Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > L513/S215/DF1 > S6365 > L705

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
28794922-A-G 26648775-A-G +
14445919-C-T 12325192-C-T CTS2723 Y+
18025402-C-T 15913522-C-T Y+
17919852-AAAG-A 15807972-AAAG-A +
17562009-TA-T 15450129-TA-T +
17466998-A-G 15355118-A-G Y26835 YY+
16721273-C-T 14609393-C-T Y+
16292543-A-T 14180663-A-T YY+
15111585-C-T 12999672-C-T YY+
15094267-G-T 12982355-G-T YY+
15076196-TG-T 12964286-TG-T +
15037752-A-ACC 12925840-A-ACC +
14668282-C-T 12556348-C-T Y+
14614767-T-C 12502965-T-C Z34374 Y+
14443735-C-T 12323008-C-T CTS2718 Y+
18857590-TG-T 16745710-TG-T +
14022715-T-G 11902009-T-G YY+
13932347-A-C 11811641-A-C Y+
13898780-TGACGGTG-T 11778074-TGACGGTG-T +
13747097-G-C 11591421-G-C +
13640577-A-G 11484901-A-G +
13640567-A-T 11484891-A-T +
13633123-G-T 11477447-G-T Y138294 +
13620868-T-A 11465192-T-A +
13611422-G-GA 11455746-G-GA +
13566948-C-T 11411272-C-T 12×AT+
13436414-G-C 11280738-G-C F18153 +
13428295-T-C 11272619-T-C +
13319375-C-G 11163699-C-G S531 +
18743593-T-C 16631713-T-C YY+
19044570-G-A 16932690-G-A YY+
13284814-C-T 11129138-C-T +
22956347-A-T 20794461-A-T YY+
58861967-T-A 56728904-A-T +
28587083-C-T 26440936-C-T +
28587061-T-C 26440914-T-C +
28577682-G-A 26431535-G-A +
28573108-A-T 26426961-A-T CTS12313 +
24895715-G-T 22749568-G-T g1 +
24485671-A-AT 22339524-A-AT +
24383529-TC-T 22237382-TC-T +
23415335-TATATATA-T 21253449-TATATATA-T +
23415304-GTATGTA-G 21253418-GTATGTA-G +
23278718-T-C 21116832-T-C YY+
23045487-AC-A 20883601-AC-A +
22956373-A-G 20794487-A-G CTS11105 YY+
22609649-A-C 20447763-A-C M7143 S24473 YY+
19197733-C-T 17085853-C-T YY+
22448787-G-T 20286901-G-T DYZ19 +
22296041-T-G 20134155-T-G DYZ19 +
22253036-C-A 20091150-C-A S5961 DYZ19 +
22253017-C-A 20091131-C-A DYZ19 +
22239414-C-A 20077528-C-A DYZ19 +
22205218-A-C 20043332-A-C Y+
21620504-A-G 19458618-A-G YY+
20812328-A-C 18650442-A-C P4_Gap +
20105745-TC-T 17993865-TC-T P5_Dst +
19500199-TA-T 17388319-TA-T +
19305556-G-GT 17193676-G-GT +
19226192-G-A 17114312-G-A PF5816 YY+
19214239-A-T 17102359-A-T YY+
13308888-C-G 11153212-C-G +
13270952-C-T 11115276-C-T +
9931885-C-CT 10094276-C-CT +
14210430-A-AT 12089724-A-AT 9×T+
2936083-C-A 3068042-C-A FGC57532 +
2852369-T-G 2984328-T-G YY+
3576498-T-G 3708457-T-G +
13507935-C-A 11352259-C-A +
2987520-T-C 3119479-T-C +
26400998-T-C 24254851-T-C P1_Y1 +
23438097-G-A 21276211-G-A CTS12036 YY+
23342189-A-G 21180303-A-G CTS11905 YY+
21132049-T-C 18970163-T-C F3127 YY+
18939581-T-C 16827701-T-C FT302016 YY+
18064281-G-T 15952401-G-T F463 YY11×T+
15922922-A-G 13811042-A-G CTS4955 Y+
15111587-G-A 12999674-G-A YY+
7857433-C-T 7989392-C-T FT300262 YY8×A+
3364984-A-C 3496943-A-C +
7829890-A-C 7961849-A-C FT300254 YY+
7542304-G-A 7674263-G-A FT49692 YY+
7087086-C-T 7219045-C-T S2906 CTS919 YY+
14541144-T-G 12429345-T-G YY+
9105202-C-A 9267593-C-A Y15×A+
7579109-T-C 7711068-T-C YY+
16779007-G-A 14667127-G-A YY10×A+
5666004-T-C 5797963-T-C +
4351388-T-A 4483347-T-A +
13436375-A-C 11280699-A-C +
4351403-A-C 4483362-A-C FT129806 +
13436405-T-A 11280729-T-A +
17919853-AAG-A 15807973-AAG-A +
2993635-C-G 3125594-C-G +
3402868-G-A 3534827-G-A +
13222916-G-C 11067240-G-C +
8214881-TC-T 8346840-TC-T +
13222660-G-T 11066984-G-T +
10005992-G-A 10168383-G-A Y+
9989941-G-T 10152332-G-T Y+
9931852-C-T 10094243-C-T Y+
9930264-C-A 10092655-C-A Y+
9930258-CG-C 10092649-CG-C +
9430085-A-G 9592476-A-G Y+
9430076-G-GCCT 9592467-G-GCCT +
8985925-G-C 9148316-G-C +
8985882-C-A 9148273-C-A +
8703897-C-G 8835856-C-G FT300517 YY+
8703896-G-T 8835855-G-T BY75307 YY+
8653633-C-T 8785592-C-T M11147 YY+
8125059-AGAGAG-A 8257018-AGAGAG-A +
3454064-C-T 3586023-C-T +
8057194-TGC-T 8189153-TGC-T +
8057193-ATG-A 8189152-ATG-A +
7536076-C-T 7668035-C-T YY+
6517620-C-T 6649579-C-T FT107254 +
6158454-A-G 6290413-A-G IR3_Dst +
5644847-T-C 5776806-T-C +
5364686-G-GT 5496645-G-GT +
5364661-C-T 5496620-C-T +
4490836-A-G 4622795-A-G +
4389427-T-G 4521386-T-G +
4079714-G-A 4211673-G-A FT319455 +
3964100-T-C 4096059-T-C +
3504287-A-G 3636246-A-G +
59021927-A-AGTTTT 56875780-A-AGTTTT +

