Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > DF21/S192 > S971 > Z16267 > F24434 > Z3000/S951 > Z3006 > BY3160 > ~19651428-C-G > BY130746

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
39409
5147958-A-G 5279917-A-G A+
4386824-G-A 4518783-G-A A*
23181425-T-C 21019539-T-C YA*
6243741-T-C 6375700-T-C IR3_Dst A*
19592637-C-T 17480757-C-T P5_Prx YA*
3325988-T-A 3457947-T-A FT223219 +
13558035-A-C 11402359-A-C +
10004957-A-G 10167348-A-G FT225353 Y+
17595645-G-A 15483765-G-A FT224600 YY+
7680344-C-G 7812303-C-G FT223809 YY+
18840060-A-C 16728180-A-C FT224726 YY+
6970698-C-G 7102657-C-G FT223733 YY+
19086681-G-T 16974801-G-T FT224760 YY+
19251511-G-A 17139631-G-A FT224782 YY+
6491847-G-C 6623806-G-C FT223666 +
3260473-CAT-C 3392432-CAT-C +
16183453-A-G 14071573-A-G FT224387 Y+
21224344-C-A 19062458-C-A FT224848 YY+
21251929-C-T 19090043-C-T YY+
22030750-C-T 19868864-C-T BY137194 YY+
23189679-C-T 21027793-C-T FT225101 Y+
24388862-A-G 22242715-A-G FT225199 +
17125597-A-C 15013717-A-C FT224531 Y+
13463314-A-T 11307638-A-T *
15548847-G-GACAC 13436967-G-GACAC 18×AC*
13869410-G-A 11748704-G-A *
22537702-T-C 20375816-T-C **
22877152-A-C 20715266-A-C **
23213089-T-C 21051203-T-C **
28022972-G-GA 25876825-G-GA P1_Y2 10×A**
9804471-G-A 9966862-G-A **
33155-A-T **
56699846-GAATGGAA-G **
7338738-A-G 7470697-A-G **
6720662-C-T 6852621-C-T **
10030580-G-GT 10192971-G-GT **
15410633-CAAAA-C 13298753-CAAAA-C 28×A**
10648064-CTCCACTCCAT-C **
14784701-CTTT-C,CT 12672771-CTTT-C,CT 22×T***
17312215-G-GA 15200335-G-GA 10×A***
4213186-G-GTT 4345145-G-GTT 15×T***
14505579-T-C 12393784-T-C ***
18770049-TTA-T 16658169-TTA-T ***
14394872-G-GT 12274168-G-GT 10×T***
19042179-CAAA-C 16930299-CAAA-C 17×A***
4277201-CTT-C,CTTT 4409160-CTT-C,CTTT 20×T***
23241947-CTTTT-C,CTTT 21080061-CTTTT-C,CTTT 27×T***
6944943-C-CAAA 7076902-C-CAAA 28×A***
17641957-CTTTTT-C,CTTTT 15530077-CTTTTT-C,CTTTT 25×T***
21553403-CTTTT-C,CTT 19391517-CTTTT-C,CTT 31×T***

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: 394091496972593772148316017
Used in age calculations1496972593772148316017
Counts of SNPs159
Variant counts last updated 2020-03-21 02:39:36.



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