Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > Z251/S470 > Z16943 > CTS4157

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 STR1kG
58861966-A-C 56728905-T-G +
8740675-G-T 8872634-G-T FT281063 Y17×T+
13193951-N-C 11038275-C-. +
13193950-N-T 11038274-T-. +
22237399-T-A 20075513-T-A DYZ19 +
13494543-TAC-T 11338867-TAC-T +
22457290-G-C 20295404-G-C DYZ19 +
18246305-A-G 16134425-A-G BY180690 Y+
6954762-C-T 7086721-C-T CTS690 YY+
7111402-T-G 7243361-T-G S3742 CTS961 Y+
7353876-T-G 7485835-T-G S3730 CTS1347 YY+
8570903-C-A 8702862-C-A FT295418 YY+
8644824-T-C 8776783-T-C FT192613 YY+
8722894-C-T 8854853-C-T FT295501 YY+
13950994-C-T 11830288-C-T FT295886 Y+
14199453-C-T 12078747-C-T S3738 CTS2149 YY+
14572591-C-T 12460791-C-T CTS2930 YY+
14647958-G-A 12536023-G-A CTS3079 YY+
14904631-T-C 12792698-T-C S3731 CTS3411 YY+
14975686-A-G 12863761-A-G CTS3497 YY+
15181802-G-A 13069888-G-A CTS3790 YY+
15760775-C-T 13648895-C-T S3734 CTS4668 Y+
16269642-A-G 14157762-A-G S3739 CTS5431 YY+
16432416-G-A 14320536-G-A FT296860 YY+
16577357-G-A 14465477-G-A S3729 CTS5963 YY+
16771749-C-T 14659869-C-T CTS6254 S3737 YY+
17032730-C-A 14920850-C-A CTS6650 YY+
17192060-T-A 15080180-T-A CTS6913 S3740 YY+
18083677-G-A 15971797-G-A CTS8563 YY+
18184622-T-C 16072742-T-C CTS8763 S3736 Y+
18583135-C-A 16471255-C-A CTS8964 YY+
18724807-T-C 16612927-T-C CTS9165 YY+
18871986-T-C 16760106-T-C CTS9392 YY+
18928141-C-T 16816261-C-T CTS9488 YY+
19456743-C-T 17344863-C-T CTS10440 YY+
21121956-G-T 18960070-G-T Y+
21129438-C-T 18967552-C-T FT298245 YY+
21330925-G-A 19169039-G-A S3733 YY+
21930069-C-T 19768183-C-T S3728 YY+
21992239-T-G 19830353-T-G FT298785 YY+
22545523-A-C 20383637-A-C FT390714 Y+
23562894-C-T 21401008-C-T FGC8834 YY+
24468123-T-C 22321976-T-C FT299564 Y+
4597097-T-G 4729056-T-G +
18892293-T-TTA 16780413-T-TTA +
3030126-G-A 3162085-G-A +
3296011-T-C 3427970-T-C FT316749 +
3426041-A-T 3558000-A-T +
3571635-C-CT 3703594-C-CT +
4065357-T-C 4197316-T-C +
4113732-A-C 4245691-A-C FT319556 +
4251032-TC-T 4382991-TC-T +
4460963-CG-C 4592922-CG-C +
4461030-C-G 4592989-C-G +
4475488-C-T 4607447-C-T +
4619419-T-C 4751378-T-C FGC45643 +
4803958-G-T 4935917-G-T +
4838471-A-G 4970430-A-G +
4986288-G-A 5118247-G-A FT322349 +
5550721-G-A 5682680-G-A FT324281 +
9307390-G-C 9469781-G-C Y+
9307392-G-T 9469783-G-T Y+
9951804-A-G 10114195-A-G Y+
10101631-C-A 10264022-C-A +
13143256-CA-C 10632742-CA-C +
13143330-CA-C 10632816-CA-C +
13143334-TC-T 10632820-TC-T +
13193949-N-A 11038273-A-. +
13300664-C-CA 11144988-C-CA 9×A+
13387481-C-T 11231805-C-T +
13577516-G-A 11421840-G-A +
13602211-G-C 11446535-G-C +
13717361-G-T 11561685-G-T DYZ17 +
13717362-A-T 11561686-A-T DYZ17 +
14392886-A-C 12272182-A-C YY+
14609799-C-CAAA 12498001-C-CAAA 23×A+
14642471-TG-T 12530540-TG-T +
15315460-T-TA 13203565-T-TA +
15815814-G-A 13703934-G-A FT296640 YY+
16081109-T-C 13969229-T-C CTS5236 Y+
16293555-TG-T 14181675-TG-T +
16309587-AATAC-A 14197707-AATAC-A +
16363825-T-G 14251945-T-G YY+
17703236-T-TAAA 15591356-T-TAAA 22×A+
18006699-T-TATC 15894819-T-TATC P7_Gap +
18026019-T-A 15914139-T-A CTS8434 Y+
18393269-T-TATC 16281389-T-TATC P6_Gap +
18719747-C-G 16607867-C-G CTS9161 YY+
19073837-AGTAT-A 16961957-AGTAT-A +
19239058-C-CTATA 17127178-C-CTATA +
19411949-AG-A 17300069-AG-A +
19498816-G-A 17386936-G-A YY+
19562084-T-G 17450204-T-G Y2451 CTS10600 PF1441 Y+
21043103-T-C 18881217-T-C FT298179 Y+
21050705-A-G 18888819-A-G YY+
21096483-C-A 18934597-C-A FT314001 Y+
22237395-A-G 20075509-A-G DYZ19 +
22462709-A-T 20300823-A-T BY27586 DYZ19 +
22552638-C-A 20390752-C-A YY+
23772362-A-T 21610476-A-T Y+
24456925-T-C 22310778-T-C Y+
27861667-T-G 25715520-T-G P1_Y2 +
28463458-A-C 26317311-A-C +
28565749-G-A 26419602-G-A +
58903327-G-T 56687544-C-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.

Mutation Notes:

Manual6351101-T-A6483060-T-A3 good reads, all with an A.
Manual22253773-A-G20091887-A-G16 reads total -- 3 are G, the balance are A.
Manual4439911-TGCAGCTTCACTCCTGAGG-T4571870-TGCAGCTTCACTCCTGAGG-T2 reads, both positive.
Manual25633952-G-A23487805-G-A5 reads, all G. This is a palindromic SNP with 4 copies. As such, I don't consider this result to be a definitive no.