Tree Position

R-U106/S21 > Z2265 > Z381/S263 > Z301/S499 > L48 > L47/S170 > Z160 > S3251 > FGC8604 > ZZ66 > A688 > Exact position not yet finalized.

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
HG00131
Manual
Edits
13526327-G-A 11370651-G-A A761A761 +
19326910-T-A 17215030-T-A CTS10206 Y+
17919854-AG-A 15807974-AG-A +
13294271-A-G 11138595-A-G +
26180188-T-C 24034041-T-C P1_Y1 +
17919853-AAG-A 15807973-AAG-A +
14334341-G-GT 12213636-G-GT +
6036864-C-T 6168823-C-T +
13503964-T-C 11348288-T-C +
13503969-A-C 11348293-A-C +
14386294-C-A 12265590-C-A Y+
24408989-TG-T 22262842-TG-T +
3164640-T-C 3296599-T-C PF26 L412 +
18183453-T-C 16071573-T-C Y+
2750838-TC-T 2882797-TC-T +
2764940-T-G 2896899-T-G F14899 YY+
3029654-C-G 3161613-C-G +
3051114-T-A 3183073-T-A +
3065775-C-A 3197734-C-A +
3107628-C-T 3239587-C-T +
3181586-G-A 3313545-G-A +
3186469-T-G 3318428-T-G +
3200288-T-C 3332247-T-C +
3200289-G-A 3332248-G-A +
3200292-T-C 3332251-T-C +
3254988-C-G 3386947-C-G +
3256136-CTAT-C 3388095-CTAT-C +
3736655-T-C 3868614-T-C +
3851832-A-G 3983791-A-G +
4375416-A-T 4507375-A-T +
4462495-T-G 4594454-T-G +
4617974-G-A 4749933-G-A Y95947 BY3150FGC1891 +
4624405-A-G 4756364-A-G +
4838962-T-G 4970921-T-G +
4997473-A-C 5129432-A-C +
5023097-C-T 5155056-C-T +
5103885-C-T 5235844-C-T +
5248639-C-T 5380598-C-T +
6090136-C-A 6222095-C-A +
6447458-A-G 6579417-A-G +
7341797-G-T 7473756-G-T Y+
8650098-A-G 8782057-A-G FGC53785 YY+
9075188-C-CTTT 9237579-C-CTTT 20×T+
9086396-A-C 9248787-A-C Y+
9842770-T-G 10005161-T-G YY+
10068130-G-A 10230521-G-A +
10068156-G-C 10230547-G-C +
10068187-T-C 10230578-T-C +
13295159-C-T 11139483-C-T +
13319340-T-TTG 11163664-T-TTG +
13319342-G-GTA 11163666-G-GTA +
13347198-T-C 11191522-T-C +
13385947-C-T 11230271-C-T +
13388421-T-G 11232745-T-G +
13389990-A-G 11234314-A-G +
13393142-G-A 11237466-G-A +
13414995-G-A 11259319-G-A +
13428138-C-T 11272462-C-T +
13448734-C-CATTCG 11293058-C-CATTCG +
13450787-ACTTGG-A 11295111-ACTTGG-A +
13507675-G-A 11351999-G-A +
13606751-C-G 11451075-C-G +
13615632-T-C 11459956-T-C S14283 +
13711998-G-A 11556322-G-A +
13847229-GACT-G 11726523-GACT-G +
14003844-A-C 11883138-A-C YY+
14339125-TG-T 12218420-TG-T +
14372867-AT-A 12252163-AT-A +
14443707-A-G 12322980-A-G CTS2716 Y+
14443713-A-T 12322986-A-T CTS2717 Y+
14493173-A-C 12381370-A-C Y+
14493181-A-C 12381378-A-C Y+
14894100-A-G 12782166-A-G M4053 YY+
15065776-G-A 12953868-G-A CTS3610 YY+
16029220-A-C 13917340-A-C Y+
16242675-T-TATCG 14130795-T-TATCG +
17500836-T-G 15388956-T-G M8509 Y+
17662175-A-G 15550295-A-G YY+
17674191-G-T 15562311-G-T FT196532 YY+
17831896-C-A 15720016-C-A YY+
19326918-G-T 17215038-G-T Y+
21146292-TG-T 18984406-TG-T +
21386185-ATTATT-A 19224299-ATTATT-A +
