074-C-T 21213188-C-T Y59091 YY+
7178652-G-A 7310611-G-A Y45720 YY+
24886468-A-C 22740321-A-C BY226294 g1 +
7417418-T-C 7549377-T-C Y46020 YY+
7771261-G-T 7903220-G-T Y46389 YY+
24507344-G-A 22361197-G-A Y59887 +
9523138-A-G 9685529-A-G Y48433 +
22184412-C-G 20022526-C-G Y57732 YY+
22430441-A-C 20268555-A-C BY218008 DYZ19 **
22428550-A-G 20266664-A-G DYZ19 **
22219643-C-T 20057757-C-T DYZ19 **
19088569-G-T 16976689-G-T CTS9825 **
4049458-T-C 4181417-T-C BY57952 **
7337508-T-C 7469467-T-C Y45924 **
23726383-T-C 21564497-T-C ***
26266519-TC-T 24120372-TC-T P1_Y1 ***
24807070-G-C 22660923-G-C P3_b2 ***
24730439-C-T 22584292-C-T P3_b2 ***
9211664-G-T 9374055-G-T ***
24113486-G-A 21967339-G-A P3_b1 ***
13827164-A-AAATGG 11706458-A-AAATGG ***
22217967-T-A 20056081-T-A DYZ19 ***
19743818-C-G 17631938-C-G P5_Prx ***
22450320-G-T 20288434-G-T DYZ19 ***
19814927-A-T 17703047-A-T P5_Prx ***
22303771-G-T 20141885-G-T DYZ19 ***
22280361-G-T 20118475-G-T DYZ19 ***
22279136-T-G 20117250-T-G DYZ19 ***
22276029-G-T 20114143-G-T DYZ19 ***
22251385-G-T 20089499-G-T DYZ19 ***
22243457-T-G 20081571-T-G DYZ19 ***
19692567-G-A 17580687-G-A P5_Prx ***

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: 420691088665579395548024116
Used in age calculations1088665579395548024116
Counts of SNPs2323
Variant counts last updated 2019-11-29 02:37:54.

Big Tree Main Page