Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z272 > S450 > Z295/S1217 > ZZ77 > Z216

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
19500555-G-A 17388675-G-A BY129599 YY+
6347522-G-A 6479481-G-A BY59676 +
6696639-C-T 6828598-C-T BY60769 YY+
6733661-C-T 6865620-C-T BY60941 YY+
7317721-A-G 7449680-A-G BY64530 YY+
7473018-T-A 7604977-T-A BY65462 IR1_L +
7927981-C-G 8059940-C-G BY68822 YY+
7957794-C-G 8089753-C-G BY69057 YY+
8334416-G-A 8466375-G-A BY71765 YY+
9133693-G-A 9296084-G-A BY78397 Y+
13662735-T-C 11507059-T-C BY87479 +
13827543-G-A 11706837-G-A BY54506 +
14312819-G-T 12192113-G-T BY54616 YY+
14874879-C-T 12762949-C-T BY98158 YY+
15145969-AC-A 13034056-AC-A +
15382346-C-T 13270466-C-T BY101210 YY+
16737660-A-G 14625780-A-G BY109695 YY+
16927618-T-C 14815738-T-C BY111178 YY+
17012544-A-T 14900664-A-T BY111729 YY+
17119340-T-A 15007460-T-A BY112445 YY+
17192281-G-T 15080401-G-T BY112930 YY+
17338699-T-A 15226819-T-A BY113955 YY+
18067624-G-C 15955744-G-C BY119633 YY+
19519225-A-T 17407345-A-T BY129750 YY+
21222074-G-A 19060188-G-A BY131216 YY+
21444682-T-C 19282796-T-C YY+
21473693-C-A 19311807-C-A BY133186 YY+
21656363-A-G 19494477-A-G BY134527 YY+
21783285-G-A 19621399-G-A BY135436 YY+
22034091-C-A 19872205-C-A BY137224 YY+
22201449-C-T 20039563-C-T BY138411 YY+
22213828-G-A 20051942-G-A BY138516 Y+
22467372-C-T 20305486-C-T BY221908 DYZ19 +
22476889-T-G 20315003-T-G BY223681 DYZ19 +
22478320-G-T 20316434-G-T BY224000 DYZ19 +
23050153-G-T 20888267-G-T BY142571 YY+
23160208-C-A 20998322-C-A BY143498 Y+
23248246-G-A 21086360-G-A BY144074 YY+
23437458-A-G 21275572-A-G BY145291 YY+
24455396-C-T 22309249-C-T BY150080 Y+
28580027-T-A 26433880-T-A CTS12341 **
28580126-C-T 26433979-C-T CTS12342 **
28580131-A-C 26433984-A-C CTS12343 **
16275407-C-A 14163527-C-A **
19664367-A-G 17552487-A-G P5_Prx **
13817557-T-C 11696851-T-C ***
13138099-A-T 10627585-A-T ***
13862047-A-T 11741341-A-T ***
13858643-T-A 11737937-T-A ***
18353116-GTA-G 16241236-GTA-G P6_Prx 8×TA***
13421327-T-A 11265651-T-A ***
13421338-G-A 11265662-G-A ***
22469862-T-C 20307976-T-C DYZ19 ***
22469846-T-G 20307960-T-G BY12496 DYZ19 ***
13857619-T-A,C 11736913-T-A,C ***
10013444-G-A 10175835-G-A ***
58985398-C-A 56839251-C-A ***
13868093-A-T 11747387-A-T ***
7448282-C-T 7580241-C-T IR1_L ***
9934772-G-T 10097163-G-T ***
13858589-GCAAGT-G,GGAATT 11737883-GCAAGT-G,GGAATT ***
20789136-G-A 18627250-G-A P4_Prx ***
21397822-TA-T 19235936-TA-T 9×A***
22224236-G-A 20062350-G-A DYZ19 ***
22309948-T-G 20148062-T-G DYZ19 ***
22345129-C-T 20183243-C-T DYZ19 ***
22431055-T-G 20269169-T-G DYZ19 ***
22438487-C-T 20276601-C-T DYZ19 ***
22451517-C-A 20289631-C-A DYZ19 ***
22451518-C-A 20289632-C-A DYZ19 ***
22455745-C-A 20293859-C-A DYZ19 ***
22469397-T-C 20307511-T-C BY222213 DYZ19 ***
22489615-G-A 20327729-G-A DYZ19 ***
23181733-C-T 21019847-C-T ***
23718170-G-A 21556284-G-A ***
24164460-G-A 22018313-G-A P3_b1 ***
24186759-A-C 22040612-A-C P3_b1 ***
24244979-A-G 22098832-A-G P3_b1 ***
24673173-G-GCACA 22527026-G-GCACA P3_b2 16×CA***
24915397-C-A 22769250-C-A g1 ***
25164242-T-C 23018095-T-C g1 ***
25342404-A-G 23196257-A-G P2_r1 ***
25602341-A-T 23456194-A-T P1_gr1 ***
26797985-T-C 24651838-T-C P1_g2 ***
58985390-A-T 56839243-A-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.