Tree Position

A0-T-YP2191 > P305 > L413/PF1409/V31 > M168/PF1416 > P143 > M89/PF2746 > F1329/M3658 > F929 > IJK > K > P295 > M242 > 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
14604440-G-A 12492642-G-A Z17581Z17581 Y4954 YY+
16711960-TTC-T 14600080-TTC-T +
16054765-A-G 13942885-A-G Y26587 YY+
16273119-C-G 14161239-C-G YP5754 Y+
16519247-T-G 14407367-T-G YP5746 YY+
16556552-TG-T 14444672-TG-T +
16622405-C-A 14510525-C-A YP5755 Y+
16680268-G-A 14568388-G-A Y26588 YY+
16696452-C-A 14584572-C-A Y26589 YY+
16738262-C-T 14626382-C-T YP5764 YY+
15869065-T-A 13757185-T-A Y26586 YY+
16955182-C-T 14843302-C-T SK1978 YY+
17104392-G-A 14992512-G-A Y26590 YY+
17374774-G-C 15262894-G-C Y26591 Y+
17800104-C-T 15688224-C-T Y26592 YY+
17866611-T-A 15754731-T-A Y26593 YY+
17909830-A-T 15797950-A-T Y26594 YY+
18122131-C-T 16010251-C-T Y26595 YY+
15979832-A-G 13867952-A-G SK1976 YY+
15798888-T-C 13687008-T-C Y26585 YY+
18153614-G-A 16041734-G-A Y+
14447092-G-A 12326365-G-A YP5739 Y+
14003426-A-G 11882720-A-G Y26574 YY+
14054523-A-G 11933817-A-G Y26575 YY+
14079211-G-A 11958505-G-A Y26576 YY+
14169818-A-T 12049112-A-T Y26577 YY+
14235158-C-T 12114452-C-T YY+
14258873-C-T 12138167-C-T Y26578 Y+
14327778-C-G 12207072-C-G Y26579 YY+
14555799-T-G 12444000-T-G YP5740 YY+
15683514-C-T 13571634-C-T Y+
14587383-C-T 12475583-C-T Y26580 YY+
14783130-A-AG 12671200-A-AG +
14813764-A-C 12701835-A-C YP5742 YY+
15282361-G-T 13170460-G-T YP5743 Y+
15330838-A-G 13218956-A-G Y26581 YY+
15345215-C-G 13233334-C-G Y26582 YY+
15391576-G-C 13279696-G-C Y26583 YY+
15673619-T-C 13561739-T-C Y+
18149024-C-G 16037144-C-G Y26596 YY+
18256335-C-T 16144455-C-T YP5747 +
13880013-T-C 11759307-T-C Y26573 Y+
23044582-G-GA 20882696-G-GA +
22472058-G-T 20310172-G-T DYZ19 +
22649468-A-C 20487582-A-C Y26603 YY+
22649933-C-T 20488047-C-T Y26604 YY+
22692190-C-T 20530304-C-T Y+
22856028-T-C 20694142-T-C YP5752 Y+
22914954-G-C 20753068-G-C Y26605 YY+
23018415-A-T 20856529-A-T Y38275 Y+
23049558-G-A 20887672-G-A YP5753 YY+
22464047-G-A 20302161-G-A DYZ19 +
23110700-C-T 20948814-C-T Y+
23207629-G-A 21045743-G-A Y26606 Y+
23775134-G-A 21613248-G-A YP5760 Y+
23857512-G-A 21695626-G-A Y26607 Y+
23985823-G-T 21839676-G-T Y26608 Y+
24502838-C-T 22356691-C-T BZ270 +
28543031-C-T 26396884-C-T YP5769 +
28643876-CAAAA-C 26497729-CAAAA-C +
22472057-G-T 20310171-G-T BY53040 DYZ19 +
22445611-G-A 20283725-G-A DYZ19 +
18395083-T-C 16283203-T-C YP5756 P6_Gap +
19247021-C-T 17135141-C-T YP5748 YY+
18427359-C-G 16315479-C-G YP5766 P6_Gap +
18677217-A-G 16565337-A-G SK1977 YY+
18685720-T-A 16573840-T-A YP5765 YY+
18715192-G-T 16603312-G-T Y26597 YY+
18852045-A-G 16740165-A-G SK1979 YY+
19057775-A-G 16945895-A-G YP5757 YY+
19127299-A-C 17015419-A-C Y26598 YY+
19452928-T-C 17341048-T-C Y26599 YY+
22440546-G-T 20278660-G-T DYZ19 +
19824892-AAAG-A 17713012-AAAG-A P5_Prx +
21059320-C-T 18897434-C-T Y+
