Tree Position

R-M269 > L23 > Z2103 > Y4364 > 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
25955976-CTG-C 23809829-CTG-C P1_Y1 16×TG+
2907304-T-C 3039263-T-C YY+
58987993-T-A 56841846-T-A +
59004639-A-G 56858492-A-G +
59019546-ACACACAAG-A 56873399-ACACACAAG-A +
59019547-CACACAA-C 56873400-CACACAA-C +
59019549-CACAA-C 56873402-CACAA-C FGC80623 +
59019550-ACAAG-A 56873403-ACAAG-A +
13435159-A-T 11279483-A-T +
13435166-T-C 11279490-T-C +
14399063-A-C 12278359-G-C YY+
2855072-G-A 2987031-G-A YY+
3744668-A-T 3876627-A-T +
58891004-T-C 56699867-A-G +
3883882-G-A 4015841-G-A +
4013275-G-A 4145234-G-A +
4419571-C-G 4551530-C-G +
4772326-G-A 4904285-G-A Z7302 +
5083526-A-C 5215485-A-C FT254262 +
5084931-A-T 5216890-A-T +
6634566-G-A 6766525-G-A FT289161 YY+
6799121-C-T 6931080-C-T FT289208 YY+
7270270-TC-T 7402229-TC-T +
7401224-A-C 7533183-A-C YY+
7682693-G-C 7814652-G-C FT289454 YY+
8064391-C-T 8196350-C-T FT289565 Y+
8121261-T-G 8253220-T-G FT289592 YY+
8184545-CTG-C 8316504-CTG-C +
58970173-TA-T 56824026-TA-T 11×A+
58869341-T-C 56721530-A-G +
9015610-G-C 9178001-G-C FT289864 +
22936277-A-G 20774391-A-G YY+
21515891-G-A 19354005-G-A YY+
21966566-C-T 19804680-C-T Y+
21978376-C-G 19816490-C-G YY+
22015082-A-T 19853196-A-T Y+
22237305-A-G 20075419-A-G DYZ19 +
22237307-A-G 20075421-A-G DYZ19 +
22237376-C-A 20075490-C-A FGC21861 DYZ19 +
22237501-A-T 20075615-A-T DYZ19 +
22237516-G-T 20075630-G-T DYZ19 +
22289550-T-C 20127664-T-C DYZ19 +
22289605-T-C 20127719-T-C DYZ19 +
22827079-A-C 20665193-A-C YY+
22868312-AC-A 20706426-AC-A +
22995397-TG-T 20833511-TG-T +
28792471-TG-T 26646324-TG-T +
23074967-T-G 20913081-T-G YY+
23777994-T-G 21616108-T-G Y+
23802120-T-G 21640234-T-G Y+
23802155-T-G 21640269-T-G Y+
23802160-T-G 21640274-T-G Y+
23881874-T-A 21719988-T-A Y+
24326616-G-A 22180469-G-A P3_t1 +
24389879-A-C 22243732-A-C Y+
24432855-G-A 22286708-G-A Y+
24432872-G-A 22286725-G-A Y+
28370015-T-TATAG 26223868-T-TATAG P1_gr2 16×AG+
28545696-C-CAAA 26399549-C-CAAA 26×A+
28761176-G-A 26615029-G-A +
28761180-G-A 26615033-G-A +
8479294-C-T 8611253-C-T FT289705 YY+
9384438-C-G 9546829-C-G BY46731 Y+
20603841-G-A 18441955-G-A BY13277 P5_Dst 18×GA+
23302575-C-A 21140689-C-A FT292498 YY+
19409420-C-A 17297540-C-A YY+
21216419-A-G 19054533-A-G FT291830 YY+
21347745-T-A 19185859-T-A Y+
21451701-C-G 19289815-C-G FT291945 YY+
21464560-AG-A 19302674-AG-A +
21634240-G-A 19472354-G-A FT292030 Y+
22275441-T-G 20113555-T-G DYZ19 +
22457930-T-A 20296044-T-A DYZ19 +
22458649-T-C 20296763-T-C BY42254 DYZ19 +
22466035-G-C 20304149-G-C DYZ19 +
22777606-T-C 20615720-T-C Y+
23009602-C-A 20847716-C-A FT292391 Y+
23268410-A-C 21106524-A-C FT292485 YY+
23399063-G-T 21237177-G-T A370 Y+
18615931-CCT-C 16504051-CCT-C +
23435237-A-T 21273351-A-T YY+
