Tree Position

A0-T-YP2191 > P305[A1] > L413/PF1409/V31 > M168/PF1416[CT] > P143[CF] > M89/PF2746[F] > F1329/M3658[GHI > F929[HIJK] > IJK > IJ > J > J2 > 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
HG02490
13454333-G-A 11298657-G-A BY32935 +
18931544-C-T 16819664-C-T Y8507 YY+
18384188-C-A 16272308-C-A Y8503 P6_Gap +
18386103-G-A 16274223-G-A Y7707 P6_Gap +
18565186-T-C 16453306-T-C Y8505 YY+
18573196-T-C 16461316-T-C Y8506 SK1334 YY+
18715794-G-A 16603914-G-A Y28880 YY+
18727829-C-T 16615949-C-T Y7708 Z29414 YY+
18776610-G-T 16664730-G-T YY+
18966139-C-A 16854259-C-A Y28881 YY+
18233184-C-T 16121304-C-T b38:7808642-T-CY7706 Y+
19025613-A-T 16913733-A-T Y+
19083923-C-T 16972043-C-T Y21797 Y+
19255390-C-T 17143510-C-T Y8518 YY+
19313919-A-G 17202039-A-G Y8519 YY+
19335412-C-T 17223532-C-T Y28882 YY+
19464893-G-A 17353013-G-A YY+
21062809-T-C 18900923-T-C YY+
18270604-A-G 16158724-A-G Y15413 +
17916890-T-A 15805010-T-A Y7705 YY+
21147503-T-C 18985617-T-C Y7709 YY+
17169312-A-C 15057432-A-C Y7701 YY+
16590433-T-C 14478553-T-C Y8498 YY+
16621694-C-T 14509814-C-T Y21789 Y+
16824697-T-A 14712817-T-A Y7700 SK1332 YY+
16945125-C-T 14833245-C-T Y21790 Y+
16967894-C-G 14856014-C-G YY+
17029248-C-A 14917368-C-A Y14413 YY+
17094772-C-T 14982892-C-T YY+
17187514-T-A 15075634-T-A Y14679 YY+
17909502-C-T 15797622-C-T Y8502 YY+
17428402-T-C 15316522-T-C Y21791 YY+
17430591-G-T 15318711-G-T Y+
17589473-C-T 15477593-C-T Y7702 YY+
17604824-C-T 15492944-C-T Y8500 YY+
17647680-G-A 15535800-G-A Y7703 YY+
17749123-G-T 15637243-G-T Y7704 YY+
17793052-A-G 15681172-A-G Y28883 YY+
17796916-C-T 15685036-C-T Y21793 Y+
21123596-C-T 18961710-C-T Y+
21274543-C-G 19112657-C-G Y+
16377123-A-G 14265243-A-G Y7699 YY+
24462921-T-C 22316774-T-C Y8529 Y+
22801299-C-T 20639413-C-T Y+
22865098-G-A 20703212-G-A YY+
22948502-T-C 20786616-T-C YY+
23074684-T-C 20912798-T-C BY185839 YY+
23605972-C-T 21444086-C-T YY+
23989782-T-C 21843635-T-C BY20018Y8528 Y+
24417103-A-G 22270956-A-G M809 Y+
27976062-G-A 25829915-G-A BY33004 P1_Y2 +
22720579-A-G 20558693-A-G Y14672 YY+
28479017-C-G 26332870-C-G +
28549913-G-A 26403766-G-A Y14673 +
28596209-A-G 26450062-A-G +
28710535-G-T 26564388-G-T +
28748271-G-A 26602124-G-A +
28776339-C-T 26630192-C-T +
28789322-G-A 26643175-G-A Y7717 5×AATCA+
22786731-T-G 20624845-T-G Y8526 YY+
22550953-C-T 20389067-C-T Y7716 YY+
21353059-A-G 19191173-A-G Y+
21751330-G-A 19589444-G-A M47 YY+
21374136-G-C 19212250-G-C Y7710 YY+
21377774-T-A 19215888-T-A Y+
21380876-G-T 19218990-G-T Y7711 Y+
21490443-T-A 19328557-T-A Y7712 YY+
21492977-G-C 19331091-G-C Y7713 YY+
21498489-A-G 19336603-A-G Y+
21594149-T-G 19432263-T-G Y8521 YY+
21792107-C-T 19630221-C-T Y+
22549115-T-A 20387229-T-A Y8525 YY+
21878995-A-C 19717109-A-C L290 YY+
21915778-G-A 19753892-G-A Y7714 YY+
21951312-T-G 19789426-T-G BY185742 YY+
22071505-A-G 19909619-A-G Y8523 YY+
22151326-G-A 19989440-G-A Y+