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:

Manual17387271-CAT-C15275391-CAT-CTwo reads cover this deletion. The read which barely covers it does not show the deletion. The other read does.
Manual9522589-A-T9684980-A-T2 reads cover this position. One shows an A to N transition, and the other A to T.
Manual7030497-T-A7162456-T-A5 good reads, all are A.
Manual15003291-C-T12891376-C-T2 good reads, both T.
Manual8584704-CT-C8716663-CT-C3 good reads, all show the deletion.
Manual23771183-C-T21609297-C-T4 reads, all are C.
Manual22098199-A-C19936313-A-CNo coverage.
Manual21603292-G-A19441406-G-AOne read, a G.
Manual19565254-A-G17453374-A-G2 reads, both A.
Manual18264528-G-T16152648-G-T4 good reads, 1 okay read, all T.
Manual15564936-C-T13453056-C-TOne poor read, but it is a T.
Manual3436215-G-T3568174-G-T3 okay reads, all T.
Manual14516492-A-G12404693-A-GOne read, an N.
Manual19261105-T-C17149225-T-C2 reads, both T.
Manual22462900-T-A20301014-T-A3 good reads, 1 okay, all with A.
Manual22462902-A-C20301016-A-C4 good reads, all with C. One poor read, an A.
Manual3436218-G-A3568177-G-A1 read not aligned correctly. 1 poor read with a T. 2 ok reads with an A. 1 poor read with a C.
Manual28307441-CT-C26161294-CT-C4 reads, one of them shows the deletion.

Uncertain Mutations

NGS tests don't always cover all of the Y chromosome and, even when they do, the results can be inconclusive. The following mutations don't have clear results and have been assumed to be positive or negative. For those mutations that are assumed to be positive, the assumed SNP/INDEL will likely be found on the tree in some upstream block. It is unclear if it should be placed upstream of your results or parallel to them. The situation is reversed for mutations assumed negative. Those SNPs/INDELs will likely be found on a parallel branch on the tree, and it is unclear if they should be positioned upstream. As more results come in, the ambiguity may resolve itself, or it may be necessary to consult the BAM file for your test (available from FamilyTreeDNA or FullGenomes Corp) or by direct SNP testing (Sanger Sequencing - YSEQ or FamilyTreeDNA).


BlockRegionPOS-REF-ALT (hg19)POS-REF-ALT (hg38)NamesNotes
718 14516492-A-G 12404693-A-G Z16403 Uncertain, but assumed negative.
718 22098199-A-C 19936313-A-C Z16412 Uncertain, but assumed negative.

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