Tree Position

R-P312/S116 > Y18209

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
21441595-C-A 19279709-C-A Y17622Y17622 YY+
22294237-G-T 20132351-G-T Z14528 DYZ19 +
22715636-G-A 20553750-G-A Y48 YY+
6145980-G-A 6277939-G-A BY59295 IR3_Dst +
7091836-T-C 7223795-T-C BY63293 YY+
7401855-A-C 7533814-A-C Y45997 YY+
7612957-C-A 7744916-C-A Y46179 YY+
7781903-A-G 7913862-A-G Y46400 YY+
7901871-C-T 8033830-C-T Y46587 YY+
8466885-G-C 8598844-G-C Y47359 YY+
8553597-C-A 8685556-C-A Y47535 YY+
8792598-T-G 8924557-T-G Y47899 YY+
8808795-C-A 8940754-C-A Y47928 YY+
9153309-G-A 9315700-G-A Y48263 Y+
9760636-A-G 9923027-A-G Y48461 Y+
9899178-C-A 10061569-C-A Y48630 Y+
13684435-A-G 11528759-A-G BY88357 +
14017980-T-C 11897274-T-C Y48872 YY+
14276620-G-T 12155914-G-T Y49276 YY+
14398540-T-C 12277836-T-C FGC21633 YY+
14495471-T-C 12383668-T-C Y49606 YY+
14497711-C-T 12385916-C-T Y49611 YY+
15338189-T-C 13226307-T-C Y50534 YY+
16444076-T-C 14332196-T-C Y51862 YY+
16587678-C-T 14475798-C-T Y52084 YY+
16612293-G-A 14500413-G-A Y52122 YY+
16612823-G-T 14500943-G-T Y52123 YY+
16780081-G-C 14668201-G-C Y52315 YY+
18061329-G-T 15949449-G-T Y54144 YY+
18636332-GC-G 16524452-GC-G +
18899378-T-C 16787498-T-C Y55032 YY+
19495035-C-T 17383155-C-T Y55988 YY+
21188937-G-T 19027051-G-T Y56306 YY+
21401855-A-G 19239969-A-G Y56636 YY+
21590831-G-A 19428945-G-A FGC61743 YY+
21594104-T-G 19432218-T-G Y56947 YY+
22148728-A-G 19986842-A-G Y57693 YY+
22476053-G-T 20314167-G-T BY223506 DYZ19 +
22478631-C-G 20316745-C-G BY224064 DYZ19 +
22676579-T-C 20514693-T-C Y58128 YY+
23556317-A-G 21394431-A-G Y59342 YY+
28569918-C-T 26423771-C-T CTS12299 **
9774812-C-T 9937203-C-T Y48476 **
22522314-C-T 20360428-C-T Y57879 **
9485887-T-TCA 9648278-T-TCA 12×CA***
22501988-G-C 20340102-G-C DYZ19 ***
18365583-A-G 16253703-A-G BY121466 P6_Prx ***
6222955-T-C 6354914-T-C IR3_Dst ***
6264487-T-C 6396446-T-C IR3_Dst ***
13455993-C-A 11300317-C-A BY46498 ***
19791579-C-G 17679699-C-G BY196754 P5_Prx ***
22224907-C-G 20063021-C-G DYZ19 ***
22251927-C-G 20090041-C-G DYZ19 ***
22277557-C-G 20115671-C-G DYZ19 ***
22300190-C-G 20138304-C-G DYZ19 ***
22309748-C-A 20147862-C-A DYZ19 ***
22316827-C-T 20154941-C-T DYZ19 ***
22430828-G-T 20268942-G-T DYZ19 ***
22430836-CAG-C 20268950-CAG-C DYZ19 ***
22447872-C-A 20285986-C-A DYZ19 ***
22456078-C-G 20294192-C-G DYZ19 ***
23713727-G-A 21551841-G-A ***
24125035-G-A 21978888-G-A P3_b1 ***
24186572-G-A 22040425-G-A P3_b1 ***
24216697-T-C 22070550-T-C P3_b1 ***
24804452-A-T 22658305-A-T P3_b2 ***
25025887-G-A 22879740-G-A g1 ***
25169693-T-C 23023546-T-C g1 ***
25243776-C-A 23097629-C-A P2_r1 ***
25943588-G-A 23797441-G-A P1_Y1 ***
26227467-G-A 24081320-G-A P1_Y1 ***
26227468-G-T 24081321-G-T P1_Y1 ***

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.