Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > FGC5494 > FGC5561 > FGC7448

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
2765701-G-A 2897660-G-A A12657 YY+
19536679-G-A 17424799-G-A A12686 YY+
16565842-T-C 14453962-T-C A12676 YY+
16634404-G-A 14522524-G-A A12677 YY+
16730892-G-T 14619012-G-T A12678 YY+
16816833-G-A 14704953-G-A A12679 YY+
17769821-A-C 15657941-A-C A12680 YY+
18145388-C-T 16033508-C-T A12681 YY+
19483135-T-A 17371255-T-A A12685 Y+
22029266-T-C 19867380-T-C A12687 YY+
14878094-G-A 12766164-G-A A12674 YY+
22190861-A-T 20028975-A-T A12688 YY+
22463057-C-G 20301171-C-G DYZ19 +
22912099-T-C 20750213-T-C A12689 YY+
23232938-G-T 21071052-G-T A12690 Y+
23584749-A-G 21422863-A-G A12691 YY+
23964626-C-T 21818479-C-T A12692 Y+
19406361-TA-T 17294481-TA-T +
15877821-C-T 13765941-C-T A12675 YY+
18887669-T-C 16775789-T-C A12682 YY+
14777727-G-A 12665796-G-A A12673 YY+
9042969-C-G 9205360-C-G A12668 Y+
8367134-T-C 8499093-T-C A12663 YY+
7506992-T-C 7638951-T-C IR1_L +
8440300-C-T 8572259-C-T A12664 YY+
7291239-T-C 7423198-T-C A12661 YY+
14370573-A-G 12249869-A-G A12672 YY+
8453647-C-T 8585606-C-T A12665 YY+
9028407-T-C 9190798-T-C A12667 Y+
8652101-C-T 8784060-C-T A12666 YY+
9935140-C-T 10097531-C-T A12669 Y+
10025746-G-A 10188137-G-A A12670 Y+
6794751-T-C 6926710-T-C A12659 YY+
6760540-G-T 6892499-G-T A12658 YY+
14274344-T-C 12153638-T-C A10633 YY+
14350693-G-A 12229988-G-A A12671 YY+
7830470-A-G 7962429-A-G A12662 YY+
28182630-C-G 26036483-C-G P1_b4 **
23306170-T-C 21144284-T-C **
10016459-T-A 10178850-T-A **
28805812-C-T 26659665-C-T ***
26217744-G-C 24071597-G-C P1_Y1 ***
25929437-A-T 23783290-A-T P1_Y1 ***
25348178-C-T 23202031-C-T P2_r1 ***
25156632-C-T 23010485-C-T g1 ***
24273599-G-C 22127452-G-C P3_b1 ***
22429085-G-A 20267199-G-A DYZ19 ***
22510731-G-T 20348845-G-T DYZ19 ***
22450537-G-A 20288651-G-A DYZ19 ***
22450402-T-C 20288516-T-C DYZ19 ***
22302469-C-A 20140583-C-A DYZ19 ***
22286062-G-T 20124176-G-T DYZ19 ***
22282610-A-C 20120724-A-C DYZ19 ***
22243155-T-A 20081269-T-A DYZ19 ***
19650775-C-T 17538895-C-T P5_Prx ***
6275864-C-T 6407823-C-T IR3_Dst ***
13449630-AA-G 11293954-AA-G ***
14709302-TG-T,TT 12597369-TG-T,TT ***

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.

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