Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z41150 > Z49 > Z142/S211 > Z51 > Z50 > Z57 > Y12119 > Z52 > BY33643 > CTS11232 > Y131763

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
15324344-TG-T 13212462-TG-T +
13433114-A-T 11277438-A-T +
16050996-C-CTTTCTT 13939116-C-CTTTCTT 16×TCTT+
15855403-C-T 13743523-C-T Y+
15669963-AC-A 13558083-AC-A +
14881926-G-A 12769994-G-A M5668 YY+
14705590-A-C 12593656-A-C YY+
14326365-T-A 12205659-T-A K202 YY+
14101340-C-CT 11980634-C-CT +
14032641-TC-T 11911935-TC-T +
14001886-A-C 11881180-A-C YY+
13960639-A-G 11839933-A-G Y4×GATG+
13950946-TC-T 11830240-TC-T +
13936212-G-GAAAA 11815506-G-GAAAA +
13898398-A-G 11777692-A-G Y+
13445750-C-T 11290074-C-T +
13432823-C-T 11277147-C-T +
16277219-A-C 14165339-A-C YY+
9945815-A-G 10108206-A-G Y+
7235824-C-T 7367783-C-T YY+
7359790-A-T 7491749-A-T YY+
7425119-A-C 7557078-A-C YY+
8439234-T-TTTA 8571193-T-TTTA +
9063235-A-C 9225626-A-C Z12147 Y+
9944578-G-T 10106969-G-T Y+
13213825-GGAT-G 11058149-GGAT-G +
13432815-T-A 11277139-T-A +
13260372-T-A 11104696-T-A +
13264289-G-T 11108613-G-T +
13276382-G-T 11120706-G-T +
13312501-C-G 11156825-C-G +
13323745-G-A 11168069-G-A +
13432571-G-T 11276895-G-T +
16262781-G-T 14150901-G-T YY+
16302679-G-A 14190799-G-A Z9264 YY+
6617478-T-C 6749437-T-C Y+
24387513-C-T 22241366-C-T +
22242269-A-T 20080383-A-T DYZ19 +
22447388-G-A 20285502-G-A DYZ19 +
22457613-T-C 20295727-T-C DYZ19 +
22484739-C-A 20322853-C-A DYZ19 +
22633911-A-AAT 20472025-A-AAT +
23391724-C-A 21229838-C-A FT292524 YY+
24929441-C-T 22783294-C-T g1 +
22113230-G-A 19951344-G-A S23983 YY+
28539156-A-T 26393009-A-T +
28700799-G-A 26554652-G-A +
28817653-GGAAT-G 26671506-GGAAT-G +
59017385-GAA-G 56871238-GAA-G +
59026881-A-G 56880734-A-G +
59033610-C-A 56887463-C-A +
22241895-G-A 20080009-G-A DYZ19 +
21871431-T-C 19709545-T-C F24781 YY+
16533561-CAT-C 14421681-CAT-C +
18872082-TCTTC-T 16760202-TCTTC-T 5×CTTC+
16779004-T-TA 14667124-T-TA +
16779006-A-AG 14667126-A-AG +
17925491-C-G 15813611-C-G YY+
17946943-T-TTTAA 15835063-T-TTTAA +
18390083-C-A 16278203-C-A P6_Gap 19×A+
18825628-TC-T 16713748-TC-T +
19049508-A-ATAT 16937628-A-ATAT +
21809806-AGTT-A 19647920-AGTT-A +
19309460-T-TATATAC 17197580-T-TATATAC 11×AC+
20752168-C-T 18590282-C-T P4_Prx +
21068452-ATATAT-A 18906566-ATATAT-A +
21212706-C-A 19050820-C-A YY+
21512144-T-C 19350258-T-C FT302399 YY+
21711261-A-C 19549375-A-C M1947 YY+
7076641-ATAC-A 7208600-ATAC-A +
6617457-A-G 6749416-A-G Y+
21551793-G-A 19389907-G-A L1336 Y+
