Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > PF6551 > BY21057

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
333856
4769904-G-T 4901863-G-T BY58300 +
7997425-A-C 8129384-A-C F16533 YY+
8015298-C-A 8147257-C-A Y46725 YY+
8094248-A-C 8226207-A-C BY69885 YY+
8225615-G-C 8357574-G-C Y46976 YY+
8688709-G-T 8820668-G-T Y47747 YY+
14927571-G-A 12815636-G-A Y50065 YY+
16451422-G-A 14339542-G-A Y51875 YY+
16983085-A-T 14871205-A-T Y52625 YY+
17709466-A-G 15597586-A-G BZ1508 YY+
18049236-C-A 15937356-C-A Y54130 YY+
18573135-A-G 16461255-A-G BY58900Y54620 YY+
18914449-G-A 16802569-G-A Y55047 YY+
19060444-C-T 16948564-C-T Y55294 YY+
19230049-C-T 17118169-C-T BY55172 YY+
19365541-A-G 17253661-A-G Y55782 YY+
20835060-A-G 18673174-A-G Y56145 P4_Gap +
21514328-A-C 19352442-A-C Y56823 YY+
21516469-G-A 19354583-G-A Y56826 YY+
22464229-A-C 20302343-A-C BY52893 DYZ19 +
22864744-A-CTTGTT 20702858-A-CTTGTT PF6551 +
23347822-C-G 21185936-C-G Y59068 YY+
23576637-A-C 21414751-A-C Y59369 YY+
25648014-A-C 23501867-A-C P1_b3 +
21092276-T-C 18930390-T-C PF1015 **
9654389-AGAAG-A 9816780-AGAAG-A IR3_Prx ***
19271400-A-G 17159520-A-G CTS10118 ***
25967955-C-T 23821808-C-T P1_Y1 ***
22594751-C-T 20432865-C-T Z11188 ***
6286078-T-C 6418037-T-C IR3_Dst ***
7492278-A-C 7624237-A-C IR1_L ***
13697672-C-G 11541996-C-G ***
13818724-AG-A 11698018-AG-A ***
13818728-G-GT 11698022-G-GT ***
19998521-T-A 17886641-T-A P5_Prx ***
22221993-G-T 20060107-G-T DYZ19 ***
22225365-GA-G 20063479-GA-G DYZ19 ***
22254736-A-G 20092850-A-G DYZ19 ***
22257040-G-A 20095154-G-A DYZ19 ***
22276864-A-T 20114978-A-T DYZ19 ***
22287793-C-T 20125907-C-T DYZ19 ***
22290807-A-T 20128921-A-T DYZ19 ***
22359030-G-A 20197144-G-A DYZ19 ***
22422728-G-C 20260842-G-C DYZ19 ***
22427657-A-T 20265771-A-T DYZ19 ***
22442611-C-A 20280725-C-A DYZ19 ***
22594743-T-C 20432857-T-C FT89694 ***
24104985-C-T 21958838-C-T P3_b1 ***
25097858-C-T 22951711-C-T g1 ***
25170903-C-T 23024756-C-T g1 ***
25233519-A-G 23087372-A-G P2_r1 ***
25246812-G-A 23100665-G-A P2_r1 ***
26033646-C-T 23887499-C-T P1_Y1 ***
26244003-G-A 24097856-G-A P1_Y1 ***
26292448-G-A 24146301-G-A P1_Y1 ***
26375776-A-G 24229629-A-G P1_Y1 ***
16108702-C-CTTTCTTTTCT 13996822-C-CTTTCTTTTCT P8_Prx 10×TTTCT***
16606458-C-CTG 14494578-C-CTG 8×TG***
19412006-GAGAAAGAAAGAA-G 17300126-GAGAAAGAAAGAA-G 14×AGAA***
22594751-C-CAT 20432865-C-CAT ***

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.