Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > DF49/S474 > Z2980 > Z2976 > DF23 > ZP112 > Y29872 > b38:6532654-G-A

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
NA12154
Manual
Edits
28613387-G-C 26467240-G-C CTS12561 +
13258558-CTTTTTTT-C 11102882-CTTTTTTT-C 20×T+
14881732-GTA-G 12769800-GTA-G +
14695992-C-CAAA 12584058-C-CAAA 30×A+
14245267-A-G 12124561-A-G YY5×GGAG+
14172752-AT-A 12052046-AT-A +
14096635-AG-A 11975929-AG-A +
13691018-G-A 11535342-G-A +
13640645-T-C 11484969-T-C +
13500490-T-A 11344814-T-A +
13500215-A-T 11344539-A-T +
13500181-G-A 11344505-G-A +
13416983-C-T 11261307-C-T +
13315688-G-A 11160012-G-A +
13258572-TTTTTTTC-T 11102896-TTTTTTTC-T +
13222827-A-G 11067151-A-G +
15151525-AG-A 13039612-AG-A +
13222416-GCACT-G 11066740-GCACT-G +
9996875-C-T 10159266-C-T Y+
9976668-T-C 10139059-T-C Y+
9932524-C-T 10094915-C-T Y+
8125049-A-AAAGC 8257008-A-AAAGC +
8119069-TG-T 8251028-TG-T +
7907525-G-GC 8039484-G-GC +
7723829-GAAGAAAAGAAAAGAA-G 7855788-GAAGAAAAGAAAAGAA-G 12×AAGAA+
7717675-T-TC 7849634-T-TC +
7567753-C-CTTT 7699712-C-CTTT 25×T+
6440847-G-A 6572806-G-A PF3622 +
5933250-A-T 6065209-A-T +
5756908-A-G 5888867-A-G +
15044347-C-A 12932437-C-A YY+
15230863-C-T 13118949-C-T Y+
5354790-ATAT-A 5486749-ATAT-A +
22446630-G-T 20284744-G-T DYZ19 +
59019511-AACACACACACACACACACACAC-A 56873364-AACACACACACACACACACACAC-A 20×AC+
58971911-T-TAC 56825764-T-TAC +
58903327-G-T 56687544-C-A +
58878251-C-T 56712620-G-A +
28604299-G-A 26458152-G-A +
28542433-AG-A 26396286-AG-A +
28534907-G-T 26388760-G-T +
28470598-C-A 26324451-C-A +
24386790-CTA-C 22240643-CTA-C +
23105999-TC-T 20944113-TC-T +
22767498-AT-A 20605612-AT-A +
22765597-C-A 20603711-C-A YY+
22633911-A-AAT 20472025-A-AAT +
22273128-T-A 20111242-T-A BY52328 DYZ19 +
15733430-C-A 13621550-C-A YY+
22081175-G-A 19919289-G-A FGC64878 Y32131 YY+
21504254-TA-T 19342368-TA-T +
21251812-CA-C 19089926-CA-C +
21251811-C-CT 19089925-C-CT +
20778689-T-C 18616803-T-C P4_Prx 13×AC+
20778687-C-T 18616801-C-T P4_Prx +
19335332-A-T 17223452-A-T YY+
19138043-A-AAT 17026163-A-AAT +
19099786-A-T 16987906-A-T Y+
18401237-G-A 16289357-G-A P6_Gap +
18001539-C-A 15889659-C-A P7_Gap Y+
17219907-G-A 15108027-G-A CTS6980 S3723 Y+
17074581-T-C 14962701-T-C YY+
5702620-C-CAAA 5834579-C-CAAA 25×A+
5339690-A-G 5471649-A-G +
2807063-TAA-T 2939022-TAA-T +
8218751-A-G 8350710-A-G YY+
21894801-A-G 19732915-A-G PH5007 YY+
21525079-G-A 19363193-G-A Y+
18988712-T-C 16876832-T-C CTS9607 Y+