23100541-T-C 20938655-T-C FT292431 Y+
3248119-T-C 3380078-T-C +
3215317-T-G 3347276-T-G +
3195121-A-G 3327080-A-G FT6914 +
3166559-C-T 3298518-C-T +
3166554-A-T 3298513-A-T +
3144273-G-A 3276232-G-A +
3030126-G-A 3162085-G-A +
3178102-T-A 3310061-T-A +
13273993-C-A 11118317-C-A +
13273994-C-T 11118318-C-T +
13268914-A-G 11113238-A-G +
13253191-G-A 11097515-G-A A145 +
3446633-G-A 3578592-G-A +
28752982-G-T 26606835-G-T CTS12924 +
23084946-C-T 20923060-C-T FT332191 Y+
3256203-T-C 3388162-T-C +
18867364-G-T 16755484-G-T YY+
5937661-C-CCA 6069620-C-CCA 15×CA+
13930192-AG-A 11809486-AG-A +
19372386-T-G 17260506-T-G PH5187M756 F3032 YY+
20197205-GA-G 18035319-GA-G P5_Dst 14×A+
22443006-T-A 20281120-T-A ZS3148 DYZ19 +
13253182-C-T 11097506-C-T +
28686570-C-A 26540423-C-A CTS12734 +
19430342-T-C 17318462-T-C Z21127 YY+
7925833-G-T 8057792-G-T Y19622 YY11×T+
7194007-C-T 7325966-C-T Z29614CTS1090 YY+
13900031-C-T 11779325-C-T FT295833 YY+
15192356-C-T 13080442-C-T FT290421 YY+
15749591-C-T 13637711-C-T YY+
16242588-A-G 14130708-A-G Z9260 Y9838 YY+
3256136-CTAT-C 3388095-CTAT-C +
3404259-G-A 3536218-G-A +
6617433-C-T 6749392-C-T Y+
5797428-A-T 5929387-A-T +
5081887-T-G 5213846-T-G FTB54840 +
5241253-TG-T 5373212-TG-T +
5398982-A-G 5530941-A-G +
5400468-C-T 5532427-C-T 19×T+
5607528-T-G 5739487-T-G +
5691530-T-G 5823489-T-G +
5815616-AT-A 5947575-AT-A +
4956482-G-A 5088441-G-A FT17021 +
5887202-G-T 6019161-G-T +
5977663-T-C 6109622-T-C +
5986334-T-C 6118293-T-C +
6010544-G-A 6142503-G-A +
6149998-TGG-T 6281957-TGG-T IR3_Dst +
6349205-A-T 6481164-A-T +
5012499-C-T 5144458-C-T +
4911506-T-A 5043465-T-A +
3434309-CAT-C 3566268-CAT-C +
4269196-G-A 4401155-G-A +
3434648-A-G 3566607-A-G +
3459991-G-T 3591950-G-T +
3613748-A-C 3745707-A-C +
3619767-G-A 3751726-G-A +
4022247-C-T 4154206-C-T +
4049389-C-A 4181348-C-A +
4346565-A-ATT 4478524-A-ATT 22×T+
4834357-C-T 4966316-C-T FT349788 +
4365584-T-C 4497543-T-C +
4367372-C-A 4499331-C-A +
4367394-G-GAA 4499353-G-GAA 9×A+
4656459-A-T 4788418-A-T +
4748667-T-C 4880626-T-C PF3145 +
4788859-C-T 4920818-C-T +
59033638-C-A 56887491-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:

Manual21527519-T-TA19365633-T-TA4 reads positive, 1 negative.
Manual22220675-T-G20058789-T-G3G 1T
Manual22230942-A-C20069056-A-C2A 3C 1N
Manual22248567-A-T20086681-A-T2A 3T
Manual19854803-G-A17742923-G-A1G 3A + 1 extra misaligned read
Manual22344958-G-C20183072-G-C3C 6G
Manual25977565-C-T23831418-C-T1C 1T

Big Tree Main Page