23881876-C-A 21719990-C-A Y18×A+
23984100-C-A 21837953-C-A Y+
24404182-T-G 22258035-T-G M8156 +
24893393-T-C 22747246-T-C g1 +
26544618-G-T 24398471-G-T P1_g2 14×AT+
28642811-C-CAG 26496664-C-CAG +
28755774-C-T 26609627-C-T CTS12939 Y+
28761211-A-G 26615064-A-G +
19048976-C-A 16937096-C-A YY+
18203546-C-G 16091666-C-G FT291367 YY+
9991634-CA-C 10154025-CA-C +
15009972-C-T 12898057-C-T YY+
13194053-C-T 11038377-C-T +
13354835-G-A 11199159-G-A FT443163 +
13402293-A-G 11246617-A-G +
13589910-C-T 11434234-C-T FGC55701 +
13632837-C-T 11477161-C-T +
13841787-G-A 11721081-G-A FT328661 +
14062071-C-A 11941365-C-A YY+
14085691-A-C 11964985-A-C FT290066 YY+
14123846-C-A 12003140-C-A CTS1928 Y+
14134153-T-G 12013447-T-G Y+
14292324-A-C 12171618-A-C FT290167 Y+
14654388-C-A 12542453-C-A Y4366 YY+
14938676-G-A 12826750-G-A FT290352 YY+
15250214-C-A 13138300-C-A CTS3900 Y+
18128223-AG-A 16016343-AG-A +
15368403-T-G 13256523-T-G FT290460 Y+
15713124-C-A 13601244-C-A YY+
15959790-G-T 13847910-G-T Y+
16216782-A-G 14104902-A-G YY+
16312084-G-A 14200204-G-A S18121 YY+
16994535-C-T 14882655-C-T Y37981 Y+
17265748-G-A 15153868-G-A M12162 Y+
17569307-T-G 15457427-T-G YY+
17717463-G-A 15605583-G-A A18667 YY+
17773360-G-A 15661480-G-A CTS7973 Z1737 YY+
17794249-TTTCG-T 15682369-TTTCG-T +
17828101-A-G 15716221-A-G CTS8084 Y+
17941227-C-T 15829347-C-T Y100713 YY+
17946915-G-GTT 15835035-G-GTT +
21464187-G-A 19302301-G-A BY55257 YY12×GAAA+
19391082-A-T 17279202-A-T YY+
18892281-T-A 16780401-T-A E160 YY+
3038446-A-AG 3170405-A-AG +
6617129-A-G 6749088-A-G Y+
28721518-G-A 26575371-G-A +
7541451-T-C 7673410-T-C YY+
9951729-A-G 10114120-A-G Y+
17281261-T-G 15169381-T-G A3149FGC34921 YY+
28798957-G-GT 26652810-G-GT +
17385421-C-A 15273541-C-A YY15×A+
8703678-G-T 8835637-G-T YY+
58893241-A-C 56697630-T-G +
5523893-A-T 5655852-A-T +
3172144-G-C 3304103-G-C FT371421 +
5400465-G-T 5532424-G-T +
13933734-T-A 11813028-T-A Y+
3083069-A-C 3215028-A-C +
14418189-ATG-A 12297464-ATG-A +
3302125-T-C 3434084-T-C +
3403623-G-C 3535582-G-C +
3426238-C-T 3558197-C-T +
3963813-A-G 4095772-A-G +
3989162-T-G 4121121-T-G A4993 +
4123372-T-TAAA 4255331-T-TAAA +
4480829-T-G 4612788-T-G +
4936083-A-T 5068042-A-T +
4997517-C-CAGAGAGAG 5129476-C-CAGAGAGAG +
5032237-A-ATT 5164196-A-ATT 13×T+
5395944-C-T 5527903-C-T S9041 +
5400468-C-T 5532427-C-T 19×T+
5409742-TTC-T 5541701-TTC-T +
5784062-C-CAA 5916021-C-CAA 21×A+
18270302-G-T 16158422-G-T +
13129491-C-T 10618977-C-T +
6398634-T-A 6530593-T-A +
59004635-A-G 56858488-A-G +
26834745-G-A 24688598-G-A BY226817 P1_g2 12×AAGA+
14213636-G-GAGGA 12092930-G-GAGGA 7×AGGA+
8403300-AG-A 8535259-AG-A +
8353655-A-C 8485614-A-C YY+
13735888-G-C 11580212-G-C +
13669463-C-A 11513787-C-A +
5084560-A-T 5216519-A-T Y82046 +
13254002-G-T 11098326-G-T BY43060 17×T+
