Tree Position

R-P312/S116 > L238/S182 > Z2245 > Z2247

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
20596727-G-A 18434841-G-A P5_Dst A+
19589847-T-C 17477967-T-C P5_Prx YA+
19589848-T-C 17477968-T-C P5_Prx YA+
6333662-T-C 6465621-T-C IR3_Dst A*
19583046-C-T 17471166-C-T P5_Prx YA*
19725541-T-C 17613661-T-C P5_Prx A*
19868205-T-A 17756325-T-A P5_Prx A*
28816719-A-C 26670572-A-C A*
28817057-G-A 26670910-G-A A*
28705598-G-T 26559451-G-T FTA42232 +
8481611-C-T 8613570-C-T Z43991 YY+
18995575-G-A 16883695-G-A Y26995 YY+
22910671-T-C 20748785-T-C Y85669Y110089 YY+
22729450-C-A 20567564-C-A FTB38501 YY+
14502096-A-G 12390301-A-G FTB36269 Y+
13924681-C-A 11803975-C-A FTA38905 Y+
19139727-G-A 17027847-G-A BY42605BY43540 YY+
2879921-A-G 3011880-A-G FTA37851 YY+
3217033-T-C 3348992-T-C FTA43331 +
3245160-A-G 3377119-A-G FTA43339 +
3613063-T-C 3745022-T-C FTA43373 +
3644996-T-C 3776955-T-C FTB58963 +
3791316-C-G 3923275-C-G FTA43408 +
4222673-T-C 4354632-T-C FTB58969 +
4703117-A-C 4835076-A-C FTA42734 +
5143650-G-C 5275609-G-C FTA43619 +
5497139-A-C 5629098-A-C FTB58993 +
5972095-A-G 6104054-A-G FTB59002 +
6536826-C-T 6668785-C-T FTB59014 +
6615445-A-G 6747404-A-G FTB59016 +
7224342-G-T 7356301-G-T FTA38082 YY+
7705280-G-A 7837239-G-A FTA38250 Y+
7870461-T-C 8002420-T-C FTB35541 YY+
7988136-CATT-C 8120095-CATT-C +
8485028-G-C 8616987-G-C FTB35735 YY+
8516320-C-A 8648279-C-A FTB35747 YY+
9055462-G-A FTB59017 +
9110088-C-G 9272479-C-G FTA38787 Y+
10865344-A-T FT434646 +
13578537-AT-A 11422861-AT-A +
13628354-G-A 11472678-G-A +
13864790-G-A 11744084-G-A FTA43870 +
13901617-T-C 11780911-T-C FTA38896 Y+
13924681-C-CA 11803975-C-CA +
14261839-C-A 12141133-C-A FTA39065 YY+
14868201-A-G 12756271-A-G YY+
15181870-T-C 13069956-T-C FTA39432 YY+
15772755-A-C 13660875-A-C FTA39624 YY+
15781759-A-G 13669879-A-G FTB36690 YY+
15955548-A-T 13843668-A-T FTA39698 YY+
16346547-CCTAA-C 14234667-CCTAA-C +
16414734-C-T 14302854-C-T FTB36890 YY+
16689922-A-G 14578042-A-G FTA39997 YY+
16990069-A-T 14878189-A-T YY+
17149851-C-A 15037971-C-A FTA40177 YY+
17238810-A-G 15126930-A-G FTA40210 YY+
17413972-A-T 15302092-A-T FTB37226 YY+
17500651-C-T 15388771-C-T FTA40324 Y+
17714845-T-C 15602965-T-C FTA40424 YY+
17766921-G-T 15655041-G-T FTA40445 YY+
18017112-T-G 15905232-T-G BY196852 Y+
18078111-T-C 15966231-T-C FTA40581 YY+
18111446-C-A 15999566-C-A FTA40599 YY+
18199593-C-T 16087713-C-T FTA40637 YY+
18220894-T-C 16109014-T-C FTA40646 Y+
18563274-C-T 16451394-C-T FTA40707 YY+
18669125-C-T 16557245-C-T FTB37618 YY+
18773595-A-G 16661715-A-G FTB37660 YY+
19118364-C-A 17006484-C-A FTA40919 YY+
19411351-C-A 17299471-C-A FTA41046 YY+
19422768-T-C 17310888-T-C BY128974 YY+
21240952-C-T 19079066-C-T FTB38056 YY+
21478572-G-A 19316686-G-A FTA41321 YY+
21638708-T-G 19476822-T-G FTB38212 YY+
22061801-G-A 19899915-G-A FTA41532 YY+
22186260-G-A 20024374-G-A FTB38409 YY+
22436988-A-T 20275102-A-T DYZ19 +
22595085-G-A 20433199-G-A FTA41634 YY+
23088382-C-T 20926496-C-T FTB38626 YY+
23089154-G-A 20927268-G-A FTB38628 YY+
23243723-T-C 21081837-T-C FTA41907 YY+
23551368-T-A 21389482-T-A FTA42019 YY+
23551468-G-C 21389582-G-C FTA42020 YY+
28625947-C-G 26479800-C-G FTA42198 Y+
59026209-G-C 56880062-G-C *
26152175-C-T 24006028-C-T P1_Y1 *
27810264-G-A 25664117-G-A P1_Y2 *
56844471-A-G *
22474171-C-T 20312285-C-T Z15263 DYZ19 **
14301818-C-A 12181112-T-A FTB54232 **
17825292-G-A 15713412-G-A **
18358478-A-T 16246598-A-T P6_Prx **
20311570-A-T 18149684-A-T P5_Dst **
22302199-C-G 20140313-C-G DYZ19 **
22436989-A-T 20275103-A-T DYZ19 **
22439569-T-C 20277683-T-C DYZ19 **
22443769-G-T 20281883-G-T DYZ19 **
24628572-C-T 22482425-C-T P3_t2 **
25885854-AG-A 23739707-AG-A P1_Y1 ***
15323659-AC-A 13211777-AC-A ***
13452173-CACTCA-C,CACTCC 11296497-CACTCA-C,CACTCC ***
4997519-CAGAGAGAG-C 5129478-CAGAGAGAG-C 16×AG***
10910739-A-G ***
15491909-A-ATG 13380029-A-ATG 16×TG***
22317378-AG-A 20155492-AG-A DYZ19 ***
16232-A-T ***

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.