Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > L1335/S530 > L1065 > Z16325 > S744 > S691 > BY3127 > S7361 > S3679 > BY45127 > CTS110

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
20105742-TTATC-T 17993862-TTATC-T P5_Dst 14×TATC+
14537957-T-C 12426158-T-C YY+
13686909-ACACG-A 11531233-ACACG-A +
13738889-A-G 11583213-A-G +
13853311-T-A 11732605-T-A Y29262 +
13859440-G-C 11738734-G-C +
13931735-C-T 11811029-C-T Y+
13931739-C-T 11811033-C-T Y22×T+
13960892-T-C 11840186-T-C Y+
14015392-T-G 11894686-T-G Y+
14025561-G-GAAAA 11904855-G-GAAAA +
14063655-G-C 11942949-G-C CTS1777 YY+
14102397-C-CTATG 11981691-C-CTATG +
14881732-GTA-G 12769800-GTA-G +
13622184-G-T 11466508-G-T +
14986717-TGCAC-T 12874785-TGC-T +
15263363-T-TAAA 13151453-T-TAAA +
15276900-AG-A 13164989-AG-A +
15305888-T-TAATAG 13193990-T-TAATAG 11×AG+
15305889-AG-A 13193991-AG-A +
15329065-C-T 13217183-C-T CTS4003 YY+
15379781-C-T 13267901-C-T Y+
15557159-ATATT-A 13445279-ATATT-A +
15882099-AG-A 13770219-AG-A +
16021881-C-CT 13910001-C-CT +
16244821-GTGTA-G 14132941-GTGTA-G +
13622191-C-T 11466515-C-T +
13602316-C-G 11446640-C-G +
16406852-TA-T 14294972-TA-T +
13322986-T-TTTC 11167310-T-TTTC +
9941960-T-G 10104351-T-G Y+
10006625-A-C 10169016-A-C Y+
10104556-N-G 10266947-N-G +
10104558-N-T 10266949-N-T +
10104559-N-C 10266950-N-C +
10104560-N-G 10266951-N-G +
13222616-GGAGA-G 11066940-GGAGA-G +
13255133-G-T 11099457-G-T +
13260605-TTC-T 11104929-TTC-T +
13275119-A-G 11119443-A-G +
13311501-G-A 11155825-G-A +
13334362-G-C 11178686-G-C +
13535681-ATG-A 11380005-ATG-A 9×TG+
13383888-T-G 11228212-T-G +
13388103-A-G 11232427-A-G +
13388173-T-C 11232497-T-C +
13414762-T-A 11259086-T-A +
13414853-G-A 11259177-G-A +
13415224-G-A 11259548-G-A +
13431505-T-C 11275829-T-C +
13447117-C-T 11291441-C-T +
13500604-A-T 11344928-A-T +
13500639-C-T 11344963-C-T +
13500658-T-A 11344982-T-A +
16406824-G-T 14294944-G-T YY+
16986067-G-T 14874187-G-T YY+
9307403-T-TTC 9469794-T-TTC +
28628430-ATATT-A 26482283-ATATT-A +
24408990-GA-G 22262843-GA-G +
24600498-TTC-T 22454351-TTC-T P3_t2 +
24600509-T-C 22454362-T-C P3_t2 +
24895715-G-T 22749568-G-T g1 +
27399223-A-G 25253076-A-G P1_g3 +
27399225-G-A 25253078-G-A P1_g3 +
27454144-G-C 25307997-G-C P1_Y2 +
28478036-TATAG-T 26331889-TATAG-T +
28611428-G-A 26465281-G-A +
28620602-G-GA 26474455-G-GA +
28628428-ATATATT-A 26482281-ATATATT-A +
28628432-ATT-A 26482285-ATT-A +
23829792-G-A 21667906-G-A M4658 Y+
28642837-C-G 26496690-C-G M3959 +
28663199-A-T 26517052-A-T +
28686464-C-A 26540317-C-A +
28698846-A-G 26552699-A-G +
28734730-ACTGAG-A 26588583-ACTGAG-A +
58873959-T-C 56716912-A-G +
59001389-AAAG-A 56855242-AAAG-A +
59009233-C-CCAAA 56863086-C-CCAAA +
59009240-AAC-A 56863093-AAC-A +
59009241-AC-A 56863094-AC-A +
59026874-C-CT 56880727-C-CT +
