Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z367/S255 > L20/S144

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
843604
15095373-G-A 12983461-G-A FT21819 YY+
13832359-G-T 11711653-G-T BY90902 +
5657265-C-T 5789224-C-T FT17859 +
22440241-C-A 20278355-C-A BY46643 DYZ19 +
22294425-C-G 20132539-C-G DYZ19 +
19232807-C-T 17120927-C-T BY127517 YY+
9026135-C-G 9188526-C-G BY77471 Y+
9858162-A-C 10020553-A-C FT20578 YY+
21486020-G-A 19324134-G-A BY133312 YY+
13551318-G-A 11395642-G-A FT56478 +
21471766-G-A 19309880-G-A BY133159 YY+
13943360-C-T 11822654-C-T FT20849 Y+
23187971-T-A 21026085-T-A BY143658 Y+
13998846-T-C 11878140-T-C FT20930 YY+
14248077-C-G 12127371-C-G BY94313 YY+
16690087-C-T 14578207-C-T BY211642 YY+
21293526-A-T 19131640-A-T FT25232 YY+
17231633-G-A 15119753-G-A FT23317 YY+
17737470-A-C 15625590-A-C FT23737 YY+
17904953-G-A 15793073-G-A BY118281 YY+
18253538-T-A 16141658-T-A FT24199 Y+
18703788-G-A 16591908-G-A FT24397 YY+
18892529-AC-A 16780649-AC-A +
23053623-T-C 20891737-T-C YY+
8069219-A-G 8201178-A-G BY69713 YY+
4900563-C-T 5032522-C-T FT16973 +
3685374-C-G 3817333-C-G FT15573 +
10038407-G-A 10200798-G-A FGC34244 +
28633819-A-G 26487672-A-G FT27199 Y+
28616637-C-T 26470490-C-T +
19047531-G-T 16935651-G-T BY43538 YY12×T+
24357998-A-T 22211851-A-T BY149308 +
3609767-G-A 3741726-G-A FT15484 +
3662978-CAT-C 3794937-CAT-C +
19234247-C-T 17122367-C-T FT24798 YY+
3705570-G-A 3837529-G-A FT15594 +
3863821-A-G 3995780-A-G FT15797 +
23612013-T-A 21450127-T-A BY146707 YY+
23969135-G-C 21822988-G-C BY148860 Y+
23654742-A-C 21492856-A-C FT26783 Y+
17737627-AAAAAAG-A 15625747-AAAAAAG-A 4×AAAAAG*
4678058-G-GTT 4810017-G-GTT 15×T*
13688270-C-T 11532594-C-T *
19014431-C-T 16902551-C-T **
17624529-C-A 15512649-C-A **
10969986-T-G **
18057133-T-C 15945253-T-C **
17876105-CT-C 15764225-CT-C **
18401022-G-A 16289142-G-A P6_Gap **
19324551-T-C 17212671-T-C **
56886677-C-G **
6495031-C-A 6626990-C-A **
16319220-G-T 14207340-G-T **
16064456-T-C 13952576-T-C **
19014389-AC-A 16902509-AC-A **
22289289-G-T 20127403-G-T BY52376 DYZ19 **
10973582-T-TATTCC **
22461875-T-G 20299989-T-G DYZ19 **
13488426-C-A 11332750-C-A **
7213264-A-G 7345223-A-G **
6770439-C-T 6902398-C-T **
21417513-C-A 19255627-C-A **
24435616-T-C 22289469-T-C **
5275759-T-C 5407718-T-C FT12115 BY11119FGC4545 **
27967355-TAGAGAGAGAGAGAG-T 25821208-TAGAGAGAGAGAGAG-T P1_Y2 14×AG**
28542225-G-C 26396078-G-C ***
20816924-CAAAA-C,CAAA 18655038-CAAAA-C,CAAA P4_Gap 22×A***
23194817-CT-C,CTT 21032931-CT-C,CTT 24×T***
28542224-G-A 26396077-G-A ***
21095931-C-G 18934045-C-G ***
21391650-CT-C,CTT 19229764-CT-C,CTT 14×T***
21230509-TAA-T 19068623-TAA-T 14×A***
19048348-A-ATT 16936468-A-ATT ***
4130101-ATT-A 4262060-ATT-A 13×T***
13477239-C-T 11321563-C-T ***
15865539-G-C 13753659-G-C ***
3969793-TA-T 4101752-TA-T 10×A***
23802081-T-A 21640195-T-A ***
21664054-GA-G 19502168-GA-G 10×A***
23197360-C-A 21035474-C-A Y79445 17×A***
9942043-ATTTTTTTTT-A 10104434-ATTTTTTTTT-A 28×T***
3243060-T-C 3375019-T-C FT203073 ***
3833256-GAA-G 3965215-GAA-G 10×A***
3941037-TA-T 4072996-TA-T ***
3941043-TA-T 4073002-TA-T ***
5218350-T-C 5350309-T-C ***
18761846-G-T 16649966-G-T ***
5230813-T-C 5362772-T-C ***
7296874-C-A 7428833-C-A ***
7383851-CAAAA-C,CAAAAA 7515810-CAAAA-C,CAAAAA 24×A***
8030053-AAAAGAAC-A,GAAC 8162012-AAAAGAAC-A,GAAC ***
10810533-T-G ***
13323494-CAAAA-C,CAAA 11167818-CAAAA-C,CAAA 24×A***
13585512-T-G 11429836-T-G ***
13911543-A-G 11790837-A-G ***
15374441-GTTT-G,GTT 13262561-GTTT-G,GTT 20×T***
16768641-G-T 14656761-G-T ***
17228618-A-G 15116738-A-G ***
17737625-AAAAAAAAG-A 15625745-AAAAAAAAG-A ***
12395-G-A ***

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)

AllMcDonaldYFull
Kit: 8436041468864292140788219369
Used in age calculations1468864292140788219369
Counts of SNPs2122
Variant counts last updated 2020-03-31 02:49:59.



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