Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > ZZ10 > Z253 > ZZ6 > 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
HG01136
Manual
Edits
13735888-G-C 11580212-G-C +
14882306-G-T YY+
13611422-G-GA 11455746-G-GA +
13950946-TC-T 11830240-TC-T +
14263268-G-A 12142562-G-A S15717 YY+
14334340-G-GT 12213635-G-GT +
14613457-TCC-T 12501655-TCC-T +
14709281-A-AC 12597348-A-AC +
14832653-G-T 12720720-G-T YY+
14986712-T-C 12874780-T-C Z45602 YY+
13256857-TG-T 11101181-TG-T +
15066204-CT-C 12954296-CT-C +
15092755-TC-T 12980844-TC-T +
15151525-AG-A 13039612-AG-A +
15255767-TGG-T 13143853-TGG-T +
15262458-C-CAAA 13150542-C-CAAA 30×A+
15358787-AGCAG-A 13246907-AGCAG-A +
15491537-C-CG 13379657-C-CG +
13260605-TTC-T 11104929-TTC-T +
13193949-N-A 11038273-A-. +
15842560-T-TCTTTC 13730680-T-TCTTTC +
7613833-G-GAAA 7745792-G-GAAA 31×A+
5999361-AGC-A 6131320-AGC-A +
6444869-C-T 6576828-C-T +
6449423-G-A 6581382-G-A +
6601006-A-C 6732965-A-C +
6765634-TG-T 6897593-TG-T +
7050077-T-C 7182036-T-C YY+
7201820-G-T 7333779-G-T S9955 Y+
8218013-TTTTCTTTCTTTCTTTC-T 8349972-TTTTCTTTCTTTCTTTC-T 15×TTTC+
10020201-C-CA 10182592-C-CA +
8550862-G-A 8682821-G-A S11626 YY+
8575956-A-ATTTTT 8707915-A-ATTTTT 28×T+
8785009-C-T 8916968-C-T YY+
9385010-G-A 9547401-G-A Y+
9489389-G-A 9651780-G-A +
9900478-GTA-G 10062869-GTA-G +
9934685-T-C 10097076-T-C Y+
9983041-G-A 10145432-G-A Y+
15842556-T-TCTTC 13730676-T-TCTTC +
15976275-G-T 13864395-G-T YY+
5906857-GCA-G 6038816-GCA-G +
22868312-AC-A 20706426-AC-A +
22325187-AAG-A 20163301-AAG-A DYZ19 +
22428261-T-A 20266375-T-A DYZ19 +
22445631-G-T 20283745-G-T DYZ19 +
22471477-G-C 20309591-G-C DYZ19 +
22476081-T-A 20314195-T-A DYZ19 +
22478251-A-T 20316365-A-T DYZ19 +
22511871-C-T 20349985-C-T DYZ19 +
22953918-T-G 20792032-T-G M4422 YY+
22240998-A-T 20079112-A-T DYZ19 +
23234708-CTTCTTTCTTTCT-C 21072822-CTTCTTTCTTTCT-C 17×TTCT+
24447205-T-G 22301058-T-G Y+
24447211-C-G 22301064-C-G Y+
24485690-TAG-T 22339543-TAG-T +
27055711-TC-T 24909564-TC-T P1_r4 +
28620605-G-GC 26474458-G-GC +
58852577-A-C 56738294-T-G +
22319026-A-T 20157140-A-T DYZ19 +
22215217-C-CTT 20053331-C-CTT 17×T+
16001185-C-T 13889305-C-T Y+
17678618-T-C 15566738-T-C YY+
16183116-C-T 14071236-C-T CTS5282 Y+
16309587-AATAC-A 14197707-AATAC-A +
16535053-C-CTT 14423173-C-CTT 35×T+
16652006-T-G 14540126-T-G YY+
16718625-TA-T 14606745-TA-T +
17474943-TTC-T 15363063-TTC-T +
17529810-C-A 15417930-C-A YY+
18281496-C-T 16169616-C-T P6_Prx +
22197267-G-T 20035381-G-T Y+
18857590-TG-T 16745710-TG-T +
19127642-AAATATATAT-A 17015762-AAATATATAT-A +
19412004-AAGAG-A 17300124-AAGAG-A +
20684855-A-G 18522969-A-G P4_Prx +
21169238-G-A 19007352-G-A YY+
21251809-T-TTC 19089923-T-TTC +
21665560-T-G 19503674-T-G YY+
21914642-C-A 19752756-C-A Y+
5966272-C-A 6098231-C-A +
5846180-G-GAAAA 5978139-G-GAAAA 39×A+
13735890-G-C 11580214-G-C +
14805177-C-G 12693248-C-G CTS3290 YY+
