Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > ZZ39 > Z229 > Y16019 > Y16018 > BY21399 > B342

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
HG00742
Manual
Edits
8140401-G-A 8272360-G-A Z101 YY+
16050917-T-C 13939037-T-C FTB28917 YY+
9945050-C-A 10107441-C-A Y+
24600382-C-T 22454235-C-T BY23042 P3_t2 +
17477484-G-A 15365604-G-A YY14×A+
14737352-C-T 12625420-C-T Y+
16834465-C-T 14722585-C-T FT297024 YY+
28686545-T-C 26540398-T-C +
7185273-G-A 7317232-G-A FT109081 Y+
7531843-G-A 7663802-G-A YY+
9072433-G-T 9234824-G-T Y+
9393408-G-A 9555799-G-A YY+
9431955-G-C 9594346-G-C Y+
14155700-C-A 12034994-C-A Y+
14255547-G-A 12134841-G-A FT311675 Y+
14769433-T-C 12657502-T-C YY+
15046195-C-T 12934285-C-T YY+
16195659-A-G 14083779-A-G FT296756 YY+
16244276-G-T 14132396-G-T YY+
16500331-T-C 14388451-T-C FT296881 Y+
17755531-A-G 15643651-A-G FT297397 YY+
22613899-C-G 20452013-C-G FT299004 YY+
22828227-C-A 20666341-C-A BY205407 YY+
22880047-C-A 20718161-C-A Y+
23059737-C-G 20897851-C-G F25744 YY+
23358597-C-A 21196711-C-A CTS11924 Y+
23398592-T-C 21236706-T-C FT89732 Y+
23533434-G-T 21371548-G-T Z22716 YY+
28544473-C-T 26398326-C-T +
28621218-G-T 26475071-G-T Y+
13254991-A-G 11099315-A-G 12×T+
2824725-CA-C 2956684-CA-C +
2845158-C-A 2977117-C-A M9438 YY+
3068281-C-T 3200240-C-T +
3329703-A-G 3461662-A-G +
3412053-A-T 3544012-A-T +
3443608-C-T 3575567-C-T +
3557336-A-G 3689295-A-G +
3557391-TTC-T 3689350-TTC-T +
3845768-G-C 3977727-G-C FT318697 +
3890112-T-C 4022071-T-C +
4208576-TGA-T 4340535-TGA-T +
4446217-C-G 4578176-C-G FT88556 +
4467445-T-G 4599404-T-G FT88563 +
4658785-A-T 4790744-A-T +
5144178-A-G 5276137-A-G FT88728 +
5316596-A-G 5448555-A-G FT88766 +
5482850-A-T 5614809-A-T +
5607528-T-G 5739487-T-G +
5860836-A-T 5992795-A-T FT325310 +
5860837-C-A 5992796-C-A FT325311 +
6532701-G-A 6664660-G-A +
6861300-T-TTC 6993259-T-TTC +
7142452-C-T 7274411-C-T Y+
7509721-C-T 7641680-C-T Y+
8026917-CTCT-C 8158876-CTCT-C +
8088189-AT-A 8220148-AT-A +
8288838-AGG-A 8420797-AGG-A +
8580250-G-A 8712209-G-A F17257 YY+
8977951-C-T 9140342-C-T Y+
9377013-G-A 9539404-G-A Y+
9451278-T-C 9613669-T-C YY+
9610591-C-T 9772982-C-T FTB16854 IR3_Prx +
9771624-C-A 9934015-C-A Y+
9785300-G-T 9947691-G-T Y+
9914423-G-A 10076814-G-A Y+
13108698-C-A 10598184-C-A +
13251569-C-A 11095893-C-A +
13500490-T-A 11344814-T-A +
13623045-G-T 11467369-G-T 11×T+
13865957-ACTGAG-A 11745251-ACTGAG-A +
13868036-G-GAATGC 11747330-G-GAATGC +
13976252-G-C 11855546-G-C Y+
13990887-C-T 11870181-C-T YY+
14090602-C-T 11969896-C-T YY+
14556154-G-A 12444355-G-A YY+
14708421-T-A 12596487-T-A YY+
15248715-T-C 13136801-T-C FT296415 Y+
15733904-AG-A 13622024-AG-A +
15771103-C-T 13659223-C-T BY103976 YY+
15944372-A-G 13832492-A-G M9154 YY+
16301001-TG-T 14189121-TG-T +
16451113-A-G 14339233-A-G YY+
16852378-T-C 14740498-T-C YY+
17669819-C-T 15557939-C-T YY+
17713845-A-T 15601965-A-T YY+
17764119-C-A 15652239-C-A YY+
18171605-A-T 16059725-A-T YY+
18267125-C-T 16155245-C-T Y138703 +
18899948-T-A 16788068-T-A YY+
18926889-AG-A 16815009-AG-A +
19277251-C-T 17165371-C-T YY+
21341602-A-G 19179716-A-G YY+
21574161-G-A 19412275-G-A FGC24699 Y+
22962201-TG-T 20800315-TG-T +
28642787-T-TCC 26496640-T-TCC +
28686506-A-G 26540359-A-G +
28808392-A-G 26662245-A-G +

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:

Kit POSITION-REF-ALT (hg19) POSITION-REF-ALT (hg38) Note
Manual16051979-G-A13940099-G-A1A
Manual28660482-G-A26514335-G-A1A
Manual6778488-A-T6910447-A-T1T
Manual8108942-T-C8240901-T-C1C
Manual9932290-T-C10094681-T-C2C
Manual14265018-G-A12144312-G-A1A
Manual17308037-G-GT15196157-G-GT2 reads, both positive.
Manual17366705-G-T15254825-G-T1T
Manual19908359-C-T17796479-C-T2T
Manual20024468-C-G17912588-C-G2C 1G
Manual22010873-C-T19848987-C-T2T
Manual22231464-G-C20069578-G-C1C
Manual22282447-T-C20120561-T-C1T 2C
Manual22432173-G-T20270287-G-T1T
Manual22828155-A-G20666269-A-G1G
Manual25967914-G-A23821767-G-A1G 3A
Manual25984314-G-A23838167-G-A2G 1A