Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > S14469 > FGC8158 > Y61423

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 STRBigY3
5332430-G-A 5464389-G-A A+
20330694-C-T 18168808-C-T P5_Dst A+
3195860-T-C 3327819-T-C A+
5743043-A-G 5875002-A-G A+
20660306-A-G 18498420-A-G P4_Prx A*
23181284-C-T 21019398-C-T YA*
19603530-C-A 17491650-C-A P5_Prx YA*
19730770-C-T 17618890-C-T P5_Prx A*
19840576-G-A 17728696-G-A P5_Prx A*
28817366-G-T 26671219-G-T A*
19849082-G-A 17737202-G-A P5_Prx A*
28817501-G-T 26671354-G-T A*
28817365-G-T 26671218-G-T A*
25883914-C-T 23737767-C-T P1_Y1 A*
26300050-C-T 24153903-C-T P1_Y1 A*
26376262-T-C 24230115-T-C P1_Y1 A*
20995344-T-TG 18833458-T-TG P4_Dst A*
19684200-G-A 17572320-G-A BY211905 P5_Prx A*
15487325-T-C 13375445-T-C FT22073 YY+
15473740-T-A 13361860-T-A FT22063 YY+
15469958-G-A 13358078-G-A FT22062 YY+
14401928-C-T 12281225-C-T YY+
15283353-G-A 13171452-G-A FT21912 Y+
21798909-G-A 19637023-G-A FT25662 YY+
14497969-A-T 12386174-A-T FT21412 YY+
16437466-C-T 14325586-C-T FT76585 YY+
14189528-C-T 12068822-C-T FT21127 YY+
16342183-G-T 14230303-G-T FT22626 YY+
18250814-CA-C 16138934-CA-C +
17118616-C-T 15006736-C-T FT23242 YY+
17211183-C-G 15099303-C-G FT23294 YY+
17357414-C-T 15245534-C-T FT23402 YY+
21323906-C-T 19162020-C-T FT25273 Y+
18081449-C-T 15969569-C-T FT24036 YY+
18118230-C-A 16006350-C-A FT24087 YY+
13856148-G-T 11735442-G-T FT20708 +
18407315-C-A 16295435-C-A FT24262 P6_Gap +
19381324-T-C 17269444-T-C FT24933 YY+
21320875-C-T 19158989-C-T FT25267 Y+
21233457-A-G 19071571-A-G FT25180 YY+
19787353-C-T 17675473-C-T P5_Prx +
21881417-T-G 19719531-T-G FT25744 YY+
22465755-G-C 20303869-G-C DYZ19 +
13666671-G-A 11510995-G-A +
22761391-C-G 20599505-C-G FT26150 YY+
23265227-G-C 21103341-G-C FT26537 YY+
2997875-C-T 3129834-C-T FT14785 +
3047238-C-CA 3179197-C-CA +
3078921-G-T 3210880-G-T FT14877 +
3128797-A-T 3260756-A-T FT14937 +
22915995-A-G 20754109-A-G FT26270 YY+
5039469-G-A 5171428-G-A FT17124 +
5416634-A-G 5548593-A-G FT17544 +
5531818-T-G 5663777-T-G FT17675 +
5548203-G-A 5680162-G-A FT17692 +
22214553-C-T 20052667-C-T FT25997 Y+
5898333-A-T 6030292-A-T FT18137 +
7288059-C-A 7420018-C-A FT19101 YY+
21038272-A-C 18876386-A-C FT25067 Y+
9650423-G-A 9812814-G-A FT20482 IR3_Prx +
9929562-G-A 10091953-G-A Y+
10665402-C-G +
22611791-G-A 20449905-G-A FT26063 YY+
7291412-T-A 7423371-T-A FT19105 YY+
22437717-C-G 20275831-C-G DYZ19 +
6941484-T-TTCTC 7073443-T-TTCTC 13×TC*
22255265-A-G 20093379-A-G DYZ19 *
3275928-C-G 3407887-C-G *
4479867-G-A 4611826-G-A *
7828740-C-T 7960699-C-T YY*
28808164-C-T 26662017-C-T BY227434 *
22444273-G-T 20282387-G-T DYZ19 **
22471169-A-T 20309283-A-T DYZ19 **
24291300-G-A 22145153-G-A P3_t1 **
14858843-A-AT 12746909-A-AT **
19627675-A-C 17515795-A-C P5_Prx **
13483009-A-T 11327333-A-T **
4776622-AACACAC-A 4908581-AACACAC-A 20×AC**
19627653-A-C 17515773-A-C P5_Prx **
13482983-C-A 11327307-C-A **
13482997-A-T 11327321-A-T **
13337459-T-C 11181783-T-C **
13609888-T-A 11454212-T-A **
14114388-A-T 11993682-A-T **
17483098-C-T 15371218-C-T **
13522940-A-G 11367264-A-G ***
13522941-T-G 11367265-T-G ***
7004133-T-G 7136092-T-G ***
3334419-A-C 3466378-A-C ***
4711950-G-A 4843909-G-A ***
14565004-T-A 12453204-T-A ***
24751223-T-C 22605076-T-C P3_b2 ***
24931798-C-T 22785651-C-T g1 ***
18846011-CAAAAA-C 16734131-CAAAAA-C 25×A***
13535639-G-GTA 11379963-G-GTA 21×TA***
56862630-TTTTTT-T,TTTTTG ***

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.

Age Analysis Information (work in progress)

Kit: 3600031527795895743978393873
Used in age calculations1527795895743978393873
Counts of SNPs3224
Variant counts last updated 2020-07-03 02:53:04.

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