Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > S1026 > BY173538 > FT5949

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
IN26698
13451386-C-T 11295710-C-T A*
20414083-T-A 18252197-T-A P5_Dst A*
20414086-G-C 18252200-G-C P5_Dst A*
19817394-C-T 17705514-C-T P5_Prx A*
13450945-C-G 11295269-C-G A*
6275544-G-C 6407503-G-C IR3_Dst A*
6284249-T-C 6416208-T-C IR3_Dst A*
6548328-C-A 6680287-C-A A*
18285566-C-T 16173686-C-T P6_Prx A*
19676750-G-T 17564870-G-T P5_Prx A*
20503028-C-A 18341142-C-A P5_Dst A*
22290088-C-A 20128202-C-A DYZ19 A*
26171247-G-A 24025100-G-A P1_Y1 A*
26301278-A-G 24155131-A-G P1_Y1 A*
56832968-C-CCATTCCATTT A*
2722909-A-G 2854868-A-G PH24 YY+
3240322-C-T 3372281-C-T FGC2907 Z11712 +
22458394-G-T 20296508-G-T Z17069 DYZ19 +
23586617-C-T 21424731-C-T Y111969 YY+
3684655-G-T 3816614-G-T FT3706 +
2875209-T-C 3007168-T-C FT3463 YY+
3264995-T-A 3396954-T-A FT3575 +
3319786-ATCTC-A 3451745-ATCTC-A 8×TC+
4114198-T-C 4246157-T-C FT3847 +
4303406-G-C 4435365-G-C FT3922 +
4433628-G-A 4565587-G-A FT3954 +
4593287-C-T 4725246-C-T FT4013 +
4744371-A-T 4876330-A-T FT4056 +
5066672-C-T 5198631-C-T FT4179 +
5165605-T-C 5297564-T-C FT4213 +
5576286-A-G 5708245-A-G FT4335 +
5992840-ACTT-A 6124799-ACTT-A +
6986373-A-T 7118332-A-T FT4658 YY+
8185906-C-T 8317865-C-T FT4856 YY+
8361396-C-T 8493355-C-T FT4883 YY+
8481772-C-T 8613731-C-T YY+
8572221-C-T 8704180-C-T FT4916 YY+
8617642-TTGAGGGGCACAGTGGATTCCCCA-T 8749601-TTGAGGGGCACAGTGGATTCCCCA-T +
9120891-T-C 9283282-T-C FT4999 Y+
9477057-T-C 9639448-T-C FT5021 +
9775859-G-A 9938250-G-A FT5045 Y+
10833731-A-G FT433301 +
10942973-A-T FT437560 +
10982328-T-A FT439100 +
13540350-A-T 11384674-A-T FT445020 +
15563657-G-C 13451777-G-C FT5403 YY+
17494281-C-T 15382401-C-T FT5708 YY+
17754107-T-G 15642227-T-G FT5758 YY+
17996327-G-A 15884447-G-A FT5803 P7_Gap Y+
18069887-C-T 15958007-C-T FT5815 YY+
18144425-G-A 16032545-G-A FT5832 YY+
18216148-G-A 16104268-G-A FT5850 YY+
19207115-A-G 17095235-A-G FT5976 YY+
22294022-G-T 20132136-G-T BY216460 DYZ19 +
22760186-G-A 20598300-G-A FT6307 YY+
22800610-T-C 20638724-T-C FT6318 Y+
23026310-C-T 20864424-C-T FT6366 YY+
23251805-G-A 21089919-G-A FT6403 YY+
24430900-C-A 22284753-C-A FT6521 Y+
21368207-A-ATTATGTTATG 19206321-A-ATTATGTTATG 10×TTATG*
2780632-G-GAC 2912591-G-GAC 14×AC*
3249466-T-TTGTGTG 3381425-T-TTGTGTG 17×TG*
6964748-C-CT 7096707-C-CT *
13246010-A-G 11090334-A-G *
13504620-T-G 11348944-T-G *
27896007-CA-C 25749860-CA-C P1_Y2 12×A**
17989583-C-CAT 15877703-C-CAT P7_Prx **
6150049-G-ATA 6282008-G-ATA IR3_Dst **
7710345-G-C 7842304-G-C **
7852430-C-T 7984389-C-T **
7897658-G-A 8029617-G-A **
13289077-C-G 11133401-C-G **
15683588-G-A 13571708-G-A **
16564319-A-G 14452439-A-G **
19330595-A-G 17218715-A-G **
21535194-G-A 19373308-G-A **
22443166-A-G 20281280-A-G DYZ19 **
22950072-G-A 20788186-G-A **
13844028-T-A 11723322-T-A FTB70613 DYZ17 ***
17004618-C-CAA 14892738-C-CAA 14×A***
10049793-C-A 10212184-C-A ***
7646961-A-G 7778920-A-G ***
18804525-AGC-A 16692645-AGC-A ***
4200053-AC-A 4332012-AC-A ***
13587384-A-G 11431708-A-G ***
8982999-C-T 9145390-C-T ***
14995217-T-C 12883302-T-C ***
16593945-CATATAT-C,CATAT 14482065-CATATAT-C,CATAT 11×AT***
19325883-A-G 17214003-A-G ***
23007979-T-C 20846093-T-C ***

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.