Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > FGC5494 > Y15901 > Y9089

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
58909239-T-C 56681632-A-G +
13577575-TTGA-T 11421899-TTGA-T +
16175584-GCA-G 14063704-GCA-G +
16171030-T-C 14059150-T-C FT346868 Y+
15961942-T-TGG 13850062-T-TGG +
15874334-AG-A 13762454-AG-A +
15866371-C-G 13754491-C-G S17682 YY+
15863183-G-A 13751303-G-A YY+
15507258-G-T 13395378-G-T YY+
15247995-C-G 13136081-C-G Y+
15231944-T-C 13120030-T-C Y+
14986649-TCG-T 12874717-TCG-T +
14979100-T-C 12867176-T-C YY+
14200750-A-AT 12080044-A-AT +
13885999-T-G 11765293-T-G M9067 Y+
13621577-C-G 11465901-C-G +
13529275-G-A 11373599-G-A +
16277219-A-C 14165339-A-C YY+
13521064-A-G 11365388-A-G +
13521041-T-G 11365365-T-G +
13436543-T-C 11280867-T-C +
13430670-G-A 11274994-G-A +
13430646-GTCT-G 11274970-GTCT-G +
13402442-T-C 11246766-T-C +
13326061-A-C 11170385-A-C +
13319342-G-GTA 11163666-G-GTA +
13311501-G-A 11155825-G-A +
13309681-C-T 11154005-C-T +
13269016-G-T 11113340-G-T +
13222419-C-G 11066743-C-G +
9945028-T-C 10107419-T-C Y+
9945024-C-T 10107415-C-T Y+
16247957-T-C 14136077-T-C YY+
16410142-G-T 14298262-G-T YY+
9643202-T-C 9805593-T-C IR3_Prx +
22507426-G-A 20345540-G-A FGC31820 DYZ19 +
58891004-T-C 56699867-A-G +
58881594-G-T 56709277-C-A +
58881591-A-C 56709280-T-G +
58881588-A-C 56709283-T-G +
58881584-T-A 56709287-A-T +
58831113-C-A 56759758-G-T +
28817653-GGAATGGAAT-G 26671506-GGAATGGAAT-G +
28760897-A-C 26614750-A-C Y+
28553464-T-C 26407317-T-C +
28491352-G-A 26345205-G-A +
23984113-C-A 21837966-C-A FT369642 Y+
23252216-G-T 21090330-G-T M8030 YY+
23209796-A-C 21047910-A-C Y+
23011286-T-G 20849400-T-G YY+
21152835-G-A 18990949-G-A Y+
17038333-C-T 14926453-C-T S19127 YY+
20827065-A-G 18665179-A-G P4_Gap +
19288830-C-T 17176950-C-T M7150 YY+
19143952-A-T 17032072-A-T FGC37894 BY1504 YY+
19052390-G-T 16940510-G-T YY+
18863053-T-G 16751173-T-G Y+
18710160-A-C 16598280-A-C YY+
18035631-C-T 15923751-C-T YY+
17999518-G-C 15887638-G-C P7_Gap Y+
17948277-A-C 15836397-A-C YY+
17794499-G-A 15682619-G-A YY+
17695537-C-A 15583657-C-A M9229 YY+
17593413-T-G 15481533-T-G YY+
17500808-G-C 15388928-G-C Y+
17136924-A-T 15025044-A-T YY+
9930934-C-G 10093325-C-G Y+
8826707-ACAG-A 8958666-ACAG-A +
22269465-A-G 20107579-A-G DYZ19 +
15143093-G-A 13031180-G-A Y+
5632865-T-A 5764824-T-A +
7241839-C-G 7373798-C-G Y+
5632856-G-T 5764815-G-T 8×A+
13568858-T-C 11413182-T-C +
16224920-T-G 14113040-T-G YY+
6929129-TTGC-T 7061088-TTGC-T +
58859677-C-T 56731194-G-A +
58849244-C-A 56741627-G-T +
