Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z367/S255 > Z34/S368 > Z33/S212 > ZZ71 > Z29519 > Exact position not yet finalized.

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 STR1kG
7092235-TCATC-T 7224194-TCATC-T 8×CATC+
14724279-A-C 12612347-A-C YY+
22260723-G-T 20098837-G-T DYZ19 +
22802868-A-ATTTT 20640982-A-ATTTT 32×T+
15909050-CCATT-C 13797170-CCATT-C 9×CATT+
21620553-T-C 19458667-T-C BY41434 YY+
14007942-C-A 11887236-C-A YY15×A+
8360291-C-A 8492250-C-A FT334412 YY+
8593359-G-A 8725318-G-A Y87400 YY+
9019954-A-G 9182345-A-G FT334860 Y+
9140994-A-G 9303385-A-G FT334935 Y+
14683802-C-T 12571868-C-T Y+
15591261-G-A 13479381-G-A FT336248 YY+
16720801-C-A 14608921-C-A FT336994 Y+
19380980-C-A 17269100-C-A FT338698 YY+
21506605-G-A 19344719-G-A BY168335 YY+
21770980-A-G 19609094-A-G Y+
21923226-T-G 19761340-T-G FT339500 YY+
22149131-A-T 19987245-A-T FT339643 YY+
22939834-C-G 20777948-C-G FT339983 YY+
22987580-G-A 20825694-G-A Y+
23137429-G-A 20975543-G-A FT340145 YY+
24862285-C-A 22716138-C-A IR1_R +
25876151-T-G 23730004-T-G P1_Y1 +
20209001-T-C 18047115-T-C A13707 P5_Dst +
5886194-TC-T 6018153-TC-T +
15309739-C-CAAAA 13197843-C-CAAA 41×A+
2675423-A-G 2807382-A-G FT333369 Y+
2736221-C-T 2868180-C-T FT315367 YY+
3010751-T-G 3142710-T-G +
3259124-G-A 3391083-G-A +
3403597-C-G 3535556-C-G +
3403623-G-C 3535582-G-C +
3403650-A-C 3535609-A-C FT250625 +
3403666-A-C 3535625-A-C +
4395752-A-G 4527711-A-G +
4465789-G-A 4597748-G-A +
4554780-A-G 4686739-A-G +
5278431-G-A 5410390-G-A +
5377803-G-A 5509762-G-A +
5381038-G-A 5512997-G-A +
5425698-T-A 5557657-T-A +
5513091-A-T 5645050-A-T +
5818139-T-TAGAC 5950098-T-TAGAC +
5831797-G-T 5963756-G-T +
6010040-T-C 6141999-T-C +
6177527-G-GTT 6309486-G-GTT IR3_Dst +
6347805-A-AG 6479764-A-AG +
6419045-CAT-C 6551004-CAT-C +
6566077-C-T 6698036-C-T +
8977029-C-A 9139420-C-A Y16×A+
9522029-T-C 9684420-T-C FT426477 +
13308578-G-A 11152902-G-A +
13415704-C-G 11260028-C-G +
13442124-G-A 11286448-G-A +
13499938-C-T 11344262-C-T +
13507335-G-T 11351659-G-T +
13529783-TAAAAAA-T 11374107-TAAAAAA-T 16×A+
13798921-T-C 11678215-T-C +
13817802-G-A 11697096-G-A +
14026940-TTTGA-T 11906234-TTTGA-T +
14724273-A-G 12612341-A-G YY+
14926462-C-CAAA 12814527-C-CAAA 26×A+
14940072-T-A 12828146-T-A YY+
14986751-CACA-C 12874817-CACA-C +
15604354-C-CAA 13492474-C-CAA 20×A+
15888872-A-C 13776992-A-C Y69064 Y+
15891845-T-C 13779965-T-C FT336452 Y+
17648007-AC-A 15536127-AC-A +
18409713-G-T 16297833-G-T FT338060 P6_Gap +
18465469-G-GAA 16353589-G-GAA P6_Dst 26×A+
19126433-C-CCAAAA 17014553-C-CCAAAA +
19205430-C-A 17093550-C-A M9281 YY+
22246381-T-G 20084495-T-G FGC24651 DYZ19 +
22293176-T-C 20131290-T-C DYZ19 +
22293180-G-A 20131294-G-A DYZ19 +
22294894-C-T 20133008-C-T DYZ19 +
22353123-T-G 20191237-T-G DYZ19 +
22466716-C-T 20304830-C-T BY30012 DYZ19 +
22486316-G-A 20324430-G-A DYZ19 +
23034308-TG-T 20872422-TG-T +
23209789-T-C 21047903-T-C Y+
23572570-A-C 21410684-A-C ZS7894 YY+
23881874-T-A 21719988-T-A Y+
24328649-T-G 22182502-T-G BY22869 P3_t1 +
28763385-A-T 26617238-A-T FT354001 +
58971884-GTACATATA-G 56825737-GTACATATA-G +
59030572-TTA-T 56884425-TTA-T 8×TA+
59030915-T-A 56884768-T-A +
24842116-A-C 22695969-A-C ZZ71_2 IR1_R *
28316534-A-C 26170387-A-C ZZ71_4 P1_b4 *

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.

Mutation Notes:

Manual21527519-T-TA19365633-T-TA4 reads, all match the hg19 reference sequence.
Manual25646368-T-G23500221-T-G3T 1G
Manual24842116-A-C22695969-A-C2A 3C
Manual28316534-A-C26170387-A-C3A 2C