21632648-T-C 19470762-T-C YP5749 Y+
22018844-T-G 19856958-T-G YP5758 YY+
22106084-C-T 19944198-C-T YP5759 YY+
22123960-C-G 19962074-C-G Y26601 YY+
22208111-A-G 20046225-A-G Y26602 YY+
22287902-A-C 20126016-A-C DYZ19 +
13893425-C-T 11772719-C-T Y+
13833116-G-A 11712410-G-A YP5773 +
13436080-AT-A 11280404-AT-A 8×T+
6498458-G-A 6630417-G-A +
5440247-A-T 5572206-A-T +
5584328-A-G 5716287-A-G +
5637527-T-C 5769486-T-C +
5907508-T-G 6039467-T-G YP5736 +
5914854-C-T 6046813-C-T +
6071408-T-C 6203367-T-C +
6422924-C-T 6554883-C-T YP5767 +
6698908-G-C 6830867-G-C Y26547 YY+
4894855-C-T 5026814-C-T +
6702974-G-A 6834933-G-A YP5768 YY+
6835354-A-G 6967313-A-G Y26548 YY+
6845623-C-T 6977582-C-T Y26549 YY+
6847451-G-A 6979410-G-A Y26550 YY+
7121921-C-G 7253880-C-G Y+
7353111-GA-G 7485070-GA-G +
7548499-A-G 7680458-A-G SK1973 YY+
5003091-A-C 5135050-A-C +
4837537-C-A 4969496-C-A +
7654363-G-A 7786322-G-A Y26551 YY+
4256999-C-A 4388958-C-A +
2940485-C-T 3072444-C-T +
3041540-ATTTAT-A 3173499-ATTTAT-A +
3486204-T-A 3618163-T-A +
3567540-A-C 3699499-A-C +
3799493-C-T 3931452-C-T +
3888581-G-A 4020540-G-A +
4002422-G-A 4134381-G-A +
4362511-T-G 4494470-T-G +
4827463-A-G 4959422-A-G +
4366560-A-C 4498519-A-C +
4376002-C-T 4507961-C-T +
4494209-C-T 4626168-C-T +
4564289-C-T 4696248-C-T +
4570030-C-G 4701989-C-G +
4576868-A-G 4708827-A-G +
4710489-T-C 4842448-T-C +
4746727-GT-G 4878686-GT-G +
7558554-G-A 7690513-G-A SK1974 YY+
7672315-A-G 7804274-A-G Y26552 YY+
13814742-C-A 11694036-C-A YP5741 +
10009022-G-C 10171413-G-C Y+
9464721-T-C 9627112-T-C Y26570 Y+
9786101-T-C 9948492-T-C Y26571 Y+
9821644-GCTA-G 9984035-GCTA-G +
9895907-C-A 10058298-C-A YP5772 Y+
9898699-A-G 10061090-A-G Y26572 Y+
9955711-T-C 10118102-T-C Y+
9968712-A-G 10131103-A-G Y+
10027249-C-A 10189640-C-A Y+
9401357-T-C 9563748-T-C Y38133 YY+
10075489-T-C 10237880-T-C YP5737 +
10093722-C-T 10256113-C-T +
13212452-A-C 11056776-A-C +
13456998-A-G 11301322-A-G +
13575385-A-T 11419709-A-T +
13577467-T-G 11421791-T-G +
13624664-G-T 11468988-G-T +
13798769-A-C 11678063-A-C +
9440234-A-G 9602625-A-G Y26569 YY+
9197006-A-G 9359397-A-G Y+
7676068-A-T 7808027-A-T Y26553 YY+
8306124-A-G 8438083-A-G Y26561 YY+
7843564-T-C 7975523-T-C Y26554 YY+
7929840-G-A 8061799-G-A Y26555 YY+
7934704-T-G 8066663-T-G Y26556 YY+
8008399-T-G 8140358-T-G Y26557 YY+
8047054-T-G 8179013-T-G Y26558 YY+
8086114-G-T 8218073-G-T Y26559 YY+
8105751-A-T 8237710-A-T Y26560 YY+
8344350-AT-A 8476309-AT-A +
9168921-A-G 9331312-A-G Y26568 Y+
8353233-G-A 8485192-G-A Y26562 YY+
8445638-G-C 8577597-G-C Y26563 YY+
8581071-T-C 8713030-T-C Y26564 YY+
8601165-C-T 8733124-C-T Y26565 YY+
8704106-C-G 8836065-C-G Y26566 YY+
8789011-G-A 8920970-G-A YP5763 YY+
8986389-G-T 9148780-G-T +
9012775-A-C 9175166-A-C Y26567 Y+
28667072-G-A 26520925-G-A YP5770 +

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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