Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z41150 > Y11667 > 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
19231319-C-T 17119439-C-T YY24×T+
13562979-C-A 11407303-C-A +
13374821-A-G 11219145-A-G +
13374833-G-C 11219157-G-C +
13441827-A-G 11286151-A-G +
13441838-T-C 11286162-T-C +
13449888-ATTT-A 11294212-ATTT-A +
13472458-C-T 11316782-C-T +
13503141-C-G 11347465-C-G +
13602357-A-G 11446681-A-G +
13311851-C-T 11156175-C-T +
13606604-C-G 11450928-C-G +
13606922-T-C 11451246-T-C +
13840186-G-A 11719480-G-A FGC82221 +
13950947-C-CTTT 11830241-C-CTTT 23×T+
14172759-AC-A 12052053-AC-A +
14200754-A-AT 12080048-A-AT +
14991346-A-C 12879431-A-C YY+
13311862-A-G 11156186-A-G +
13305231-T-C 11149555-T-C +
15963963-A-AC 13852083-A-AC +
9825002-CAT-C 9987393-CAT-C +
8597005-GCA-G 8728964-GCA-G +
8708627-C-T 8840586-C-T Z10329 V2479 YY+
8785009-C-T 8916968-C-T YY+
9381817-C-T 9544208-C-T Z14884 Y+
9451238-T-A 9613629-T-A YY+
9516750-TC-T 9679141-TC-T +
9771053-TA-T 9933444-TA-T +
9931329-A-C 10093720-A-C Y+
13301196-T-C 11145520-T-C +
13143953-T-TC 10633439-T-TC +
13252600-C-T 11096924-C-T +
13254614-TC-T 11098938-TC-T +
13255975-A-G 11100299-A-G +
13265768-C-T 11110092-C-T +
13291559-A-G 11135883-A-G +
13295002-G-A 11139326-G-A +
13296233-C-T 11140557-C-T +
15882129-T-A 13770249-T-A YY+
16205677-AAT-A 14093797-AAT-A +
7832267-A-G 7964226-A-G Z7349 YY+
28237933-TGG-T 26091786-TGG-T P1_b4 +
22892163-G-T 20730277-G-T M7079 YY+
22962008-G-GTTT 20800122-G-GTTT 27×T+
23008713-T-G 20846827-T-G Y+
23843634-C-CTATT 21681748-C-CTATT +
24425365-ATG-A 22279218-ATG-A 8×TG+
24432872-G-A 22286725-G-A Y+
25173629-T-C 23027482-T-C g1 +
28482310-C-T 26336163-C-T +
22472403-G-C 20310517-G-C DYZ19 +
28496017-A-T 26349870-A-T +
28598575-G-T 26452428-G-T CTS12504 +
28604029-A-G 26457882-A-G CTS12538 +
28697477-TAC-T 26551330-TAC-T +
28777425-T-G 26631278-T-G CTS12992 +
58856395-T-C 56734476-A-G +
58985837-G-A 56839690-G-A +
58985849-T-C 56839702-T-C +
22538698-A-G 20376812-A-G FT298952 Y+
22458903-G-T 20297017-G-T FT457379 DYZ19 +
16692784-AG-A 14580904-AG-A +
21126302-A-C 18964416-A-C YY+
16710760-GATGT-G 14598880-GATGT-G +
16961546-C-T 14849666-C-T CTS6515 YY+
17474911-A-C 15363031-A-C YY+
17703255-A-AAAAG 15591375-A-AAAAG 6×AAAG+
18575027-T-G 16463147-T-G YY+
18723886-TC-T 16612006-TC-T +
19226192-G-A 17114312-G-A PF5816 YY+
21863917-T-G 19702031-T-G YY+
22445947-A-G 20284061-A-G DYZ19 +
21978368-T-G 19816482-T-G S23811 YY+
22001693-T-C 19839807-T-C YY+
22253017-C-A 20091131-C-A DYZ19 +
22282035-C-T 20120149-C-T DYZ19 +
22294753-G-C 20132867-G-C DYZ19 +
22297320-C-A 20135434-C-A DYZ19 +
22342632-T-C 20180746-T-C DYZ19 +
22445915-G-C 20284029-G-C DYZ19 +
7938176-AG-A 8070135-AG-A +
7784897-G-A 7916856-G-A YY+
22238328-C-T 20076442-C-T DYZ19 +
8380144-T-C 8512103-T-C FT295320 YY+
6659791-A-G 6791750-A-G YY+