28798972-G-A 26652825-G-A FT462122 +
13743926-G-A 11588250-G-A +
28571558-C-G 26425411-C-G CTS12306 +
13648911-A-G 11493235-A-G +
22297555-G-A 20135669-G-A DYZ19 +
22289585-T-G 20127699-T-G DYZ19 +
22438611-C-T 20276725-C-T FGC30381 DYZ19 +
58907253-C-T 56683618-G-A +
28237965-GT-G 26091818-GT-G P1_b4 +
59033463-G-A 56887316-G-A +
27056034-T-C 24909887-T-C P1_r4 +
4123328-G-GAAAT 4255287-G-GAAAT 11×AAAT+
58834169-G-A 56756702-C-T +
26180133-T-G 24033986-T-G P1_Y1 +
22438869-A-C 20276983-A-C DYZ19 +
9951786-G-C 10114177-G-C Y+
15406960-G-A 13295080-G-A YY+
25472004-C-T 23325857-C-T FGC11716 P2_r2 +
58828807-C-T 56762064-G-A +
6493973-G-A 6625932-G-A +
5506028-C-T 5637987-C-T +
5828964-CAA-C 5960923-CAA-C +
6402493-G-A 6534452-G-A Z36464 +
18857003-G-C 16745123-G-C YY+
16629403-C-T 14517523-C-T SK2361 YY+
13923845-T-C 11803139-T-C Y+
14195748-C-G 12075042-C-G Y+
14213801-A-AAG 12093095-A-AAG +
14456501-C-A 12335774-C-A Y15×A+
14602056-TG-T 12490258-TG-T +
15516945-ATG-A 13405065-ATG-A +
15839976-AG-A 13728096-AG-A +
16247952-T-C 14136072-T-C YY+
16247962-T-C 14136082-T-C YY+
16247970-T-C 14136090-T-C YY+
16602614-A-C 14490734-A-C YY+
16652006-T-G 14540126-T-G YY+
13747097-G-C 11591421-G-C +
16809469-T-TGAGA 14697589-T-TGAGA +
16900856-C-T 14788976-C-T YY+
17030604-TG-T 14918724-TG-T +
17361085-T-G 15249205-T-G YY+
17361088-A-G 15249208-A-G YY+
17385413-T-A 15273533-T-A YY+
17385419-T-A 15273539-T-A YY+
17387952-G-T 15276072-G-T YY+
17655476-TA-T 15543596-TA-T +
17998062-G-GC 15886182-G-GC P7_Gap +
18035643-A-C 15923763-A-C FTB72278 YY+
18195143-A-C 16083263-A-C YY+
18236743-A-T 16124863-A-T FT151341 Y+
18653646-T-A 16541766-T-A YY+
13747099-G-C 11591423-G-C +
13618743-A-G 11463067-A-G +
6586809-G-T 6718768-G-T +
13292091-CCG-C 11136415-CCG-C +
7258783-C-A 7390742-C-A Y+
7451294-C-CTTT 7583253-C-CTTT IR1_L 29×T+
7618088-CTT-C 7750047-CTT-C +
8026917-CTCT-C 8158876-CTCT-C +
8066692-A-T 8198651-A-T Y+
8066693-T-C 8198652-T-C Y+
8555575-G-GTTTTTT 8687534-G-GTTTTTT +
9013093-A-T 9175484-A-T Y+
9013119-G-A 9175510-G-A Y+
13222942-A-G 11067266-A-G +
13259611-G-T 11103935-G-T +
13260609-CCA-C 11104933-CCA-C +
13265088-C-T 11109412-C-T +
13300664-C-CA 11144988-C-CA 9×A+
13618300-A-C 11462624-A-C +
13319340-T-TTG 11163664-T-TTG +
13319342-G-GTA 11163666-G-GTA +
13319344-A-ATG 11163668-A-ATG BY14118 10×TG+
13346088-A-G 11190412-A-G 8×AG+
13354873-C-A 11199197-C-A +
13384357-G-C 11228681-G-C +
13402099-T-G 11246423-T-G +
13448782-TCCACA-T 11293106-TCCACA-T +
13478842-A-C 11323166-A-C +
13478859-A-C 11323183-A-C +
13531776-AC-A 11376100-AC-A +
13577103-A-T 11421427-A-T +
13611578-C-T 11455902-C-T +
13616466-A-T 11460790-A-T +

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.

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