Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > Z251/S470 > FGC13899 > FGC18233

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 STR1kG
22113210-AG-A 19951324-AG-A +
14850507-G-A 12738573-G-A YY+
16880645-C-T 14768765-C-T YY+
16744138-T-G 14632258-T-G FT312746 YY+
16617481-A-G 14505601-A-G FT22860 Y+
16593945-C-T 14482065-C-T YY11×AT+
16064132-T-G 13952252-T-G Y+
15943632-T-G 13831752-T-G Y+
15683652-AT-A 13571772-AT-A +
15658085-CGT-C 13546205-CGT-C +
15176295-AC-A 13064381-AC-A +
14882305-CGG-C 12770373-G-C +
14667694-AT-A 12555759-AT-A +
17362456-C-A 15250576-C-A PF2438FGC18894 YY+
14286784-C-CTTTTTT 12166078-C-CTTTTTT 22×T+
14102397-C-CTATG 11981691-C-CTATG +
13930171-C-CAA 11809465-C-CAA 21×A+
13914244-A-C 11793538-A-C Y+
13630385-G-A 11474709-G-A FGC70703 +
13571934-A-G 11416258-A-G +
13571911-T-C 11416235-T-C +
13570212-A-AG 11414536-A-AG +
13457352-C-T 11301676-C-T +
13418416-A-T 11262740-A-T +
13414092-G-C 11258416-G-C +
16986973-T-A 14875093-T-A YY+
17663109-AG-A 15551229-AG-A +
13218987-AG-A 11063311-AG-A +
22483244-C-T 20321358-C-T DYZ19 +
28711352-A-C 26565205-A-C Y+
28711307-T-TG 26565160-T-TG +
28547139-G-A 26400992-G-A FT299637 +
28534958-TGC-T 26388811-TGC-T +
28457770-G-A 26311623-G-A +
25647030-A-C 23500883-A-C P1_b3 22×AC+
24960871-AAT-A 22814724-AAT-A g1 +
24388225-CTA-C 22242078-CTA-C +
23644084-A-C 21482198-A-C Y+
23369624-G-A 21207738-G-A FT348954 YY+
21965771-AG-A 19803885-AG-A +
17680076-AC-A 15568196-AC-A +
21931854-G-A 19769968-G-A BY196031 YY+
21761950-T-C 19600064-T-C YY+
21520230-TAGA-T 19358344-TAGA-T +
19346426-TCTTCTTC-T 17234546-TCTTCTTC-T +
19225667-A-T 17113787-A-T YY+
18984974-A-T 16873094-A-T Z6478 YY+
18914162-G-A 16802282-G-A BY200143 YY+
18618290-T-C 16506410-T-C Z10915 Y+
18462573-G-A 16350693-G-A P6_Dst +
17926570-G-A 15814690-G-A YY+
17784136-AC-A 15672256-AC-A +
13260750-T-G 11105074-T-G +
13140124-C-CT 10629610-C-CT +
14286775-G-A 12166069-G-A YY+
15945938-G-T 13834058-G-T PH1914 YY+
23079397-G-A 20917511-G-A 6869162-G-ABY22421 FGC70706 YY+
22950334-C-T 20788448-C-T CTS11095 YY+
21598287-A-G 19436401-A-G FGC29554 Y13466 Y+
21300544-G-A 19138658-G-A FGC70708 YY+
18877941-A-T 16766061-A-T FT301997 Y+
18863148-C-T 16751268-C-T FGC70709 Y+
17096666-G-T 14984786-G-T CTS6760 S3745 Y+
16934499-C-T 14822619-C-T PH2682 YY+
16874242-A-T 14762362-A-T PH2633 YY+
16466226-G-T 14354346-G-T FT34648 Y11×T+
15801718-C-A 13689838-C-A CTS4758 YY+
28792467-GGAGTGA-G 26646320-GGAGTGA-G +
15573451-T-C 13461571-T-C PH1759 YY+
15029509-T-A 12917597-T-A YY+
8263542-G-T 8395501-G-T FGC70711 YY+
7593363-G-A 7725322-G-A FGC70704 YY+
6955919-A-G 7087878-A-G PH341 YY+
15558435-T-G 13446555-T-G A12459 YY+
13431841-G-T 11276165-G-T +
14418313-C-T 12297588-C-T YSC0001262 CTS2667 YY+
13139021-C-CA 10628507-C-CA +
28776352-A-G 26630205-A-G CTS12986 +
19740992-C-A 17629112-C-A P5_Prx 24×A+
22902573-T-G 20740687-T-G YY+
3004917-A-G 3136876-A-G +
9960293-T-C 10122684-T-C Y+
5453891-C-T 5585850-C-T 19×T+
9885646-AC-A 10048037-AC-A +
9885644-CA-C 10048035-CA-C +
8826398-G-A 8958357-G-A Z29285 Y+
8221245-GA-G 8353204-GA-G +
8182223-AC-A 8314182-AC-A +
7683468-A-T 7815427-A-T YY+
7516539-A-G 7648498-A-G FGC70710 Y+
7199178-CA-C 7331137-CA-C +
7091211-C-T 7223170-C-T PH417 YY+
6694443-TC-T 6826402-TC-T +
5936842-C-T 6068801-C-T +
5193873-G-C 5325832-G-C +
3171895-T-C 3303854-T-C +
4979552-G-T 5111511-G-T FT322321 +
4661199-G-A 4793158-G-A FT321336 +
4532178-G-C 4664137-G-C FT320935 +
4082348-G-A 4214307-G-A FT155837 +
4035390-A-C 4167349-A-C +
4004405-A-G 4136364-A-G K349 +
3916933-CCA-C 4048892-CCA-C +
3865200-T-C 3997159-T-C FGC70707 +
3554443-A-G 3686402-A-G FGC70715 +
3554056-C-CAA 3686015-C-CAA +
3347700-G-T 3479659-G-T +
59026874-C-CT 56880727-C-CT +

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.

Mutation Notes:

Manual13696353-T-C11540677-T-C2 or 3 reads with a C, about a half dozen with a T, and another half dozen ill aligned.
Manual22299490-G-T20137604-G-T14 reads total, 5 with a T and the balance with G.
Manual25633952-G-A23487805-G-A1 read with A, 2 reads with G.
Manual6069952-C-T6201911-C-T2 reads, 1 C and 1 T.

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