Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > Z251/S470 > FGC13899

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 STRFTDNA
171804
2699821-G-A 2831780-G-A BY55857 YY+
7179071-G-A 7311030-G-A BY63699 YY+
8597476-G-C 8729435-G-C FT179449 YY+
8804033-C-T 8935992-C-T BY76023 YY+
9109786-T-G 9272177-T-G BY78180 Y+
9842951-A-G 10005342-A-G BY81368 YY+
10025657-C-T 10188048-C-T BY83124 Y+
13836542-C-T 11715836-C-T BY54515 +
14005086-G-A 11884380-G-A FTB3028 YY+
14026096-G-C 11905390-G-C BY92403 YY+
14095102-T-C 11974396-T-C BY92962 YY+
14324037-T-C 12203331-T-C BY94873 YY+
14409901-G-A 12289198-G-A BY95561 YY+
15547552-A-G 13435672-A-G BY102430 YY+
15845119-G-A 13733239-G-A BY104487 YY+
15977342-A-G 13865462-A-G BY105260 YY+
16222056-C-A 14110176-C-A BY106072 YY+
16235822-C-T 14123942-C-T BY106216 YY+
16473087-C-A 14361207-C-A BY108044 YY+
17172333-A-G 15060453-A-G BY112804 YY+
17457085-AC-A 15345205-AC-A +
18220349-G-T 16108469-G-T BY120970 Y+
18247782-G-C 16135902-G-C BY121162 Y+
19171777-C-T 17059897-C-T BY126949 Y+
19261498-C-T 17149618-C-T BY127738 YY+
19306841-A-G 17194961-A-G BY156856 YY+
19397608-C-A 17285728-C-A BY128745 YY+
19439755-C-T 17327875-C-T BY129043 YY+
21616998-T-C 19455112-T-C BY134230 YY+
21758385-G-A 19596499-G-A BY135233 YY+
22117083-A-G 19955197-A-G BY137755 YY+
22513724-C-T 20351838-C-T BY138570 Y+
22709944-G-T 20548058-G-T BY140209 YY+
22818761-T-TA 20656875-T-TA 8×A+
23823703-T-C 21661817-T-C BY148069 Y+
9654337-A-AGAT 9816728-A-AGAT IR3_Prx **
15712407-C-A 13600527-C-A FT204679 **
20378350-T-TA 18216464-T-TA P5_Dst 9×A**
28587192-C-A 26441045-C-A **
13477359-G-A 11321683-G-A ***
13459082-T-A,G 11303406-T-A,G ***
13839820-G-A 11719114-G-A ***
13680926-G-A 11525250-G-A ***
13856705-G-A 11735999-G-A ***
25461475-A-T 23315328-A-T P2_r2 ***
13140267-A-C 10629753-A-C ***
13140281-C-A 10629767-C-A ***
13855621-C-A 11734915-C-A ***
13458998-G-T 11303322-G-T ***
58819382-C-G 56771489-G-C ***
17196755-GAA-G 15084875-GAA-G ***
9030377-G-A 9192768-G-A ***
9030407-A-G 9192798-A-G ***
9993207-G-A 10155598-G-A BY82620 ***
13140256-C-T 10629742-C-T ***
13140258-T-A 10629744-T-A ***
13143784-G-C,T 10633270-G-C,T ***
13451913-C-A 11296237-C-A ***
13452815-A-C,T 11297139-A-C,T ***
13452845-CCTCCTTTT-C,T 11297169-CCTCCTTTT-C,T ***
13453294-C-A 11297618-C-A ***
13454333-G-T 11298657-G-T ***
13455090-C-T 11299414-C-T FTA2495 ***
13455112-T-A 11299436-T-A ***
13455655-A-T 11299979-A-T ***
13457427-C-CATTCCATCTG 11301751-C-CATTCCATCTG ***
13457432-C-G 11301756-C-G ***
13457442-C-T 11301766-C-T ***
13457516-C-T 11301840-C-T ***
13457522-C-G 11301846-C-G ***
13458033-TTCCACTGTGG-T 11302357-TTCCACTGTGG-T ***
13458045-T-C 11302369-T-C ***
13459105-CCAGTCGGGTT-C,GCAGTCGGGTT 11303429-CCAGTCGGGTT-C,GCAGTCGGGTT ***
13459623-T-A 11303947-T-A ***
13648938-G-T 11493262-G-T ***
13680855-G-T 11525179-G-T ***
13680859-T-A 11525183-T-A ***
13680903-A-T 11525227-A-T ***
13805397-G-A 11684691-G-A ***
13808670-G-C 11687964-G-C ***
13813535-C-G 11692829-C-G ***
13830320-GA-G 11709614-GA-G ***
13830324-G-T 11709618-G-T ***
13830326-C-G 11709620-C-G ***
13838382-G-C 11717676-G-C ***
13839760-G-C 11719054-G-C ***
13852012-G-GATTGC 11731306-G-GATTGC ***
13859334-C-G 11738628-C-G ***
13866033-C-A 11745327-C-A ***
15799232-T-C 13687352-T-C ***
16108610-A-C 13996730-A-C P8_Prx ***
16108784-C-T 13996904-C-T BY53459 P8_Prx ***
16108785-T-C 13996905-T-C P8_Prx ***
18297544-C-T 16185664-C-T BY121423 P6_Prx ***
19411918-G-T 17300038-G-T ***
19932954-C-T 17821074-C-T P5_Prx ***
19997933-A-G 17886053-A-G P5_Prx ***
22221850-C-A 20059964-C-A DYZ19 ***
22227035-C-G 20065149-C-G DYZ19 ***
22260518-C-G 20098632-C-G DYZ19 ***
22264591-T-A 20102705-T-A DYZ19 ***
22317034-G-C 20155148-G-C DYZ19 ***
22318165-C-T 20156279-C-T DYZ19 ***
22425515-C-G 20263629-C-G DYZ19 ***
22428918-G-T 20267032-G-T DYZ19 ***
23272371-T-A 21110485-T-A ***
23272399-A-G 21110513-A-G ***
24035186-C-G 21889039-C-G ***
24129239-T-C 21983092-T-C P3_b1 ***
24244124-G-A 22097977-G-A P3_b1 ***
24954484-C-T 22808337-C-T g1 ***
25786188-G-A 23640041-G-A P1_b3 ***
25879896-A-G 23733749-A-G P1_Y1 ***
25934941-TA-T 23788794-TA-T P1_Y1 10×A***
25969047-C-T 23822900-C-T P1_Y1 ***
26047590-G-T 23901443-G-T P1_Y1 ***
26265938-A-AC 24119791-A-AC P1_Y1 8×C***
26418762-C-T 24272615-C-T PR7519 P1_Y1 ***
28390820-GA-G 26244673-GA-G P1_gr2 10×A***
58855360-C-T 56735511-G-A ***
58908884-C-G 56681987-G-C ***
58908899-C-G 56681972-G-C ***
58908904-G-A 56681967-C-T ***
13857981-GAATTGAATGGAATGA-G 11737275-GAATTGAATGGAATGA-G ***
13140280-T-A,C 10629766-T-A,C ***
13856407-A-C,G 11735701-A-C,G ***
13865757-AC-A,AA 11745051-AC-A,AA ***

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.