22160646-T-C 19998760-T-C Y8524 YY+
22169195-G-T 20007309-G-T Y+
22183318-G-T 20021432-G-T Y7715 YY+
16536652-C-G 14424772-C-G YY+
16188459-G-A 14076579-G-A BY185334 YY+
8657436-G-A 8789395-G-A SK1331 Y8536 YY+
6593997-T-C 6725956-T-C +
5934661-G-A 6066620-G-A +
6007373-T-G 6139332-T-G +
6008385-C-T 6140344-C-T +
6069064-A-G 6201023-A-G +
6088892-A-G 6220851-A-G +
6205913-A-G 6337872-A-G BY184720 IR3_Dst +
6400384-G-T 6532343-G-T Y8533 +
6730172-G-A 6862131-G-A Y14410 Y+
5775130-C-T 5907089-C-T Y8497 +
7018357-A-G 7150316-A-G Y+
7046164-A-G 7178123-A-G YY+
7092048-T-A 7224007-T-A Y7689 YY+
7094202-A-G 7226161-A-G Y7690 YY+
7132507-A-G 7264466-A-G Y21801 Y+
7293311-G-T 7425270-G-T Y7691 YY+
7573233-C-G 7705192-C-G Y21802 YP1786 FGC25550 Y+
5925483-G-T 6057442-G-T +
5715472-A-G 5847431-A-G +
7632216-T-C 7764175-T-C Y21794 Y+
4216232-C-T 4348191-C-T Y21800 +
21256281-C-T 19094395-C-T FGC72599Y8520 BY1733 YY+
8043269-ATTG-A 8175228-ATTG-A 7×TTG+
14235938-G-A 12115232-G-A Y14677 YY+
2985854-T-C 3117813-T-C +
3042247-G-A 3174206-G-A +
3706429-T-A 3838388-T-A Y20897 +
3956920-T-A 4088879-T-A +
4471416-G-A 4603375-G-A Y21785 +
5613640-C-A 5745599-C-A +
4524295-G-C 4656254-G-C +
4550641-T-G 4682600-T-G +
4600041-G-T 4732000-G-T +
4938731-T-G 5070690-T-G +
4970060-C-T 5102019-C-T +
5081089-A-G 5213048-A-G Y7687 +
5264330-G-C 5396289-G-C Y21786 +
5386034-A-G 5517993-A-G +
7600768-T-C 7732727-T-C Y7692 YY+
7675076-A-T 7807035-A-T Y8531 YY+
15704216-T-C 13592336-T-C Y7698 YY+
14605769-G-A 12493971-G-A Y14412 Y+
13915477-C-T 11794771-C-T Y+
14079833-A-G 11959127-A-G Y20898 YY+
14080993-C-T 11960287-C-T YY+
14152629-T-A 12031923-T-A YY+
14229283-A-G 12108577-A-G Y8514 YY+
14359436-C-T 12238731-C-T Y8515 YY+
14452689-G-A 12331962-G-A Y14411 YY+
14627186-G-A 12515254-G-A Y21798 YY+
13530807-G-A 11375131-G-A +
14746809-A-G 12634878-A-G YY+
14936092-C-G 12824157-C-G YY+
15131345-T-C 13019432-T-C Y7697 YY+
15243473-A-G 13131559-A-G Y+
15443108-C-T 13331228-C-T Y21787 Y+
15469740-C-A 13357860-C-A M322 YY+
15643872-G-A 13531992-G-A Y21788 Y+
13645643-A-T 11489967-A-T BY32937 +
13318758-C-T 11163082-C-T BY85175 +
7713455-C-T 7845414-C-T BY67075 YY+
8551328-C-A 8683287-C-A Y8513 YY+
7722562-G-A 7854521-G-A Y7693 YY+
7787821-C-A 7919780-C-A YY+
7800326-G-A 7932285-G-A Y7694 YY+
7919722-G-T 8051681-G-T Y8532 YY+
8028497-G-T 8160456-G-T Y8510 YY+
8129960-C-A 8261919-C-A Y8511 YY+
8296155-C-T 8428114-C-T Y21795 Y+
8631042-G-A 8763001-G-A SK194 V2386 YY+
13199802-A-T 11044126-A-T BY32932 +
9026547-A-G 9188938-A-G Y7695 Y+
9036722-T-C 9199113-T-C Y8534 Y+
9383043-C-T 9545434-C-T Y+
9453521-C-A 9615912-C-A Y7696 YY+
9735939-T-C 9898330-T-C Y8535 IR3_Prx +
9779200-G-T 9941591-G-T Y+
13128773-T-G 10618259-T-G +
13131984-C-G 10621470-C-G +
28798298-G-T 26652151-G-T +

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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