18844872-T-C 16732992-T-C Y+
17367893-G-A 15256013-G-A CTS7233 S3713 YY+
16346264-G-C 14234384-G-C YY+
15373642-C-T 13261762-C-T S3720 CTS4067 YY+
14541139-T-A 12429340-T-A YY+
14541131-C-T 12429332-C-T YY+
14541126-T-G 12429327-T-G YY+
14330865-T-C 12210159-T-C YY+
14157413-G-A 12036707-G-A CTS2025 Y+
8322792-T-C 8454751-T-C Y+
6857619-C-T 6989578-C-T S3708 CTS576 YY+
28675656-T-G 26529509-T-G CTS12703 S3719 +
2889185-G-C 3021144-G-C CTS316 S3465 YY+
2714836-T-G 2846795-T-G CTS78 S3464 YY+
15520169-GA-G 13408289-GA-G 10×A+
14541144-T-G 12429345-T-G YY+
17834359-A-C 15722479-A-C YY+
9398654-C-G 9561045-C-G YY+
28619573-C-A 26473426-C-A 16×A+
5666004-T-C 5797963-T-C +
58894855-A-G 56696016-T-C +
19926979-G-T 17815099-G-T P5_Prx +
22802868-A-ATTTT 20640982-A-ATTTT 32×T+
25803150-GTA-G 23657003-GTA-G P1_b3 +
14148014-A-AAAAT 12027308-A-AAAAT 8×AAAT+
22600076-A-T 20438190-A-T PH5140 YY+
28794959-TG-T 26648812-TG-T +
5310277-A-C 5442236-A-C +
3720167-T-TCC 3852126-T-TCC +
5250681-C-T 5382640-C-T +
4737264-G-A 4869223-G-A +
4651422-GA-G 4783381-GA-G 11×A+
4521425-GCA-G 4653384-GCA-G 10×CA+
4072019-CGG-C 4203978-CGG-C +
4072018-ACG-A 4203977-ACG-A +
3924394-C-A 4056353-C-A +
3924392-C-T 4056351-C-T +
3909132-C-A 4041091-C-A +
3909131-AC-A 4041090-AC-A +
3891474-C-T 4023433-C-T +
3720185-C-CCCA 3852144-C-CCCA +
3720173-A-ACC 3852132-A-ACC +
3544896-G-GC 3676855-G-GC +
5174328-AAC-A 5306287-AAC-A 13×AC+
3544888-A-AG 3676847-A-AG +
3446607-C-CAAA 3578566-C-CAAA 25×A+
3087953-C-T 3219912-C-T +
3087945-A-T 3219904-A-T +
14491262-A-AGAGC +
59027475-A-AAAAG 56881328-A-AAAAG +
13452873-GCATTCCATTCCATTC-G 11297197-GCATTCCATTCCATTC-G 14×CATTC+
58889397-G-A 56701474-C-T +
13747419-T-A 11591743-T-A +
15309739-C-CAAAA 13197843-C-CAAA 41×A+
13446679-CCATT-C 11291003-CCATT-C +
13256858-G-GTT 11101182-G-GTT 18×T+
14882302-ACT-A 12770370-ACT-A +
13738513-A-T 11582837-A-T +
59021932-T-TTTC 56875785-T-TTTC +

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
Manual2805834-C-T2937793-C-TNegative for DF104. All 7 reads are C.
Manual4439911-TGCAGCTTCACTCCTGAGG-T4571870-TGCAGCTTCACTCCTGAGG-T2 reads, both positive.
Manual5060608-T-C5192567-T-C7C 2T. The two T reads could align to the X chromosome. Even with their mates, their position is ambiguous.
Manual22316776-G-T20154890-G-T11G 6T
Manual19851872-G-C17739992-G-C3G 7C
Manual8332772-G-A8464731-G-A2A
Manual9114686-C-G9277077-C-G3G
Manual28811476-T-A26665329-T-A5A 15T



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