7775735-A-G 7907694-A-G YY+
7862721-C-T 7994680-C-T FGC32369 Z31479 Y12929 YY+
7948891-G-C 8080850-G-C YY+
8727748-A-G 8859707-A-G YY+
14117275-T-C 11996569-T-C CTS1905 YY+
14143425-C-A 12022719-C-A YY+
14294070-C-G 12173364-C-G CTS2407 YY+
14887709-A-G 12775775-A-G CTS3394 YY+
2824645-G-C 2956604-G-C CTS221 S3385 YY+
15774049-G-T 13662169-G-T CTS4694 Y+
15799536-T-C 13687656-T-C CTS4755 YY+
16339150-G-A 14227270-G-A CTS5519 YY+
16720753-C-G 14608873-C-G CTS6194 Y+
16814070-T-C 14702190-T-C CTS6305 YY+
17055978-G-A 14944098-G-A CTS6679 YY+
17201787-G-A 15089907-G-A CTS6935 YY+
2910331-G-A 3042290-G-A S3386 YY+
13444580-C-A 11288904-C-A +
17481132-A-G 15369252-A-G CTS7438 YY+
58904251-G-C 56686620-C-G +
6918567-G-A 7050526-G-A YY+
22499885-C-A 20337999-C-A DYZ19 +
58833014-C-G 56757857-G-C +
14107471-G-T 11986765-G-T Y+
13374277-G-A 11218601-G-A 13×A+
13699899-T-A 11544223-T-A +
59018822-T-G 56872675-T-G +
4408904-G-GAAAA 4540863-G-GAAAA 13×A+
58846447-A-T 56744424-T-A +
8650022-GAGAAAGAAAGAA-G 8781981-GAGAAAGAAAGAA-G 19×AGAA+
22512483-C-T 20350597-C-T BY41280 DYZ19 +
18271891-C-A 16160011-C-A P6_Prx +
58842502-C-T 56748369-G-A +
58891110-G-A 56699761-C-T +
14334341-G-GT 12213636-G-GT +
13306490-A-G 11150814-A-G +
13738688-A-T 11583012-A-T +
17413892-C-T 15302012-C-T CTS7306 YY+
18177710-A-G 16065830-A-G CTS8748 YY+
5502705-AGCC-A 5634664-AGCC-A +
3888677-T-C 4020636-T-C +
2903232-CTCCTTCCTTCCTTCCTTCCTTCCT-C 3035191-CTCCTTCCTTCCTTCCTTCCTTCCT-C 18×TCCT+
3079557-C-CA 3211516-C-CA +
3142434-A-C 3274393-A-C +
3209056-T-A 3341015-T-A +
3346011-C-G 3477970-C-G +
3417555-A-G 3549514-A-G +
3544896-G-GC 3676855-G-GC +
4067369-T-A 4199328-T-A 26×A+
13546132-G-A 11390456-G-A +
4077717-T-C 4209676-T-C +
4304480-G-A 4436439-G-A +
4371094-T-C 4503053-T-C +
4582653-G-A 4714612-G-A +
4710908-G-A 4842867-G-A +
5130521-TG-T 5262480-TG-T +
5271458-C-T 5403417-C-T +
5409728-TTTTCTTTCTTTCTTTCTTTCTTTC-T 5541687-TTTTCTTTCTTTCTTTCTTTCTTTC-T 18×TTTC+
18872246-TTCTC-T 16760366-TTCTC-T +
13936201-A-AAAGG 11815495-A-AAAGG +
19047797-G-A 16935917-G-A CTS9738 YY+
21807013-G-A 19645127-G-A YY+
19078157-C-T 16966277-C-T CTS9805 YY+
19259862-T-C 17147982-T-C CTS10106 YY+
19327084-C-A 17215204-C-A CTS10208 Y+
19532186-C-T 17420306-C-T CTS10553 YY+
21297505-C-T 19135619-C-T Y+
21308224-C-A 19146338-C-A YY+
21334402-C-T 19172516-C-T YY+
21810534-G-A 19648648-G-A YY+
22537275-C-A 20375389-C-A Y15×A+
22571287-C-G 20409401-C-G YY+
23494523-A-G 21332637-A-G YY+
23633472-A-G 21471586-A-G YY+
28501613-G-A 26355466-G-A +
28798957-G-GT 26652810-G-GT +
4076728-G-GTA 4208687-G-GTA 10×TA+
5999363-C-A 6131322-C-A 20×A+
8703678-G-T 8835637-G-T YY+
58981992-CT-C 56835845-CT-C +

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
Manual24831157-C-T22685010-C-TYFull: 3C 2T
Manual28513202-T-A26367055-T-AYFull: 1A



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