Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > FGC11134 > A353 > Z16250 > A114 > CTS4466/S1136 > S1115 > A541 > S1121 > L270 > 19311319CTGTT>C

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
267382
FTDNA
267382
56834274-A-C A*
19591944-A-T 17480064-A-T P5_Prx Y10×ATA****
28812816-C-T 26666669-C-T A*
4473666-T-G 4605625-T-G A*
13489158-G-A 11333482-G-A A*
5540459-A-AT 5672418-A-AT 12×TA*
22844753-A-AT 20682867-A-AT 11×TA*
20775175-G-T 18613289-G-T P4_Prx 10×AA*
26328368-C-T 24182221-C-T BY226771 FT27066 P1_Y1 A*
13478040-C-T 11322364-C-T A*
26461472-T-TA 24315325-T-TA P1_Y1 17×AA*
19810780-C-T 17698900-C-T P5_Prx A****
20033097-T-TA 17921217-T-TA P5_Prx 13×AA*
13269990-T-C 11114314-T-C A*
25554712-A-G 23408565-A-G P1_gr1 A*
6634765-C-T 6766724-C-T BY60437 YY++
14945463-G-A 12833537-G-A BY54681 YY++
9398399-CA-C 9560790-CA-C 10×A*
17180153-A-AAC 15068273-A-AAC 23×AC*
15049918-CAAAA-C 12938009-CAAAA-C 18×A**
25587242-CT-C 23441095-CT-C P1_gr1 14×T**
26102905-C-A 23956758-C-A P1_Y1 **
25982142-T-G 23835995-T-G P1_Y1 **
13474156-C-G 11318480-C-G **
18316605-CT-C 16204725-CT-C P6_Prx 17×T**
25980054-A-C 23833907-A-C P1_Y1 **
25891293-G-T 23745146-G-T P1_Y1 **
24300766-G-T 22154619-G-T P3_t1 **
28819212-C-A 26673065-C-A **
28819268-G-GTTCAATGGAGT 26673121-G-GTTCAATGGAGT **
2676068-A-G 2808027-A-G **
6410949-AAAATAAAT-A 6542908-AAAATAAAT-A 10×AAAT**
9731616-GTTTTT-G 9894007-GTTTTT-G IR3_Prx 17×T**
22422491-T-A 20260605-T-A DYZ19 **
14302243-T-G 12181537-T-G **
23601618-A-G 21439732-A-G **
24341926-T-G 22195779-T-G P3_t1 **
24624603-A-ATT 22478456-A-ATT P3_t2 11×T**
22487082-T-C 20325196-T-C DYZ19 **
3376998-T-A 3508957-T-A **
20796128-A-C 18634242-A-C P4_Prx **
20796109-A-C 18634223-A-C P4_Prx **
20629057-T-G 18467171-T-G P4_Prx **
18635327-TATACA-G 16523447-TATACA-G **
13253267-A-C 11097591-A-C **
17297332-T-G 15185452-T-G **
16103359-C-A 13991479-C-A P8_Prx **
25870822-C-A 23724675-C-A P1_Y1 **
10244-A-C **
13485888-T-G 11330212-T-G ***
22072885-G-GA 19910999-G-GA 10×A***
13485897-T-C 11330221-T-C ***
13485899-A-G 11330223-A-G ***
18972400-G-T 16860520-G-T ***
5828966-AACAC-A,AAC 5960925-AACAC-A,AAC 22×AC***
21120339-TA-T,TAA 18958453-TA-T,TAA 16×A***
28812798-A-G 26666651-A-G ***
13589954-C-A 11434278-C-A ***
3387264-G-C 3519223-G-C ***
10912338-CT-C ***
13485927-C-G 11330251-C-G ***
23516739-A-G 21354853-A-G ***
6418390-GA-G 6550349-GA-G 11×A***
5364687-GT-G 5496646-GT-G 12×T***
23488834-TAAAAA-T 21326948-TAAAAA-T 30×A***
22247766-G-T 20085880-G-T DYZ19 ***
4539033-TAA-T 4670992-TAA-T 24×A***
9231646-T-TA 9394037-T-TA 10×A***
59027358-G-A 56881211-G-A ***
19138207-A-AAT 17026327-A-AAT ***
13549878-TTG-T 11394202-TTG-T 14×TG***
5366649-G-A 5498608-G-A ***
24813381-T-C 22667234-T-C P3_b2 ***
13453204-CACTCA-C 11297528-CACTCA-C ***
9508531-CTT-C 9670922-CTT-C 25×T***
18871633-GAGAA-G 16759753-GAGAA-G 8×AGAA***
13135804-A-G 10625290-A-G ***
10003917-A-T 10166308-A-T ***
13842646-CGGAAT-C 11721940-CGGAAT-C 12×GGAAT***
13143384-G-A 10632870-G-A ***
13478067-G-A 11322391-G-A ***
13221734-A-G 11066058-A-G ***
13221682-G-C 11066006-G-C ***
13478589-T-G 11322913-T-G ***
13687695-TA-T,TC 11532019-TA-T,TC ***
13463959-C-CTT 11308283-C-CTT ***
10744497-TC-T ***
10942731-C-G ***
19052414-CAAAA-C 16940534-CAAAA-C 24×A***
17276908-GA-G 15165028-GA-G 12×A***
14847004-CAAAAAA-C,CAAAAAAA 12735070-CAAAAAA-C,CAAAAAAA 20×A***
9114145-CTT-C ***
10992094-GTCCAC-G ***
16692104-AAAG-A 14580224-AAAG-A ***
15479942-CTTT-C 13368062-CTTT-C 21×T***
17703236-TAA-T 15591356-TAA-T 22×A***
19505547-A-AAT 17393667-A-AAT 8×AT***
14880241-ATT-A,AT 12768311-ATT-A,AT 17×T***
13223278-A-T 11067602-A-T ***
8724604-T-C 8856563-T-C ***
13469386-G-A 11313710-G-A ***
13135801-T-G 10625287-T-G ***
23025229-CAA-C 20863343-CAA-C 29×A***
6586786-C-CT 6718745-C-CT 22×T***
4887612-CA-C 5019571-CA-C 29×A***
12226-T-G ***

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: 2673821066968777190097788370
Kit: 2673821504552894416078356308
Used in age calculations1504552894416078356308
Counts of SNPs32
Variant counts last updated 2019-10-28 04:28:00.



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