23898750-C-T 21736864-C-T +
23364907-C-A 21203021-C-A YY+
17026006-C-T 14914126-C-T CTS6639 Y+
19386785-TA-T 17274905-TA-T +
17129928-C-T 15018048-C-T PH2842 YY+
17281981-AGAT-A 15170101-AGAT-A +
17500836-T-G 15388956-T-G M8509 Y+
17515601-AG-A 15403721-AG-A +
17807478-C-T 15695598-C-T A14348 YFS1251050 YY+
17836370-C-A 15724490-C-A Y+
17946919-G-GTTT 15835039-G-GTTT 24×T+
18393269-T-TATC 16281389-T-TATC P6_Gap +
18653646-T-A 16541766-T-A YY+
19049508-A-ATAT 16937628-A-ATAT +
19202764-AC-A 17090884-AC-A +
19411950-GAA-G 17300070-GAA-G +
23208766-A-T 21046880-A-T Y+
19415501-C-T 17303621-C-T Y8743 FGC22598 YY+
20815452-TAC-T 18653566-TAC-T P4_Gap +
21058022-A-G 18896136-A-G Y+
21146293-G-T 18984407-G-T YY+
21170322-T-G 19008436-T-G YY+
21170326-T-G 19008440-T-G YY+
21170346-C-T 19008460-C-T YY+
21248052-A-G 19086166-A-G Z34577 Y+
21330646-C-T 19168760-C-T YY+
21435381-GT-G 19273495-GT-G +
21622674-G-T 19460788-G-T Z5701 YY9×T+
22475864-G-A 20313978-G-A BY223450 DYZ19 +
9650328-T-C 9812719-T-C BY157660 IR3_Prx +
9307402-G-GTT 9469793-G-GTT +
28787589-A-G 26641442-A-G +
18200505-C-A 16088625-C-A YY+
9847274-A-T 10009665-A-T YY+
15023555-A-C 12911643-A-C S16678 F11578 YY+
8119489-G-T 8251448-G-T BY70093 YY14×T+
17841374-A-C 15729494-A-C S20279 YY+
17479396-C-A 15367516-C-A YY13×A+
22093164-G-T 19931278-G-T FT306469 YY+
6860621-A-G 6992580-A-G Y15 F46 YY+
6941518-C-T 7073477-C-T S9647 YY+
8486164-C-A 8618123-C-A Z31722 YY+
9804357-A-G 9966748-A-G Y+
17836380-C-G 15724500-C-G Y+
21476078-G-A 19314192-G-A S3682 Y+
19146564-C-T 17034684-C-T YY+
22155320-G-A 19993434-G-A S3684 Y+
13222618-AGAGG-A 11066942-AGAGG-A +
58877533-T-C 56713338-A-G +
13222637-A-G 11066961-A-G +
13294189-T-C 11138513-T-C +
58871191-C-T 56719680-G-A +
58871199-G-C 56719672-C-G +
58878324-C-T 56712547-G-A +
58894426-G-A 56696445-C-T +
13747514-T-A 11591838-T-A +
13741945-A-T 11586269-A-T +
28698742-GCTT-ACTC 26552595-GCTT-ACTC +
15799114-CCCTT-TCCTC 13687234-CCCTT-TCCTC 14×CCTT+
13738513-A-T 11582837-A-T +
58871362-C-A 56719509-G-T +
58873456-A-G 56717415-T-C +
13384812-G-A 11229136-G-A BY15623 +
21807789-G-A 19645903-G-A L705Z16411 YY8×T+
28571522-G-A 26425375-G-A CTS12305 +
58837383-G-A 56753488-C-T +
58880540-G-A 56710331-C-T +
16344414-T-TTCTTCA 14232534-T-TTCTTCA +
13456019-GATTCC-G 11300343-GATTCC-G 11×ATTCC+
10104554-N-T 10266945-N-T +
10104555-N-A 10266946-N-A +
10104557-N-A 10266948-N-A +
58871385-T-C 56719486-A-G +
14866140-C-T 12754206-C-T YY11×GT+
58871345-T-C 56719526-A-G +
13618508-T-A 11462832-T-A +
28802841-T-C 26656694-T-C +
13346809-C-T 11191133-C-T +
24388090-A-ATG 22241943-A-ATG +
13139021-C-CA 10628507-C-CA +
13311579-A-G 11155903-A-G +
58842502-C-T 56748369-G-A +
5941845-T-C 6073804-T-C +
6648613-C-T 6780572-C-T YY27×T+
