Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > S1026 > BY3928

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
17534355-G-GT 15422475-G-GT Z16250Z16250 A146 8×T+
7144388-T-G 7276347-T-G DC161DC161 YY+
9108113-C-T 9270504-C-T BY78154 Y+
22464315-T-A 20302429-T-A BY221300 DYZ19 +
2683864-A-G 2815823-A-G BY55786 YY+
2724081-A-G 2856040-A-G BY56016 YY+
6661433-G-A 6793392-G-A BY60596 YY+
8052638-C-T 8184597-C-T BY69630 YY+
8261391-A-C 8393350-A-C BY71247 YY+
8360069-T-C 8492028-T-C BY71983 YY+
8482119-C-G 8614078-C-G BY73219 YY+
8563832-A-T 8695791-A-T BY74069 YY+
8615658-G-A 8747617-G-A BY74593 YY+
13991277-G-C 11870571-G-C BY92132 YY+
15875936-C-A 13764056-C-A BY104703 YY+
16741178-G-T 14629298-G-T BY109711 YY+
16982636-T-C 14870756-T-C BY111545 YY+
17240827-A-G 15128947-A-G BY113228 YY+
18047962-A-T 15936082-A-T AM01801 YY+
18195573-G-C 16083693-G-C BY120756 YY+
18235294-A-T 16123414-A-T BY121065 Y+
18558600-A-G 16446720-A-G BY122176 YY+
18947704-T-G 16835824-T-G BY125023 YY+
21147099-A-T 18985213-A-T BY130693 YY+
22729252-A-C 20567366-A-C BY140366 YY+
22936313-T-C 20774427-T-C YY+
22967199-G-A 20805313-G-A BY142103 YY+
23115755-T-C 20953869-T-C BY143034 YY+
23331730-G-C 21169844-G-C BY144657 YY+
23492220-G-T 21330334-G-T BY145720 YY+
24390392-C-T 22244245-C-T BY149518 Y+
21164338-TA-T 19002452-TA-T +
4425818-A-T 4557777-A-T BY58158 **
6357236-G-A 6489195-G-A BY59769 **
10008363-A-C 10170754-A-C BY82813 **
13324382-C-A 11168706-C-A BY85196 **
22219719-A-C 20057833-A-C DYZ19 **
22297821-A-T 20135935-A-T DYZ19 **
22423917-G-T 20262031-G-T DYZ19 **
23188390-C-A 21026504-C-A **
28580377-G-T 26434230-G-T Y59931 **
13478791-C-T 11323115-C-T ***
9349789-A-G 9512180-A-G ***
18287082-G-T 16175202-G-T P6_Prx ***
19638323-C-T 17526443-C-T P5_Prx ***
20056181-C-T 17944301-C-T P5_Prx ***
20616257-C-G 18454371-C-G P4_Prx ***
20774768-T-C 18612882-T-C P4_Prx ***
22220743-T-A 20058857-T-A DYZ19 ***
22229342-T-C 20067456-T-C DYZ19 ***
22231381-G-T 20069495-G-T DYZ19 ***
22238003-G-C 20076117-G-C DYZ19 ***
22245308-A-T 20083422-A-T DYZ19 ***
22246834-C-A 20084948-C-A FT453624 DYZ19 ***
22246840-G-T 20084954-G-T DYZ19 ***
22247809-A-T 20085923-A-T DYZ19 ***
22276113-T-C 20114227-T-C DYZ19 ***
22277773-T-C 20115887-T-C DYZ19 ***
22284333-G-A 20122447-G-A DYZ19 ***
22287430-A-T 20125544-A-T DYZ19 ***
22314174-T-C 20152288-T-C DYZ19 ***
22316831-G-A 20154945-G-A DYZ19 ***
22357415-T-C 20195529-T-C DYZ19 ***
22423326-T-C 20261440-T-C DYZ19 ***
22423524-C-G 20261638-C-G DYZ19 ***
22449857-C-T 20287971-C-T DYZ19 ***
24267546-T-C 22121399-T-C P3_b1 ***
25183007-C-T 23036860-C-T g1 ***
25283633-G-A 23137486-G-A P2_r1 ***
26094870-C-T 23948723-C-T P1_Y1 ***
26160086-G-A 24013939-G-A P1_Y1 ***

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.