Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > FGC11134 > FGC12055 > A353 > Z3026

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
B108409
10093893-C-A 10256284-C-A FT427529 A+
3421372-G-C 3553331-G-C A*
13687503-A-G 11531827-A-G A*
24302585-G-C 22156438-G-C P3_t1 A*
25615721-G-A 23469574-G-A P1_gr1 A*
25874366-A-T 23728219-A-T P1_Y1 A*
26086690-G-T 23940543-G-T P1_Y1 A*
3240946-A-G 3372905-A-G +
27917519-G-GA 25771372-G-GA P1_Y2 9×A+
8465749-C-T 8597708-C-T M12406 YY+
6706197-C-T 6838156-C-T BY157343 YY+
3055898-C-G 3187857-C-G FT33018 +
3131967-T-C 3263926-T-C FT33035 +
3245766-C-A 3377725-C-A FT33061 +
3268452-C-T 3400411-C-T FT33066 +
3443774-T-G 3575733-T-G +
3511260-C-T 3643219-C-T FT33119 +
3901078-G-A 4033037-G-A FT33195 +
4937117-C-T 5069076-C-T FT33408 +
5369706-T-C 5501665-T-C FT33501 +
5696136-G-A 5828095-G-A FT33567 +
6535902-T-C 6667861-T-C FT33713 +
6692109-T-G 6824068-T-G FT33728 Y+
6719152-A-C 6851111-A-C BY186285 YY+
6719849-T-G 6851808-T-G BY60917 YY+
6968356-ACT-A 7100315-ACT-A +
7043949-T-C 7175908-T-C FT33772 Y+
7306889-A-G 7438848-A-G BY186383 YY+
7647153-G-C 7779112-G-C BY186453 YY+
7657126-C-T 7789085-C-T BY186456 YY+
7916380-T-G 8048339-T-G FT33902 YY+
7916381-C-A 8048340-C-A FT33903 YY+
7916382-C-CAGAAGATT 8048341-C-CAGAAGATT +
7916385-T-G 8048344-T-G FT33904 YY+
7916386-A-T 8048345-A-T FT33905 YY+
8037530-A-T 8169489-A-T BY186557 YY+
8164783-G-C 8296742-G-C BY70434 YY+
9767072-C-A 9929463-C-A FT34204 Y+
10764969-C-G FT56531 +
13665922-C-A 11510246-C-A BY156205 +
13934461-A-C 11813755-A-C FT34268 Y+
17587280-C-G 15475400-C-G BY187672 YY+
17866864-C-G 15754984-C-G BY187731 YY+
17972875-G-A 15860995-G-A FT34882 YY+
18944177-T-C 16832297-T-C BY124984 YY+
19049388-A-G 16937508-A-G BY125797 YY+
19133701-T-A 17021821-T-A BY126596 YY+
21322920-T-G 19161034-T-G FT35149 Y+
21382155-T-G 19220269-T-G FT35156 Y+
21685486-T-C 19523600-T-C FT35207 YY+
22813839-T-G 20651953-T-G BY140953 YY+
23066890-C-G 20905004-C-G FT35377 YY+
23117823-T-G 20955937-T-G FT74191 YY+
23483997-C-A 21322111-C-A BY145639 YY+
23548126-CCCAGAT-C 21386240-CCCAGAT-C +
23650469-G-A 21488583-G-A BY147062 Y+
18639018-AGTGTGT-A 16527138-AGTGTGT-A 26×GT*
22302083-G-T 20140197-G-T DYZ19 *
24425369-G-GTA 22279222-G-GTA *
28076522-CCTTT-C 25930375-CCTTT-C P1_Y2 13×CTTT**
7453566-AGTGTGT-A 7585525-AGTGTGT-A IR1_L 16×GT**
28809367-C-G 26663220-C-G **
22472078-A-T 20310192-A-T BY222707 DYZ19 **
4742528-CAT-C 4874487-CAT-C **
7142478-C-T 7274437-C-T FT248332 **
9961579-A-G 10123970-A-G BY82209 **
10081372-A-G 10243763-A-G **
10901028-C-T FT56535 **
13422198-C-T 11266522-C-T FT265208 **
12375056-A-AG **
14493459-C-G 12381656-C-G FT248971 **
15796241-C-T 13684361-C-T FTA39644 **
15837562-A-G 13725682-A-G **
16816870-T-G 14704990-T-G **
21576687-T-G 19414801-T-G **
21851805-T-G 19689919-T-G FT272577 **
22477516-G-T 20315630-G-T FT459988 DYZ19 **
26243503-G-A 24097356-G-A P1_Y1 4×AGGA**
16298499-G-GATAA 14186619-G-GATAA 11×ATAA***
3403444-TAATA-T 3535403-TAATA-T 10×AATA***
22048230-CAA-C 19886344-CAA-C 15×A***
10964821-G-T ***
10989122-C-A,T ***
17662010-ATGTGTGTG-A,ATG 15550130-ATGTGTGTG-A,ATG 21×TG***
5426365-CTTTT-C 5558324-CTTTT-C 16×T***
5225292-G-GTA 5357251-G-GTA 12×TA***
13462044-C-A 11306368-C-A ***
24242331-CAA-C 22096184-CAA-C P3_b1 16×A***
8389569-CTTTTTT-C 8521528-CTTTTTT-C 25×T***
28461975-G-A 26315828-G-A ***
13466429-A-G 11310753-A-G ***
4151936-CAAA-C 4283895-CAAA-C 17×A***
2960062-CA-C,CAAA 3092021-CA-C,CAAA 17×A***
5096105-CT-C 5228064-CT-C 9×T***
13459280-C-A 11303604-C-A ***
4375417-CTTTTT-C 4507376-CTTTTT-C 22×T***
7114865-C-G 7246824-C-G ***
7504796-A-C 7636755-A-C IR1_L ***
8314146-CTTTTT-C,CTTT 8446105-CTTTTT-C,CTTT 24×T***
13349239-T-C 11193563-T-C ***
15507783-GTTTT-G 13395903-GTTTT-G 25×T***
17648536-ATT-A,AT 15536656-ATT-A,AT 22×T***
22193185-A-G 20031299-A-G ***
22856942-G-T 20695056-G-T ***
21754509-C-A ***
28596698-GTT-G,GT 26450551-GTT-G,GT 24×T***
28606881-G-T 26460734-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.