Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > Z193 > Z40483 > BY3654 > BY3627

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
5565436-G-A 5697395-G-A A*
56834324-A-C A*
6176497-G-C 6308456-G-C IR3_Dst A*
18294990-C-T 16183110-C-T P6_Prx A*
19580874-G-A 17468994-G-A P5_Prx YA*
19598409-C-T 17486529-C-T P5_Prx YA*
19764656-G-T 17652776-G-T P5_Prx A*
20740523-C-T 18578637-C-T P4_Prx A*
24240358-A-T 22094211-A-T P3_b1 A*
25927102-C-T 23780955-C-T P1_Y1 A*
25982171-G-A 23836024-G-A P1_Y1 A*
26136067-C-A 23989920-C-A P1_Y1 A*
26317897-C-T 24171750-C-T P1_Y1 A*
17383880-G-C 15272000-G-C YP914 Z20611 YY+
21335054-C-T 19173168-C-T Z16008 Y+
22444004-A-C 20282118-A-C FT456753 DYZ19 +
7110521-T-C 7242480-T-C FT248327 YY+
19062259-C-A 16950379-C-A FT249745 YY+
3682159-G-A 3814118-G-A FT247592 +
5413674-G-A 5545633-G-A FT248005 +
7209528-A-G 7341487-A-G FT248346 YY+
7713913-T-G 7845872-T-G FT248443 YY+
7756726-G-C 7888685-G-C FT248448 Y+
7921588-C-T 8053547-C-T FT248473 YY+
8467238-C-A 8599197-C-A FT248562 YY+
10869302-C-T FT434824 +
10939463-G-A FT182978 +
13238991-G-A 11083315-G-A BY84859 +
13432686-TCTGGGG-T 11277010-TCTGGGG-T +
13680905-C-A 11525229-C-A FT448210 DYZ17 +
14126081-C-T 12005375-C-T BY54584 YY+
14235793-G-T 12115087-G-T FT248907 YY+
14268322-G-A 12147616-G-A Y+
14472264-A-G 12351533-A-G BY1096 YY+
14629821-T-A 12517890-T-A FT248995 YY+
14991507-T-A 12879592-T-A FT249048 YY+
15108814-C-T 12996901-C-T FT249069 YY+
15510347-C-A 13398467-C-A FT249141 YY+
15538050-C-T 13426170-C-T FT249146 YY+
16715807-C-T 14603927-C-T FT249351 YY+
16929843-G-A 14817963-G-A FT249381 Y+
17482881-C-T 15371001-C-T FT249469 Y+
17682279-G-A 15570399-G-A FT249520 YY+
17707200-AC-A 15595320-AC-A +
18735981-T-G 16624101-T-G FT249688 Y+
19061529-G-A 16949649-G-A YY+
19268796-G-A 17156916-G-A FT249797 YY+
21359205-C-T 19197319-C-T FT249927 YY+
21447086-C-T 19285200-C-T FT249944 YY+
21884294-T-C 19722408-T-C FT250039 YY+
22044187-G-A 19882301-G-A FT164211 YY+
22517997-C-T 20356111-C-T FT250113 Y+
22815535-T-G 20653649-T-G FT250178 YY+
22904976-T-C 20743090-T-C FT250199 YY+
28740735-C-G 26594588-C-G FT250500 +
3195331-C-A 3327290-C-A *
13453298-C-T 11297622-C-T **
16117960-G-T 14006080-G-T P8_Prx 22×A**
16581750-CAT-C 14469870-CAT-C **
20621379-T-C 18459493-T-C P4_Prx **
5117948-TCA-T 5249907-TCA-T **
5691405-G-T 5823364-G-T **
5691407-G-A 5823366-G-A **
5691408-T-C 5823367-T-C **
6902369-G-T 7034328-G-T **
7062388-C-T 7194347-C-T **
8970934-T-C 9133325-T-C **
13331533-T-C 11175857-T-C **
15209369-C-T 13097455-C-T FT398370 **
16064721-G-T 13952841-G-T **
16643406-T-C 14531526-T-C **
18917573-G-GT 16805693-G-GT 8×T**
20968352-T-C 18806466-T-C P4_Dst **
21397910-A-G 19236024-A-G **
21598779-C-CA 19436893-C-CA 8×A**
22440957-G-C 20279071-G-C DYZ19 **
22489394-G-T 20327508-G-T BY23286 DYZ19 ***
17597154-CTTTTTT-C 15485274-CTTTTTT-C 20×T***
13453339-C-CGATTG 11297663-C-CGATTG ***
13457930-C-CTTCTG 11302254-C-CTTCTG ***
9956364-TAAAAA-T 10118755-TAAAAA-T 16×A***
22540529-T-C 20378643-T-C ***
22540536-G-A 20378650-G-A ***
15171226-CTTTTT-C,CTTTT 13059312-CTTTTT-C,CTTTT 19×T***
16581744-A-AAT 14469864-A-AAT ***
6597340-TAAAAAAAAA-T 6729299-TAAAAAAAAA-T 28×A***
15865946-CTTTTTTTT-C 13754066-CTTTTTTTT-C 37×T***
3203603-T-A 3335562-T-A ***
5691397-C-G 5823356-C-G ***
5691418-C-A 5823377-C-A ***
5691422-T-C 5823381-T-C ***
5691428-C-T 5823387-C-T ***
6685778-T-C 6817737-T-C ***
15252784-A-G 13140870-A-G ***
16904731-AGTGTGT-A,AGTGT 14792851-AGTGTGT-A,AGTGT 20×GT***
21964363-C-T 19802477-C-T ***
22147789-CT-C 19985903-CT-C ***
22432275-G-A 20270389-G-A DYZ19 ***
28793797-A-C,G 26647650-A-C,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.