6794834-C-T 6926793-C-T BY61350 YY+
7421364-A-T 7553323-A-T FT294876 YY+
7746402-A-G 7878361-A-G YY+
8224781-C-T 8356740-C-T FT295250 YY+
8252474-G-A 8384433-G-A FT295263 YY+
8319264-A-C 8451223-A-C FT295295 YY+
8626132-G-A 8758091-G-A FT295460 YY+
16940897-T-A 14829017-T-A YY11×A+
8723648-G-A 8855607-G-A YY+
8883459-C-T 9015418-C-T FT295592 Y+
14031026-C-T 11910320-C-T CTS1715 YY+
14898180-T-C 12786246-T-C FT296327 YY+
14976723-C-A 12864798-C-A CTS3499 YY+
15984459-T-G 13872579-T-G FGC1492 YY10×G+
16278354-T-C 14166474-T-C Y+
16473971-C-A 14362091-C-A CTS5770 YY+
22766548-T-A 20604662-T-A YY10×A+
28742512-A-T 26596365-A-T FT14270 14×T+
16856867-A-G 14744987-A-G CTS6371 YY+
22229048-C-T 20067162-C-T BY20536BY43658 DYZ19 +
19231311-C-T 17119431-C-T YY+
9974567-G-C 10136958-G-C S3045 Y+
13703433-A-C 11547757-A-C BY25121 +
9974569-G-A 10136960-G-A Y+
59024013-A-AGGGAG 56877866-A-AGGGAG +
20232724-G-T 18070838-G-T P5_Dst +
4786062-T-G 4918021-T-G +
13139973-G-C 10629459-G-C +
28602161-T-A 26456014-T-A DF73FT285095 +
17304960-G-A 15193080-G-A Y1228 YY+
2744510-T-C 2876469-T-C CTS126CTS126 YY+
17030782-G-T 14918902-G-T YY+
9105202-C-A 9267593-C-A Y15×A+
8341874-C-A 8473833-C-A YY14×A+
14881734-A-G 12769802-A-G YY+
9398673-A-G 9561064-A-G BY11860 YY+
23025229-C-A 20863343-C-A YY29×A+
16646496-C-G 14534616-C-G CTS6067 YY+
17867391-C-A 15755511-C-A FT297457 YY+
7664508-T-C 7796467-T-C Y+
5025819-G-A 5157778-G-A Z4800 +
3767985-G-T 3899944-G-T FT38619 +
4026271-TG-T 4158230-TG-T +
4163850-C-T 4295809-C-T FT319737 +
4415347-GAT-G 4547306-GAT-G +
4431994-G-T 4563953-G-T +
4460962-CCG-C 4592921-CCG-C +
4613558-TAC-T 4745517-TAC-T +
5270198-C-T 5402157-C-T FT323337 +
3557529-A-G 3689488-A-G +
5502249-CA-C 5634208-CA-C +
5502252-CT-C 5634211-CT-C +
5502253-TC-T 5634212-TC-T +
5711255-A-G 5843214-A-G FT324844 +
5904070-C-T 6036029-C-T +
5904073-A-T 6036032-A-T +
6403454-G-A 6535413-G-A +
7534405-TG-T 7666364-TG-T +
3561369-T-G 3693328-T-G +
3509015-T-A 3640974-T-A +
18079217-G-A 15967337-G-A Z34556 YY+
24382950-T-G 22236803-T-G FT299525 Y+
18177764-G-A 16065884-G-A CTS8749 YY+
18997718-G-C 16885838-G-C FT297874 YY+
19230136-G-T 17118256-G-T FT297988 YY+
21896487-T-C 19734601-T-C FT298732 YY+
23307773-G-T 21145887-G-T FT299304 YY+
23964050-C-T 21817903-C-T Z15556 Y+
23968918-C-T 21822771-C-T FT299510 Y+
13306462-G-A 11150786-G-A +
3171120-T-A 3303079-T-A FT316304 +
28807475-A-G 26661328-A-G BY28204 +
13255204-G-A 11099528-G-A +
13255216-C-T 11099540-C-T +
3037295-T-C 3169254-T-C +
28604088-G-A 26457941-G-A +
2718879-TTC-T 2850838-TTC-T +
2718880-TC-T 2850839-TC-T +
2928514-G-A 3060473-G-A FT315463 +
59030836-AT-A 56884689-AT-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-TAJust 3 reads cover the necessary range, but all 3 show the insertion.

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