Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > Z46512 > FGC78762 > ZZ19 > Z31644 > Z42772 > BY20186

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
5252418-C-G 5384377-C-G A+
58981797-C-T 56835650-C-T A*
25614986-A-T 23468839-A-T P1_gr1 A*
56832622-G-T A*
13447997-A-T 11292321-A-T A*
56835651-T-C A*
56836793-C-A A*
6269398-C-T 6401357-C-T IR3_Dst A*
6270581-C-CATCA 6402540-C-CATCA IR3_Dst A*
16116240-T-C 14004360-T-C P8_Prx A*
18371702-C-T 16259822-C-T P6_Prx A*
19634626-G-A 17522746-G-A P5_Prx A*
19640856-A-G 17528976-A-G P5_Prx A*
19820683-G-A 17708803-G-A P5_Prx A*
25567791-G-A 23421644-G-A P1_gr1 A*
25951354-G-T 23805207-G-T P1_Y1 A*
26477267-G-C 24331120-G-C P1_Y1 A*
56826666-T-A A*
56830679-C-T A*
56833114-T-C A*
15248861-C-A 13136947-C-A FT279392 Y+
2775220-A-G 2907179-A-G FT278696 YY+
23119914-C-A 20958028-C-A FT279859 YY+
3467487-T-C 3599446-T-C FT278746 +
3667156-G-A 3799115-G-A FT278764 +
4391972-C-T 4523931-C-T FT278842 +
4916521-G-T 5048480-G-T FT278886 +
5021578-C-AT 5153537-C-AT +
5935378-A-C 6067337-A-C FT279002 +
6245514-T-C 6377473-T-C FT279025 IR3_Dst +
7078044-A-G 7210003-A-G FT279089 YY+
7828924-C-G 7960883-C-G FT279141 YY+
7881725-T-C 8013684-T-C FT279146 YY+
7926977-T-A 8058936-T-A FT279153 YY+
8116119-TA-T 8248078-TA-T +
8762192-G-A 8894151-G-A FT20120 YY+
8850180-G-A 8982139-G-A FT279214 Y+
9964895-G-A 10127286-G-A Y+
10073062-A-T 10235453-A-T +
10625345-A-T FT427970 +
10627219-G-T FT428015 +
13305883-G-T 11150207-G-T FT442526 +
13653811-G-C 11498135-G-C +
13689569-T-A 11533893-T-A FT448566 +
13691118-G-A 11535442-G-A BY211015 +
14016231-T-C 11895525-T-C FT279305 Y+
14525525-A-G 12413726-A-G FT279351 Y+
14532439-A-G 12420640-A-G FT279352 Y+
14536111-A-G 12424312-A-G FT279353 YY+
15702686-T-C 13590806-T-C FT279408 YY+
15716213-C-T 13604333-C-T FT279409 YY+
15970648-A-C 13858768-A-C FT279429 YY+
16339896-G-A 14228016-G-A FT226882 YY+
16556106-T-C 14444226-T-C FT279464 YY+
16751772-A-G 14639892-A-G FT279489 YY+
16762102-C-T 14650222-C-T FT279491 YY+
17438887-G-GT 15327007-G-GT 8×T+
17470939-G-A 15359059-G-A FT279549 YY+
18110902-T-A 15999022-T-A FT279602 YY+
18254550-A-T 16142670-A-T FT279620 Y+
18354400-G-A 16242520-G-A FT279622 P6_Prx +
18649955-G-T 16538075-G-T FT279648 YY+
18930757-A-T 16818877-A-T FT279668 YY+
18992769-T-G 16880889-T-G FT279676 YY+
19147381-T-C 17035501-T-C FT279698 YY+
21422611-T-C 19260725-T-C FT279767 YY+
21552586-T-A 19390700-T-A FT279775 Y+
21552587-TA-T 19390701-TA-T +
21620918-G-A 19459032-G-A FT119105 YY+
21950408-T-A 19788522-T-A FT279800 YY+
22469858-T-C 20307972-T-C FT459103 DYZ19 +
22480520-T-A 20318634-T-A FT460393 DYZ19 +
23145234-G-T 20983348-G-T FT279864 YY+
24369685-C-A 22223538-C-A FT279923 +
24452848-G-A 22306701-G-A FT279927 Y+
28682868-A-G 26536721-A-G FT279949 +
28757775-T-C 26611628-T-C FT285235 Y+
59016167-C-T 56870020-C-T *
13267780-T-CCC 11112104-T-CCC *
22304228-A-C 20142342-A-C DYZ19 *
10995821-T-TTCCAC *
3573048-C-T 3705007-C-T *
18337218-G-C 16225338-G-C P6_Prx *
22233655-A-C 20071769-A-C DYZ19 *
7939330-C-A 8071289-C-A **
10799945-GCACTC-G **
27540976-C-CA 25394829-C-CA P1_Y2 12×A**
13459540-C-CGGAAG 11303864-C-CGGAAG **
5404109-G-A 5536068-G-A **
6226021-T-C 6357980-T-C IR3_Dst **
7204018-T-G 7335977-T-G **
9809457-G-GA 9971848-G-GA **
13362360-C-CAAA 11206684-C-CAAA 19×A**
13459114-T-A 11303438-T-A **
13459175-G-A 11303499-G-A **
18931938-A-G 16820058-A-G **
20390710-A-G 18228824-A-G P5_Dst **
20426054-CAAAAAAAAAA-C 18264168-CAAAAAAAAAA-C P5_Dst 26×A**
20677658-T-A 18515772-T-A P4_Prx **
22420011-C-T 20258125-C-T DYZ19 **
22476429-G-C 20314543-G-C DYZ19 **
22483424-T-C 20321538-T-C DYZ19 **
28062449-T-C 25916302-T-C P1_Y2 **
28569636-G-A 26423489-G-A **
11933-T-A **
19349-T-G **
59026148-C-T 56880001-C-T ***
59028791-C-T 56882644-C-T ***
56843370-AT-A ***
17944937-TA-T 15833057-TA-T ***
4897963-CA-C,CAA 5029922-CA-C,CAA 20×A***
27462468-CA-C 25316321-CA-C P1_Y2 19×A***
56848886-C-G ***
18095736-A-G 15983856-A-G ***
4651374-C-CA 4783333-C-CA 9×A***
2677986-G-T 2809945-G-T ***
4347744-G-A 4479703-G-A ***
9915971-A-G 10078362-A-G ***
16323814-G-T 14211934-G-T ***
17944930-TATA-T 15833050-TATA-T ***
18134769-T-A 16022889-T-A ***
22333957-G-C 20172071-G-C DYZ19 ***
22446352-G-A 20284466-G-A DYZ19 ***
22460231-T-C 20298345-T-C DYZ19 ***
56861837-AACCTG-A,ACCTA ***

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.