14866163-A-G 12754233-A-G BY98097 YY+
19146569-C-T 17034689-C-T YY28×T+
13747547-A-T 11591871-A-T +
22005442-A-C 19843556-A-C YY+
8875443-G-T 9007402-G-T Y+
5702619-AC-A 5834578-AC-A +
4390157-A-T 4522116-A-T +
4396184-C-T 4528143-C-T +
4489282-T-A 4621241-T-A +
4682803-T-C 4814762-T-C Y1360 +
5043420-C-T 5175379-C-T +
5215599-C-T 5347558-C-T FT78366 +
5225316-ATG-A 5357275-ATG-A +
5268741-G-A 5400700-G-A +
5503843-C-T 5635802-C-T +
5691763-C-A 5823722-C-A +
5702618-AAC-A 5834577-AAC-A +
5962108-TCATA-T 6094067-TCATA-T +
4293797-G-T 4425756-G-T +
6454542-A-C 6586501-A-C +
6769276-C-T 6901235-C-T YY+
7025769-A-T 7157728-A-T Y+
7033240-C-A 7165199-C-A Y15×A+
7160877-A-C 7292836-A-C YY+
7200292-C-T 7332251-C-T Y+
7265849-A-G 7397808-A-G YY+
7474427-A-G 7606386-A-G IR1_L +
7915372-A-C 8047331-A-C YY+
8281028-T-C 8412987-T-C YY+
8748601-T-A 8880560-T-A YY+
4320933-G-A 4452892-G-A +
4288455-A-C 4420414-A-C +
15037755-A-AGC 12925845-A-AGC +
59027475-A-AAAAG 56881328-A-AAAAG +
24425339-G-GCATT 22279192-G-GCATT +
24425341-A-ATGCG 22279194-A-ATGCG +
22272934-CTT-C 20111048-CTT-C DYZ19 +
24447135-G-GAAAA 22300988-G-GAAAA +
24447150-A-AGAAG 22301003-A-AGAAG 4×AAAG+
24408989-TG-T 22262842-TG-T +
13446679-CCATT-C 11291003-CCATT-C +
24425343-G-GCATT 22279196-G-GCATT +
13746345-A-C 11590669-A-C +
13641262-C-T 11485586-C-T +
13641268-T-C 11485592-T-C +
4261308-C-T 4393267-C-T +
2758861-AGAAGAAG-A 2890820-AGAAGAAG-A +
3171959-T-A 3303918-T-A ZS448 +
3226950-C-T 3358909-C-T +
3256136-CTAT-C 3388095-CTAT-C +
3434302-A-T 3566261-A-T +
3572648-A-G 3704607-A-G +
3572650-T-C 3704609-T-C +
3628012-A-T 3759971-A-T 14×T+
3727485-T-C 3859444-T-C +
4098684-G-A 4230643-G-A +
4179019-AT-A 4310978-AT-A +
59032459-G-A 56886312-G-A +

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:

Manual14026048-AAG-A11905342-AAG-A2 reads, both show the deletion.
Manual21859032-C-CA19697146-C-CAOne read, it has the insertion.
Manual22069403-T-C19907517-T-COne read, a C.
Manual22121805-G-A19959919-G-ANo coverage.
Manual22285033-G-A20123147-G-A8 reads. 3 are A, 5 are G.
Manual22323252-G-A20161366-G-A3 reads. 1 A and 2 G.
Manual17542453-G-T15430573-G-T2 reads, both T.
Manual13357060-G-A11201384-G-A1G 3A
Manual5563777-C-CA5695736-C-CABoth reads show the insertion.
Manual16842867-ATGTGTGTGTGTGTGTGTGTG-A14730987-ATGTGTGTGTGTGTGTGTGTG-A1 read show the deletion.
Manual4439911-TGCAGCTTCACTCCTGAGG-T4571870-TGCAGCTTCACTCCTGAGG-TJust one read, it's positive.
Manual22443795-T-A20281909-T-A2T 3A
Manual13675388-G-A11519712-G-A1A, but it is at the very end of a read.
Manual14743395-A-T12631463-A-T3T, one of which has poor quality.
Manual23817310-A-T21655424-A-TBoth reads positive.
Manual23817307-C-CT21655421-C-CTBoth reads positive.

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