Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > Z46512 > FGC20747 > Y32765 > S4234 > Y20154

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
22436719-A-C 20274833-A-C BY52497 DYZ19 +
13620795-T-A 11465119-T-A +
14679419-G-T 12567485-G-T Y+
14557121-T-C 12445322-T-C Y+
14101351-T-C 11980645-T-C YY+
13961109-G-A 11840403-G-A Y+
13920793-C-A 11800087-C-A M1967 Y+
13838504-A-T 11717798-A-T +
13688218-A-AATGGG 11532542-A-AATGGG +
13637477-G-C 11481801-G-C +
13635612-AG-A 11479936-AG-A +
13635597-C-T 11479921-C-T +
13546242-G-A 11390566-G-A +
15528551-A-C 13416671-A-C YY+
13546218-A-C 11390542-A-C +
13529869-T-G 11374193-T-G +
13529422-G-GGAACTATAA 11373746-G-GGAACTATAA +
13506585-A-T 11350909-A-T +
13506575-C-T 11350899-C-T +
13474684-C-T 11319008-C-T +
13474672-T-C 11318996-T-C +
13472481-T-A 11316805-T-A +
13472465-C-T 11316789-C-T +
13430670-G-A 11274994-G-A +
13430646-GTCT-G 11274970-GTCT-G +
15318439-A-G 13206545-A-G YY+
15993679-GTGTA-G 13881799-GTGTA-G +
13402029-G-T 11246353-G-T +
21507462-C-A 19345576-C-A YY+
58872163-C-G 56718708-G-C +
28813481-G-A 26667334-G-A BY152144 +
28770302-A-G 26624155-A-G Y+
24444428-C-A 22298281-C-A S26179 Y+
23274486-G-GAGAA 21112600-G-GAGAA +
23274485-A-AGAGC 21112599-A-AGAGC +
23070188-A-C 20908302-A-C M5807 YY+
22724573-C-A 20562687-C-A YY+
22260984-G-T 20099098-G-T DYZ19 +
21822372-A-G 19660486-A-G YY+
21131420-C-G 18969534-C-G YY+
16074764-G-C 13962884-G-C Y+
21050883-TCAG-T 18888997-TCAG-T +
19530594-C-T 17418714-C-T YY+
18164685-A-C 16052805-A-C M8165 YY+
17860400-C-T 15748520-C-T Y+
17642283-T-G 15530403-T-G Y+
17639260-C-T 15527380-C-T Y+
17568445-C-G 15456565-C-G YY+
17561989-TG-T 15450109-TG-T +
17074139-T-TTG 14962259-T-TTG +
16874630-A-C 14762750-A-C YY+
16824041-G-A 14712161-G-A YY+
13402058-C-T 11246382-C-T +
13376189-G-A 11220513-G-A +
22220380-T-A 20058494-T-A DYZ19 +
2649680-A-G 2781639-A-G Y81125 Y+
4148928-C-T 4280887-C-T +
4015778-G-GA 4147737-G-GA +
3989490-G-A 4121449-G-A +
3945317-C-T 4077276-C-T +
3921897-T-C 4053856-T-C +
3654037-A-C 3785996-A-C +
3549745-C-A 3681704-C-A FT108668 +
3298982-C-T 3430941-C-T +
3051114-T-A 3183073-T-A +
2967614-A-C 3099573-A-C +
13392342-G-A 11236666-G-A +
4521335-A-G 4653294-A-G +
22893365-C-T 20731479-C-T YY+
21486281-T-C 19324395-T-C FT161357 YY+
16913442-A-G 14801562-A-G BY23202 YY+
15733223-G-T 13621343-G-T YY+
14043934-G-A 11923228-G-A FT109178 YY+
13957157-G-A 11836451-G-A S4237 Y+
8863063-G-T 8995022-G-T ZS686 YY+
7579118-T-C 7711077-T-C YY+
6682646-T-A 6814605-T-A S4231 Y+
13306139-T-C 11150463-T-C +
13290333-T-G 11134657-T-G +
4457118-A-T 4589077-A-T +
4709067-C-G 4841026-C-G FT108826 +
13337906-T-C 11182230-T-C +
9368339-G-GTC 9530730-G-GTC +
13337861-A-G 11182185-A-G +
13322578-C-T 11166902-C-T +
13322530-C-T 11166854-C-T FT69409 +
13291812-G-A 11136136-G-A +
13273502-A-T 11117826-A-T BY38164 +
13266437-G-A 11110761-G-A +
13260736-G-A 11105060-G-A +
9973880-G-A 10136271-G-A Y+
9973860-ATTTG-A 10136251-ATTTG-A +
9429743-T-C 9592134-T-C Y+
9368345-G-GTA 9530736-G-GTA +
9368335-G-GTT 9530726-G-GTT +
4776686-C-G 4908645-C-G +
9306568-C-A 9468959-C-A Y+
8888611-AAC-A 9020570-AAC-A +
8550878-G-T 8682837-G-T YY+
8547239-C-A 8679198-C-A YY+
7850427-G-T 7982386-G-T YY+
6946523-G-T 7078482-G-T YY+
6503664-T-G 6635623-T-G +
6158441-G-T 6290400-G-T IR3_Dst +
6000702-C-A 6132661-C-A PF2480 +
5972164-A-G 6104123-A-G +
5879664-G-A 6011623-G-A FT75419 +
59030801-A-AG 56884654-A-AG +

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:

Manual21380200-G-A19218314-G-A2 imperfect reads, but both are A.
Manual14175402-C-CA12054696-C-CAAll 5 reads show the insertion.
Manual24431356-T-TA22285209-T-TAJust one read, but it had the insertion.
Manual6375633-TA-T6507592-TA-TJust one read, but it has the deletion.
Manual7932958-CA-C8064917-CA-CJust one read, but it shows the deletion.
Manual9730464-A-ATGTG9892855-A-ATGTGJust one read, but it shows the insertion.
Manual13479594-G-A11323918-G-A3 reads with A, 4 reads with G, 1 misaligned read.
Manual13479603-T-C11323927-T-C3 reads with C, 6 reads with T, 2 misaligned reads.
Manual20674998-G-C18513112-G-C3G 1C
Manual20690528-C-T18528642-C-T1C 2T
Manual22225363-A-G20063477-A-G1A 2G
Manual22248904-T-A20087018-T-A4T 1A
Manual22250315-G-A20088429-G-A2A 1G
Manual22281594-G-A20119708-G-A2G 1A
Manual22315616-T-A20153730-T-A3T 2A
Manual22336748-G-T20174862-G-T2G 1T
Manual25091172-A-G22945025-A-G1A 1G
Manual25304024-A-G23157877-A-G1A 4G. The read with 1A is a poor match to the reference sequence.
Manual25705290-ACTCTCT-A23559143-ACTCTCT-AJust one read, but it shows the deletion.
Manual25912727-C-T23766580-C-T1C 3T

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