24862285-C-A 22716138-C-A IR1_R +
23388900-T-C 21227014-T-C FT348961 YY+
19115453-C-A 17003573-C-A FT347950 YY+
18913577-G-A 16801697-G-A FT347866 YY+
15745778-C-T 13633898-C-T Y+
15392537-G-A 13280657-G-A YY+
13928611-T-C 11807905-T-C Y5×CTC+
3253456-A-G 3385415-A-G +
9405380-T-C 9567771-T-C FT345952 YY+
7671697-T-A 7803656-T-A FT345397 YY+
7671160-T-G 7803119-T-G FT345396 YY+
7562943-G-A 7694902-G-A FT345341 YY+
7351178-G-A 7483137-G-A FT345266 YY+
7045536-G-A 7177495-G-A YY+
6968880-A-G 7100839-A-G FT345110 YY+
6908140-G-A 7040099-G-A Z28293 YY+
6684027-A-C 6815986-A-C Y+
18858611-G-A 16746731-G-A FTA12340 YY14×A+
17199319-G-T 15087439-G-T FT46447 YY13×T+
16732961-G-T 14621081-G-T YY14×T+
28600861-A-G 26454714-A-G Y+
22269504-A-G 20107618-A-G DYZ19 +
2767044-C-A 2899003-C-A YY+
3275791-C-A 3407750-C-A +
8706660-C-T 8838619-C-T YY+
5275715-G-C 5407674-G-C FT39512 +
8232955-CAGTTAAG-C 8364914-CAGTTAAG-C +
7536378-T-G 7668337-T-G YY+
7461024-C-G 7592983-C-G IR1_L +
6929130-TGC-T 7061089-TGC-T +
6906890-A-C 7038849-A-C YY+
6617559-A-G 6749518-A-G Y+
6617557-T-C 6749516-T-C Y+
6473285-T-G 6605244-T-G +
6093500-C-A 6225459-C-A +
5980955-A-G 6112914-A-G +
5729121-G-T 5861080-G-T FT114634 +
5519058-G-A 5651017-G-A FT114468 +
5458725-C-A 5590684-C-A +
5365581-A-G 5497540-A-G FT12169 +
5177733-A-C 5309692-A-C +
3403258-ATCC-A 3535217-ATCC-A +
5127018-A-G 5258977-A-G +
5022690-GTT-G 5154649-GTT-G +
4765852-G-T 4897811-G-T Z20455 +
4704840-CAATT-C 4836799-CAATT-C +
4674602-A-G 4806561-A-G +
4584815-G-A 4716774-G-A +
4304450-G-A 4436409-G-A +
4256127-C-G 4388086-C-G +
4152114-C-A 4284073-C-A +
4148830-A-G 4280789-A-G +
4025209-T-C 4157168-T-C +
3859766-C-G 3991725-C-G FT132587 +
3529586-C-T 3661545-C-T FT27608 +
3432581-C-A 3564540-C-A +
58976431-ATTCC-A 56830284-ATTCC-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:

Manual22231381-G-A20069495-G-A9 reads - 4G and 5A.
Manual14331769-AAG-A12211063-AAG-A4 reads, all show the insertion.
Manual16242812-T-A14130932-T-AJust one read, an A.
Manual17995655-T-C15883775-T-CJust one read, a C.
Manual18351464-A-G16239584-A-G1A 2G
Manual19785865-G-A17673985-G-A1G 2A
Manual19851474-T-A17739594-T-A1T 2A
Manual20668566-G-A18506680-G-A1G 1A
Manual20744295-G-A18582409-G-A1G 5A
Manual22278139-G-T20116253-G-T10G 8T
Manual22284207-G-A20122321-G-A8G 4A
Manual22427591-C-T20265705-C-T5C 4T
Manual25276308-T-A23130161-T-A4T 2A
Manual26118776-G-A23972629-G-A1G 2A
Manual22590488-T-TA20428602-T-TA2 reads, both positive.

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