Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > Z251/S470 > Z16943 > A6078 > A6077

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
231656
6958056-T-A 7090015-T-A BY23461 YY+
8234842-C-T 8366801-C-T BY23557 YY+
8509097-T-G 8641056-T-G BY23587 YY+
8591862-G-T 8723821-G-T BY23600 YY+
8909873-T-G 9041832-T-G BY23628 +
10010222-G-A 10172613-G-A BY23691 Y+
13833842-G-A 11713136-G-A FT212329 DYZ17 +
14010437-G-A 11889731-G-A BY23795 YY+
14638383-G-A 12526452-G-A ZS7832 YY+
14881233-A-G 12769303-A-G BY23863 YY+
15089718-C-G 12977807-C-G FT212581 YY+
15328599-C-A 13216717-C-A BY23891 YY+
16172619-C-G 14060739-C-G BY23935 Y+
16329795-G-A 14217915-G-A BY23954 YY+
16366595-C-G 14254715-C-G BY23958 YY+
16366619-A-G 14254739-A-G BY23959 YY+
16782415-T-C 14670535-T-C YP5708 YY+
16786335-A-G 14674455-A-G BY23987 YY+
17850423-T-C 15738543-T-C BY24092 YY+
18026704-A-G 15914824-A-G BY24102 Y+
19179416-C-A 17067536-C-A BY24205 Y+
19206927-T-A 17095047-T-A BY24207 YY+
21110673-C-T 18948787-C-T BY24262 YY+
21259853-C-A 19097967-C-A BY24276 YY+
22579928-C-A 20418042-C-A BY24674 YY+
27643867-G-A 25497720-G-A BY24878 P1_Y2 +
14405584-C-CT 12284881-C-CT +
17586208-TA-T 15474328-TA-T 9×A+
6753372-T-A 6885331-T-A **
6753377-G-T 6885336-G-T **
7260177-G-C 7392136-G-C F937 **
7897251-A-G 8029210-A-G **
16191528-G-T 14079648-G-T **
22461469-G-C 20299583-G-C PF2399 DYZ19 **
23309242-A-C 21147356-A-C PR7349 **
13817108-T-G 11696402-T-G DYZ17 ***
19947314-G-C 17835434-G-C P5_Prx ***
19947315-G-A 17835435-G-A P5_Prx ***
9146934-A-G 9309325-A-G S190PF4673 ***
9146937-C-T 9309328-C-T S190Z16261 ***
13676521-T-C 11520845-T-C DYZ17 ***
6230245-G-A 6362204-G-A IR3_Dst ***
9364131-C-A 9526522-C-A ***
9371416-T-A 9533807-T-A ***
13572952-G-A 11417276-G-A FT445588 ***
13720472-T-C 11564796-T-C FT60424 DYZ17 ***
21067503-C-CA 18905617-C-CA ***
21157313-GTGAGTTTGAGAA-G 18995427-GTGAGTTTGAGAA-G ***
21369924-G-A 19208038-G-A S7478 PF2175 ***
22302763-C-A 20140877-C-A FGC32023 DYZ19 ***
22310799-A-G 20148913-A-G DYZ19 ***
22369493-T-G 20207607-T-G DYZ19 ***
22424853-G-A 20262967-G-A DYZ19 ***
22425985-G-C 20264099-G-C BY197904 DYZ19 ***
22427431-T-G 20265545-T-G DYZ19 ***
22438321-C-A 20276435-C-A BY2012 DYZ19 ***
22438336-T-A 20276450-T-A DYZ19 ***
22444111-G-C 20282225-G-C DYZ19 ***
22471090-T-G 20309204-T-G DYZ19 ***
23589262-G-A 21427376-G-A FT171380 ***
24125495-G-C 21979348-G-C P3_b1 ***
24942238-C-A 22796091-C-A g1 ***
24970583-G-A 22824436-G-A g1 ***
25209172-A-G 23063025-A-G P2_r1 ***
25986574-C-G 23840427-C-G P1_Y1 ***
25999231-A-T 23853084-A-T P1_Y1 ***
26378025-C-A 24231878-C-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.