Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z41150 > Z49 > Z142/S211 > FT32075

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
B469453
6339608-A-C 6471567-A-C IR3_Dst A*
13449622-T-TTTCCA 11293946-T-TTTCCA A*
24258457-G-A 22112310-G-A P3_b1 A*
24295429-C-G 22149282-C-G P3_t1 A*
6174109-G-A 6306068-G-A IR3_Dst A*
26147343-G-A 24001196-G-A P1_Y1 A*
26364568-A-G 24218421-A-G P1_Y1 A*
19680570-G-A 17568690-G-A P5_Prx A*
19860190-T-C 17748310-T-C P5_Prx A*
18313658-C-T 16201778-C-T P6_Prx A*
19955632-A-G 17843752-A-G P5_Prx A*
18321971-C-CTA 16210091-C-CTA P6_Prx A*
56833856-A-ACTCTT A*
13512129-G-A 11356453-G-A +
13648850-G-A 11493174-G-A +
13694472-G-A 11538796-G-A +
19317325-T-C 17205445-T-C FT193899 YY+
13826182-G-C 11705476-G-C FT192781 +
14173376-C-A 12052670-C-A FT192907 YY+
19292222-C-T 17180342-C-T BY128021 YY+
13222438-G-T 11066762-G-T +
10935250-C-G +
10933615-C-G +
10929616-C-G +
10883011-T-C +
14102326-AATCT-A 11981620-AATCT-A +
15350898-C-T 13239017-C-T FT193121 YY+
18950026-T-A 16838146-T-A FT193813 YY+
18719115-C-T 16607235-C-T FT193770 YY+
18665982-A-G 16554102-A-G FT193754 YY+
17604525-A-C 15492645-A-C FT193547 YY+
17596558-G-T 15484678-G-T FT193545 YY+
17421800-C-T 15309920-C-T FT193503 YY+
17249856-C-T 15137976-C-T FT193473 Y+
17191799-C-G 15079919-C-G FT193465 YY+
17067802-AC-A 14955922-AC-A +
18813746-G-T 16701866-G-T FT193788 YY+
14320463-G-A 12199757-G-A FT192947 YY+
16621991-C-T 14510111-C-T FT193350 Y+
16233843-T-A 14121963-T-A FT193276 YY+
18840905-A-G 16729025-A-G FT193791 YY+
15720063-T-C 13608183-T-C FT193193 YY+
15701676-G-T 13589796-G-T FT193187 YY+
15466333-G-A 13354453-G-A FT193143 YY+
14703185-T-A 12591251-T-A FT193014 YY+
14611045-C-A 12499251-C-A YY+
10832038-C-T +
8045756-C-T 8177715-C-T FT192488 YY+
9519444-T-C 9681835-T-C FT192731 +
28577582-C-T 26431435-C-T FT112374 +
23037286-G-T 20875400-G-T FT194341 YY+
23354909-A-AC 21193023-A-AC +
23556719-C-A 21394833-C-A FT194440 YY+
9842377-A-G 10004768-A-G FT192755 YY+
13196431-A-T 11040755-A-T +
24361070-A-T 22214923-A-T FT194517 +
28584349-A-T 26438202-A-T FT194575 +
8663075-C-T 8795034-C-T FT192622 YY+
28676382-A-G 26530235-A-G FT194597 +
28705245-G-A 26559098-G-A FT194608 +
13938577-G-A 11817871-G-A FT192832 Y+
9964622-T-C 10127013-T-C Y+
8202918-C-G 8334877-C-G ZS654 YY+
28713177-C-T 26567030-C-T FT194612 +
28801077-AGGAGT-A 26654930-AGGAGT-A 4×GGAGT+
22618814-C-T 20456928-C-T FT194270 YY+
22468022-G-A 20306136-G-A DYZ19 +
3163386-T-C 3295345-T-C FT191322 +
5620998-C-G 5752957-C-G FT191976 +
8512539-C-G 8644498-C-G FT192586 YY+
7857918-A-T 7989877-A-T FT192450 YY+
7845794-A-G 7977753-A-G FT192443 YY+
7162059-G-T 7294018-G-T FT192300 YY+
21485229-T-C 19323343-T-C FT194061 YY+
21824530-G-A 19662644-G-A FT194153 Y+
22163136-T-G 20001250-T-G FT194219 YY+
5619803-C-G 5751762-C-G FT191975 +
22466332-G-T 20304446-G-T DYZ19 +
4980912-C-T 5112871-C-T FT191818 +
3953847-G-A 4085806-G-A FT191535 +
3922963-C-T 4054922-C-T FT191525 +
3723500-A-G 3855459-A-G FT191465 +
22444827-G-A 20282941-G-A DYZ19 +
18059422-T-C 15947542-T-C FT193643 Y+
22278772-C-T 20116886-C-T DYZ19 *
23181726-T-C 21019840-T-C Y*
56858546-TTA-T,TTT *
3406701-C-T 3538660-C-T *
3662996-C-T 3794955-C-T Z12639 *
56830293-CA-C *
3427484-C-T 3559443-C-T *
6388622-A-C 6520581-A-C FT259406 *
3662995-G-A 3794954-G-A FT11661 *
22438897-G-T 20277011-G-T BY51709 DYZ19 **
16818681-T-A 14706801-T-A ZS2445 **
13475526-A-T 11319850-A-T **
13493885-A-T 11338209-A-T **
20648565-AGAAAAG-A 18486679-AGAAAAG-A P4_Prx **
25030238-T-C 22884091-T-C g1 **
13475500-G-GC 11319824-G-GC **
19719342-A-G 17607462-A-G P5_Prx **
10632864-A-T **
17859461-T-C 15747581-T-C **
17981253-TTTG-T 15869373-TTTG-T **
5465984-A-T 5597943-A-T 8×T**
5704984-G-A 5836943-G-A **
17006448-G-A 14894568-G-A **
14291093-C-A 12170387-C-A **
13475491-T-C 11319815-T-C **
56839093-C-T ***
15940294-A-G 13828414-A-G ***
3663058-C-T 3795017-C-T FT58 ***
3689841-A-G 3821800-A-G PF1466 ***
21934791-TA-T 19772905-TA-T ***
16648115-GT-G,GTT 14536235-GT-G,GTT 29×T***
16818682-AT-A 14706802-AT-A ***
9401937-C-CA 9564328-C-CA 9×A***
7160894-CTTT-C,CTTTT 7292853-CTTT-C,CTTTT 16×T***
9899389-G-C 10061780-G-C ***
18969242-T-C 16857362-T-C ***
3532154-T-C 3664113-T-C ***
13442359-T-C 11286683-T-C ***
13357436-G-T 11201760-G-T ***
13455722-T-A 11300046-T-A ***
6074688-A-ATGTG 6206647-A-ATGTG 22×TG***
13705785-G-A 11550109-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.

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: B4694531497238893815348312257
Used in age calculations1497238893815348312257
Counts of SNPs4033
Variant counts last updated 2020-03-20 02:34:41.



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