22253017-C-A 20091131-C-A DYZ19 +
22282035-C-T 20120149-C-T DYZ19 +
22293253-CAG-C 20131367-CAG-C DYZ19 +
22293305-G-A 20131419-G-A DYZ19 +
22658142-T-G 20496256-T-G YY+
24408990-GA-G 22262843-GA-G +
24470935-A-C 22324788-A-C Y+
58971875-T-TGA 56825728-T-TGA +
58971882-G-GTA 56825735-G-GTA +
59019549-CACAA-C 56873402-CACAA-C FGC80623 +
59025459-T-A 56879312-T-A +
59025462-G-C 56879315-G-C +
2652127-C-T 2784086-C-T Y+
2778996-T-C 2910955-T-C S3898 CTS167 YY+
2988947-G-A 3120906-G-A +
3378779-G-A 3510738-G-A Z24252 +
3829247-T-C 3961206-T-C +
3829882-AAAC-A 3961841-AAAC-A +
4438742-T-C 4570701-T-C +
4714162-A-G 4846121-A-G FGC29398 +
5538242-G-A 5670201-G-A +
6090165-A-G 6222124-A-G +
6090173-C-G 6222132-C-G +
6092987-TGC-T 6224946-TGC-T +
6401907-C-T 6533866-C-T Y15296 +
6498633-C-T 6630592-C-T +
6903347-A-G 7035306-A-G CTS615 Y+
8340058-C-T 8472017-C-T S3250 YY+
8611867-A-C 8743826-A-C YY+
8650103-AG-A 8782062-AG-A +
10068204-A-C 10230595-A-C +
10091975-A-G 10254366-A-G +
13240412-C-T 11084736-C-T +
13240437-G-A 11084761-G-A +
13258240-G-A 11102564-G-A FT441974 +
13332699-G-A 11177023-G-A FT92364 +
13414960-T-C 11259284-T-C +
13486843-A-T 11331167-A-T +
13596039-G-A 11440363-G-A +
13633482-C-T 11477806-C-T +
13950369-G-A 11829663-G-A FT290015 Y+
13961373-T-G 11840667-T-G Y+
14420440-A-G 12299715-A-G Y+
14888078-T-A 12776144-T-A YY+
14991270-A-G 12879355-A-G Y13229 YY+
15437412-A-G 13325532-A-G FT290484 YY+
16979630-C-T 14867750-C-T Z22420 Y+
17258820-G-C 15146940-G-C CTS7048 Y+
17709779-T-C 15597899-T-C FT313163 YY+
17868443-G-C 15756563-G-C S3893 CTS8190 YY+
18017783-G-T 15905903-G-T CTS8418 Y+
18717451-A-G 16605571-A-G YY+
18886683-CCCTT-C 16774803-CCCTT-C 4×CCTT+
19180289-C-T 17068409-C-T CTS9974 S3904 Y+
19458046-G-T 17346166-G-T YY+
19471671-G-A 17359791-G-A S3253 CTS10467 YY+
21164639-G-T 19002753-G-T Z26507 YY+
21965262-C-T 19803376-C-T Y+
22052685-T-C 19890799-T-C S3254 YY+
22484776-T-C 20322890-T-C DYZ19 +
22863383-C-T 20701497-C-T CTS10973 YY+
23354908-CA-C 21193022-CA-C +
24432882-T-C 22286735-T-C Y+
59006970-A-AAG 56860823-A-AAG +
59019539-CACACACACACACAA-C 56873392-CACACACACACACAA-C +
59019540-ACACACACACACAAG-A 56873393-ACACACACACACAAG-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:

Kit POSITION-REF-ALT (hg19) POSITION-REF-ALT (hg38) Note
Manual23316016-C-CTTTA21154130-C-CTTTATwo reads, both positive.
Manual7064229-AT-A7196188-AT-AAll 6 reads show the deletion.
Manual19950519-A-C17838639-A-C1A 3C
Manual20760825-C-A18598939-C-A3C 2A
Manual22253953-G-T20092067-G-T6G 2T and 2 misaligned reads
Manual22312272-G-A20150386-G-A2A
Manual23379062-GT-G21217176-GT-GBoth reads show the deletion.
Manual24392929-A-G22246782-A-G1G
Manual25893925-G-A23747778-G-A2G 2A
Manual16552811-A-G14440931-A-G1G