Tree Position

R-P312/S116 > Z40481 > FGC84729 > ZZ37 > ZZ38 > Z39300

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
5370008-G-A 5501967-G-A A+
20322647-A-G 18160761-A-G P5_Dst A+
19669186-A-C 17557306-A-C P5_Prx A*
6220300-G-C 6352259-G-C IR3_Dst A*
6282966-G-A 6414925-G-A IR3_Dst A*
13449235-C-A 11293559-C-A A*
13449290-T-A 11293614-T-A A*
18291947-G-A 16180067-G-A P6_Prx A*
18364207-C-T 16252327-C-T P6_Prx A*
18517157-C-T 16405277-C-T P6_Dst A*
19857128-T-C 17745248-T-C P5_Prx A*
20379351-A-T 18217465-A-T P5_Dst A*
20635804-T-C 18473918-T-C P4_Prx A*
21008367-A-G 18846481-A-G P4_Dst YA*
25922387-C-T 23776240-C-T P1_Y1 A*
26009999-A-G 23863852-A-G P1_Y1 A*
26065639-T-A 23919492-T-A P1_Y1 A*
26129959-G-A 23983812-G-A P1_Y1 A*
26205426-G-A 24059279-G-A P1_Y1 A*
26338086-G-A 24191939-G-A P1_Y1 A*
28032086-G-GT 25885939-G-GT P1_Y2 10×TA*
56831954-A-T A*
4401665-G-A 4533624-G-A Z10007 +
21907529-GT-G 19745643-GT-G 9×T+
21230021-C-T 19068135-C-T FT140355 YY+
3161670-G-GC 3293629-G-GC +
5160560-G-C 5292519-G-C FT136432 +
6030259-T-C 6162218-T-C FT136899 +
6426227-G-A 6558186-G-A +
6702475-G-A 6834434-G-A FT137090 YY+
6704439-T-C 6836398-T-C FT137091 YY+
6796727-C-A 6928686-C-A FT137119 YY+
7530709-G-A 7662668-G-A FT137367 YY+
7599562-C-T 7731521-C-T FT137393 YY+
7746764-C-A 7878723-C-A FT137462 YY+
8240780-A-T 8372739-A-T FT137606 YY+
8453779-C-T 8585738-C-T FT137674 YY+
9169574-T-A 9331965-T-A FT137946 Y+
9404719-A-G 9567110-A-G FT137964 YY+
13324286-T-C 11168610-T-C FT376983 +
11656696-A-G FT376984 +
13860168-T-C 11739462-T-C FT138112 +
14642414-T-G 12530483-T-G FT138517 YY+
15587515-A-G 13475635-A-G FT138858 YY+
17296207-A-G 15184327-A-G FT139432 YY+
17766530-T-C 15654650-T-C FT139617 YY+
18068344-C-A 15956464-C-A FT139738 YY+
18083554-C-T 15971674-C-T FT139747 YY+
18442954-CTCTT-C 16331074-CTCTT-C P6_Dst +
18555017-C-T 16443137-C-T FT139869 YY+
18747352-G-A 16635472-G-A FT139940 YY+
18885133-T-C 16773253-T-C FT139991 YY+
18950652-G-A 16838772-G-A FT140015 YY+
19010633-C-A 16898753-C-A FT140039 YY+
21478242-A-C 19316356-A-C FT140462 YY+
21904428-A-C 19742542-A-C FT140643 YY+
22562482-T-C 20400596-T-C FT140791 YY+
23048058-C-T 20886172-C-T FT140964 Y+
23079649-T-C 20917763-T-C FT140975 YY+
23193698-A-T 21031812-A-T FT141024 Y+
23531033-C-T 21369147-C-T FT141142 YY+
21717648-A-ATGTG 19555762-A-ATGTG 17×TG*
9587403-C-T 9749794-C-T FT374637 IR3_Prx *
10955388-T-TTCCAC *
20312789-T-TG 18150903-T-TG P5_Dst **
25966272-C-A 23820125-C-A P1_Y1 **
14100957-C-G 11980251-C-G **
21002535-T-TTCTC 18840649-T-TTCTC P4_Dst 16×TC**
18492546-CTTTT-C 16380666-CTTTT-C P6_Dst 27×T**
15121967-G-A 13010054-G-A **
2789866-A-G 2921825-A-G **
2806158-A-T 2938117-A-T FTB9256 **
14135531-T-C 12014825-T-C **
14179580-G-A 12058874-G-A FTB20459 **
19663299-GT-G 17551419-GT-G P5_Prx **
19763408-T-G 17651528-T-G P5_Prx **
20312816-C-T 18150930-C-T P5_Dst **
20384302-CT-C 18222416-CT-C P5_Dst 8×T**
22508101-G-A 20346215-G-A FT460706 DYZ19 **
24296362-AAAAG-A 22150215-AAAAG-A P3_t1 **
25939443-G-T 23793296-G-T P1_Y1 **
25996182-C-A 23850035-C-A P1_Y1 **
28000282-T-TTA 25854135-T-TTA P1_Y2 **
14005951-TAATAAATA-T 11885245-TAATAAATA-T 10×AATA***
14420787-C-CTT 12300062-C-CTT 18×T***
28565731-T-C 26419584-T-C ***
17926534-CAAA-C,CAA 15814654-CAAA-C,CAA 25×A***
4277201-CT-C,CTTT 4409160-CT-C,CTTT 20×T***
7016147-C-CAA 7148106-C-CAA 16×A***
10973613-ATTCCGTTCCG-A ***
16357126-G-A 14245246-G-A ***

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.