Tree Position

R-P312/S116 > L238/S182 > Z2245 > Z2247 > CTS11638

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
2810149-G-A 2942108-G-A BY42603 YY+
13840089-C-T 11719383-C-T PF626 +
22858992-C-T 20697106-C-T FGC53741Z26866 YY+
2892303-A-G 3024262-A-G BY57161 YY+
6938566-A-G 7070525-A-G BY62386 YY+
7511180-G-A 7643139-G-A BY65511 Y+
7662633-C-T 7794592-C-T V1349 YY+
8040257-C-T 8172216-C-T BY69550 YY+
8267642-G-A 8399601-G-A BY71297 YY+
8478504-G-A 8610463-G-A BY73184 YY+
8573749-G-A 8705708-G-A V2291 YY+
9023032-T-A 9185423-T-A BY77443 Y+
9883895-T-G 10046286-T-G BY81767 YY+
14630239-A-C 12518308-A-C BY54656 YY+
14894849-T-C 12782915-T-C BY98317 YY+
15327564-T-C 13215682-T-C BY100853 YY+
15975917-C-T 13864037-C-T BY105244 YY+
16235952-G-A 14124072-G-A BY106218 YY+
17131901-G-T 15020021-G-T BY112519 YY+
17143188-C-A 15031308-C-A BY112624 YY+
17144323-C-T 15032443-C-T BY54904 YY+
17441783-G-A 15329903-G-A BY52070 YY12×TATC+
17563779-T-C 15451899-T-C BY115748 YY+
17594743-C-T 15482863-C-T BY115999 YY+
17602602-C-T 15490722-C-T BY116078 YY+
17637170-G-C 15525290-G-C BY116293 YY+
17675827-T-C 15563947-T-C BY116569 YY+
18559879-T-C 16447999-T-C BY122189 YY+
18936931-AT-A 16825051-AT-A +
19179544-T-C 17067664-T-C BY126981 Y+
19497728-C-T 17385848-C-T BY129570 YY+
21118088-A-G 18956202-A-G BY130525 YY+
21784224-G-C 19622338-G-C BY135450 YY+
22681646-C-A 20519760-C-A BY140017 YY+
23962947-A-G 21816800-A-G BY148784 Y+
28784314-T-C 26638167-T-C BY151215 +
16470941-C-A 14359061-C-A **
14724656-C-A 12612724-C-A ***
6243232-C-A 6375191-C-A IR3_Dst ***
6321551-C-T 6453510-C-T IR3_Dst ***
6361488-C-T 6493447-C-T ***
13294404-T-G 11138728-T-G ***
13693287-A-G 11537611-A-G BY88765 ***
13700315-C-T 11544639-C-T ***
13826015-T-A 11705309-T-A ***
19669951-C-T 17558071-C-T P5_Prx ***
22224931-A-C 20063045-A-C DYZ19 ***
22237548-A-G 20075662-A-G DYZ19 ***
22283561-T-A 20121675-T-A DYZ19 ***
22289202-T-G 20127316-T-G BY201310 DYZ19 ***
22359045-C-A 20197159-C-A DYZ19 ***
22364957-C-T 20203071-C-T DYZ19 ***
22453221-C-T 20291335-C-T DYZ19 ***
22474599-T-G 20312713-T-G BY223172 DYZ19 ***
22506794-A-G 20344908-A-G BY198114 DYZ19 ***
24101564-C-T 21955417-C-T P3_b1 ***
24170627-C-G 22024480-C-G P3_b1 ***
24823436-T-G 22677289-T-G P3_b2 ***
24860212-A-G 22714065-A-G IR1_R ***
24955064-A-G 22808917-A-G g1 ***
24983825-C-A 22837678-C-A g1 ***
25121595-G-C 22975448-G-C g1 ***
25143418-C-G 22997271-C-G g1 ***
25192272-C-T 23046125-C-T g1 ***
25244052-G-A 23097905-G-A P2_r1 ***
25959830-A-T 23813683-A-T P1_Y1 ***
26106456-A-C 23960309-A-C P1_Y1 ***
26159068-T-C 24012921-T-C P1_Y1 ***
28806066-G-C 26659919-G-C ***

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.