Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > DF41/S524 > BY39034

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 STRBigY3
22216217-G-A 20054331-G-A YA+
24294914-C-T 22148767-C-T P3_t1 A*
6214404-C-CA 6346363-C-CA IR3_Dst A*
6240037-C-T 6371996-C-T IR3_Dst A*
6310986-A-T 6442945-A-T IR3_Dst A*
13687749-A-G 11532073-A-G DYZ17 A*
18324141-C-A 16212261-C-A P6_Prx A*
19587005-A-G 17475125-A-G P5_Prx YA*
19673463-C-T 17561583-C-T P5_Prx A*
19796786-C-T 17684906-C-T P5_Prx A*
19857356-A-G 17745476-A-G P5_Prx A*
24268218-G-C 22122071-G-C P3_b1 A*
26029919-A-T 23883772-A-T P1_Y1 A*
26030626-A-T 23884479-A-T P1_Y1 A*
26468051-C-T 24321904-C-T P1_Y1 A*
26519143-C-T 24372996-C-T P1_Y1 A*
18419540-C-T 16307660-C-T FGC41293 P6_Gap +
17832094-C-T 15720214-C-T Z12510 Z15303 YY+
13600394-A-C 11444718-A-C BY86647BY86647 +
13828277-G-A 11707571-G-A FT212324 DYZ17 +
2909637-C-T 3041596-C-T FT211087 YY+
3985179-C-G 4117138-C-G FT211307 +
4125406-T-C 4257365-T-C FT211347 +
4652564-G-C 4784523-G-C FT211464 +
4923496-C-T 5055455-C-T FT211511 +
5138328-C-T 5270287-C-T FT211557 +
5525071-A-G 5657030-A-G FT211643 +
5574700-T-G 5706659-T-G FT211653 +
6584454-T-G 6716413-T-G FT211822 +
6887921-A-C 7019880-A-C FT211864 YY+
7597233-G-A 7729192-G-A FT211973 YY+
8241833-A-G 8373792-A-G FT212087 YY+
8361287-C-A 8493246-C-A FT212109 YY+
8485694-T-C 8617653-T-C FT212128 YY+
8528309-C-T 8660268-C-T FT212137 YY+
8592783-G-T 8724742-G-T FT212154 YY+
9465602-T-C 9627993-T-C FT212275 Y+
10064743-G-T 10227134-G-T FT354067 +
13254169-G-A 11098493-G-A FT354068 +
14232965-C-T 12112259-C-T FT116557 YY+
14352429-G-A 12231724-G-A FT212467 Y+
14658701-T-C 12546766-T-C FT212522 YY+
15290643-G-A 13178742-G-A FT212610 Y+
15307937-C-T 13196039-C-T FT212616 YY+
15783061-AG-A 13671181-AG-A +
16178901-C-T 14067021-C-T FT212752 Y+
16506779-A-T 14394899-A-T FT212806 YY+
16514492-T-A 14402612-T-A FT212808 YY+
16794271-T-C 14682391-T-C FT212876 YY+
17246367-T-A 15134487-T-A FT212960 Y+
18421129-A-C 16309249-A-C FT213154 P6_Gap +
18780110-G-A 16668230-G-A FT139952 YY+
19265782-A-T 17153902-A-T FT213291 YY+
19484472-A-T 17372592-A-T FT213330 Y+
21298113-G-A 19136227-G-A FT213386 YY+
21582584-C-A 19420698-C-A FT213447 Y+
21860219-T-C 19698333-T-C FT149925 YY+
22142330-A-G 19980444-A-G FT213548 YY+
22461776-G-T 20299890-G-T FT354069 DYZ19 +
22808045-C-G 20646159-C-G FT213602 YY+
22865682-C-T 20703796-C-T FT213607 YY+
23056428-T-C 20894542-T-C YY+
23806116-A-G 21644230-A-G FT213757 Y+
23822203-T-A 21660317-T-A FT213759 Y+
28552886-C-T 26406739-C-T FT213830 +
28757277-C-T 26611130-C-T FT285229 Y+
6972416-T-TTTG 7104375-T-TTTG 5×TTG*
18831662-C-A 16719782-C-A **
17283113-G-GTT 15171233-G-GTT 13×T**
22427828-A-G 20265942-A-G DYZ19 **
4417693-A-G 4549652-A-G FT349690 **
4505035-C-A 4636994-C-A FT349712 **
8409026-C-G 8540985-C-G **
8807415-GT-G 8939374-GT-G **
8835750-A-G 8967709-A-G **
13467912-G-C 11312236-G-C **
14142830-A-G 12022124-A-G **
19464722-T-A 17352842-T-A **
22427827-G-C 20265941-G-C DYZ19 **
22461212-G-A 20299326-G-A BY49804 DYZ19 **
22512120-C-A 20350234-C-A DYZ19 **
13947521-GAA-G 11826815-GAA-G 13×A***
13545823-TAA-T 11390147-TAA-T 12×A***
2718881-CTTTT-C,CTTT 2850840-CTTTT-C,CTTT 21×T***
28461722-CTT-C,CT 26315575-CTT-C,CT 19×T***
4196934-CAAA-C,CAA 4328893-CAAA-C,CAA 16×A***
3259217-T-C 3391176-T-C ***
3949406-CAAA-C,CAA 4081365-CAAA-C,CAA 20×A***
6447774-GTT-G,GT 6579733-GTT-G,GT 16×T***
6541140-A-G 6673099-A-G ***
8170300-C-T 8302259-C-T ***
8273841-T-C 8405800-T-C ***
8550838-A-T 8682797-A-T ***
10047867-A-G 10210258-A-G ***
14488269-C-G 12367538-C-G ***
14517393-CAAA-C 12405594-CAAA-C ***
18219035-A-G 16107155-A-G ***
18727703-C-T 16615823-C-T ***
18925560-G-A 16813680-G-A ***
19223224-C-T 17111344-C-T ***
21054379-CAAA-C,CAAAA 18892493-CAAA-C,CAAAA 18×A***
21220984-A-G 19059098-A-G ***
22128520-T-C 19966634-T-C ***
23528788-C-T 21366902-C-T ***
23537639-T-C 21375753-T-C ***
23802453-G-A 21640567-G-A ***
28747676-A-G 26601529-A-G ***

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.