Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > CTS1751 > Z17966 > Y18513 > Y47709

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
22304457-C-A 20142571-C-A DYZ19 A*
28816668-G-T 26670521-G-T A*
16115193-G-GTATT 14003313-G-GTATT P8_Prx 7×TATTA*
6322270-T-C 6454229-T-C IR3_Dst A*
13448000-C-A 11292324-C-A A*
19585719-G-A 17473839-G-A P5_Prx YA*
19620676-G-A 17508796-G-A P5_Prx YA*
19680407-C-T 17568527-C-T P5_Prx A*
19680993-C-T 17569113-C-T P5_Prx A*
19696334-C-T 17584454-C-T P5_Prx A*
19795600-G-A 17683720-G-A P5_Prx A*
19864046-A-G 17752166-A-G P5_Prx A*
20483439-G-A 18321553-G-A P5_Dst A*
24269788-G-T 22123641-G-T P3_b1 A*
26271873-G-A 24125726-G-A P1_Y1 A*
26517508-A-G 24371361-A-G P1_Y1 A*
4381160-T-G 4513119-T-G Y21410FGC34853 6×TTG+
18108468-T-A 15996588-T-A FGC43319Z33595 YY+
5825833-C-T 5957792-C-T FGC3611 +
22582438-C-T 20420552-C-T BY139272 YY+
9811530-G-A 9973921-G-A BY20408 YY+
22273097-G-A 20111211-G-A BY171773 DYZ19 +
10874185-C-A FT434998 +
7256247-C-T 7388206-C-T FT185183 Y+
2670926-G-A 2802885-G-A FT109507 Y+
2947605-A-G 3079564-A-G FT183248 +
3544740-T-A 3676699-T-A FT183509 +
4039024-T-C 4170983-T-C FT183735 +
4399216-G-T 4531175-G-T FT183930 +
4849633-C-G 4981592-C-G FT184176 +
4968001-C-G 5099960-C-G FT184225 +
5557381-A-G 5689340-A-G FT184514 +
6459922-A-G 6591881-A-G FT184870 +
7047977-T-C 7179936-T-C FT185085 YY+
7323590-C-T 7455549-C-T FT185195 YY+
7464580-T-C 7596539-T-C FT185249 IR1_L +
7554472-G-A 7686431-G-A FT185272 YY+
7701951-T-C 7833910-T-C FT185332 YY+
7731782-C-A 7863741-C-A FT121395 YY+
8324899-A-G 8456858-A-G FT185575 Y+
8892500-G-T 9024459-G-T FT185851 Y+
8912043-C-A 9044002-C-A FT185859 +
9109314-A-C 9271705-A-C FT185907 Y+
10678965-T-G FT428858 +
10690625-C-G FT429198 +
13585593-C-T 11429917-C-T +
13711114-T-A 11555438-T-A FT449354 11×GAATG+
13883096-G-A 11762390-G-A FT186140 Y+
14079484-C-T 11958778-C-T FT186295 YY+
14234932-G-T 12114226-G-T FT186406 YY+
14377104-G-A 12256400-G-A FT163194 YY+
12379334-T-C FT186539 +
14970468-AC-A 12858543-AC-A +
15659389-C-T 13547509-C-T FT187006 YY+
16402873-T-C 14290993-T-C FT187297 YY+
16445548-C-T 14333668-C-T FT187310 YY+
16458139-A-T 14346259-A-T FT187319 YY+
16953776-CA-C 14841896-CA-C +
17064207-A-G 14952327-A-G FT187579 YY+
17289719-CT-C 15177839-CT-C +
17468908-A-G 15357028-A-G FT187737 YY+
18788949-G-A 16677069-G-A YY+
19155194-G-A 17043314-G-A FT188449 YY+
19227437-T-C 17115557-T-C FT188476 YY+
21832591-T-C 19670705-T-C FT188963 Y+
22459238-A-G 20297352-A-G BY220279 DYZ19 +
22915658-G-A 20753772-G-A YY+
23272991-A-T 21111105-A-T FT189376 YY+
23310487-T-C 21148601-T-C FT182692 YY+
23805916-T-C 21644030-T-C FT189559 Y+
24000752-T-C 21854605-T-C FT189602 Y+
24880099-G-A 22733952-G-A FT461124 g1 +
16236233-A-AAAAC 14124353-A-AAAAC 8×AAAC*
9533796-A-ATG 9696187-A-ATG IR3_Prx 8×TG*
5811498-G-A 5943457-G-A **
18486204-A-AG 16374324-A-AG P6_Dst **
3031667-A-G 3163626-A-G **
7175815-G-A 7307774-G-A **
8740234-T-C 8872193-T-C **
9804652-T-C 9967043-T-C **
13467475-G-A 11311799-G-A **
13577990-G-T 11422314-G-T **
11675426-G-A **
14739541-A-G 12627609-A-G **
15298837-A-G 13186936-A-G **
16422026-A-C 14310146-A-C **
17839892-A-G 15728012-A-G **
19097571-C-A 16985691-C-A **
20312013-A-T 18150127-A-T P5_Dst **
21598197-G-GA 19436311-G-GA **
22272357-G-T 20110471-G-T DYZ19 **
22298129-G-T 20136243-G-T BY157011 DYZ19 **
22419937-C-T 20258051-C-T DYZ19 **
22433624-C-T 20271738-C-T DYZ19 **
16247-C-T **
23174-C-G **
14776923-CA-C,CAA 12664992-CA-C,CAA 15×A***
4583115-C-CTT 4715074-C-CTT 22×T***
6336567-G-GCA 6468526-G-GCA IR3_Dst 8×CA***
9900492-A-T 10062883-A-T BY81905 ***
14456634-C-A 12335907-C-A ***
17027718-T-A 14915838-T-A ***
19036875-A-G 16924995-A-G ***
19203886-A-G 17092006-A-G ***
19204157-T-C 17092277-T-C ***
22113305-T-C 19951419-T-C ***
22304319-T-C 20142433-T-C DYZ19 ***
22438358-G-T 20276472-G-T DYZ19 ***
22876964-T-TA,TAA 20715078-T-TA,TAA 20×A***
23019767-T-C 20857881-T-C ***
23416511-C-CTT 21254625-C-CTT 16×T***

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.