Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > ZZ10 > Z253 > Z2534 > ZZ5 > Z2185 > BY44331 > A287 > BY62794

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
4631167-C-G 4763126-C-G A*
5138579-A-G 5270538-A-G FT95616 A*
58973600-A-T 56827453-A-T A*
20644789-G-A 18482903-G-A P4_Prx A*
20616180-G-A 18454294-G-A P4_Prx A*
56830903-G-T A*
56833849-C-T A*
3107813-C-T 3239772-C-T A*
3241054-A-T 3373013-A-T FT254039 A*
4023268-A-T 4155227-A-T A*
4631017-T-A 4762976-T-A A*
4631172-G-A 4763131-G-A A*
6156776-C-T 6288735-C-T IR3_Dst A*
6165616-A-T 6297575-A-T IR3_Dst A*
6189646-C-A 6321605-C-A IR3_Dst A*
6298853-G-GT 6430812-G-GT IR3_Dst A*
6370246-A-G 6502205-A-G A*
13449635-G-A 11293959-G-A A*
13451297-C-A 11295621-C-A A*
18337005-T-G 16225125-T-G P6_Prx A*
18375991-T-A 16264111-T-A P6_Prx A*
18472089-A-C 16360209-A-C P6_Dst A*
19582026-G-A 17470146-G-A P5_Prx YA*
19889928-C-A 17778048-C-A P5_Prx A*
20801209-C-T 18639323-C-T P4_Prx A*
25552134-G-A 23405987-G-A P1_gr1 A*
26118833-G-A 23972686-G-A P1_Y1 A*
56830879-G-A A*
56831314-T-C A*
56831858-C-T A*
56833565-C-T A*
56836342-C-CCAT A*
56836851-C-CTGCAT A*
22270575-A-G 20108689-A-G BY33360 DYZ19 +
19479728-T-C 17367848-T-C FGC2741 M12421 YY+
2817189-CT-C 2949148-CT-C +
2725900-G-A 2857859-G-A FT127859 YY+
3139372-G-A 3271331-G-A FT33041 +
3586174-A-G 3718133-A-G FT127952 +
3694674-C-A 3826633-C-A FT127966 +
3786363-T-G 3918322-T-G FT127981 +
5090047-A-G 5222006-A-G FT128118 +
5557100-G-A 5689059-G-A FT128177 +
5616055-G-A 5748014-G-A FT128183 +
6042960-C-A 6174919-C-A FT128232 +
7133223-GA-G 7265182-GA-G +
7153774-C-T 7285733-C-T FT128327 YY+
7323909-A-G 7455868-A-G FT128338 YY+
8028204-G-C 8160163-G-C FT128413 YY+
8615882-A-C 8747841-A-C FT128466 YY+
9015984-G-A 9178375-G-A FT128502 Y+
9391789-T-G 9554180-T-G FT128522 Y+
9772363-C-T 9934754-C-T FT128539 Y+
10093341-G-A 10255732-G-A FT427493 +
10876701-C-T FT435108 +
10929281-C-T FT436919 +
13578211-GC-G 11422535-GC-G +
13954892-C-T 11834186-C-T FT128581 Y+
14238711-TG-T 12118005-TG-T +
14515951-C-T 12404152-C-T FT128653 YY+
14638011-G-C 12526080-G-C FT128667 YY+
15045220-T-C 12933310-T-C FT128706 Y+
15051740-T-C 12939831-T-C FT128707 YY+
15332609-C-T 13220727-C-T FT128729 YY+
15788224-T-A 13676344-T-A FT128791 YY+
16525838-A-T 14413958-A-T FT128872 YY+
17093313-T-C 14981433-T-C FT128933 Y+
17471527-G-A 15359647-G-A FT128978 YY+
18122874-T-A 16010994-T-A FT129045 YY+
18266463-G-C 16154583-G-C FT129060 +
18609277-T-G 16497397-T-G FT129073 YY+
19281815-T-C 17169935-T-C FT129152 YY+
21168486-C-A 19006600-C-A FT129179 YY+
21307058-CA-C 19145172-CA-C +
22178155-C-T 20016269-C-T FT129301 YY+
22540408-G-T 20378522-G-T FT129309 Y+
23081489-A-G 20919603-A-G FT129357 YY+
13633018-C-CTCT 11477342-C-CTCT 9×TCT*
8622199-G-GAC 8754158-G-GAC 12×AC*
3110476-G-A 3242435-G-A *
3110518-C-T 3242477-C-T *
3110565-C-CCTG 3242524-C-CCTG *
3440416-C-T 3572375-C-T *
4248747-T-C 4380706-T-C *
5056856-T-C 5188815-T-C *
5458725-C-A 5590684-C-A *
3241219-C-T 3373178-C-T FT241025 *
3241264-T-C 3373223-T-C *
3242531-A-G 3374490-A-G *
3425831-A-G 3557790-A-G *
5051179-A-G 5183138-A-G *
5051181-T-C 5183140-T-C *
16012485-G-A 13900605-G-A Y*
5241786-T-TAC 5373745-T-TAC 16×AC*
10990086-T-TACTCC *
5050063-T-C 5182022-T-C *
3436990-T-C 3568949-T-C *
4128344-A-ATT 4260303-A-ATT 10×T*
5022411-A-G 5154370-A-G *
5050260-C-CTA 5182219-C-CTA *
5050263-C-AT 5182222-C-AT *
5050281-A-G 5182240-A-G *
5051253-T-TC 5183212-T-TC *
5408510-G-A 5540469-G-A *
22232972-G-T 20071086-G-T DYZ19 *
22233451-T-A 20071565-T-A DYZ19 *
22254166-G-A 20092280-G-A DYZ19 *
28807989-A-G 26661842-A-G *
56845912-C-T *
13460134-T-C 11304458-T-C **
14862939-ATT-A 12751005-ATT-A 12×T**
27651841-C-A 25505694-C-A P1_Y2 **
13279997-TC-T 11124321-TC-T **
24582837-CAAAA-C 22436690-CAAAA-C P3_t2 17×A**
25557519-C-CTT 23411372-C-CTT P1_gr1 10×T**
3504662-AG-A 3636621-AG-A **
5403978-T-C 5535937-T-C **
5975996-A-T 6107955-A-T **
13556103-TA-T 11400427-TA-T **
13699247-T-C 11543571-T-C **
14590575-C-T 12478775-C-T 4×AAAT**
15221384-A-G 13109470-A-G **
16482316-T-C 14370436-T-C **
21786226-T-A 19624340-T-A **
22463904-C-A 20302018-C-A DYZ19 **
26254986-A-G 24108839-A-G P1_Y1 **
28559734-A-G 26413587-A-G **
22335127-G-T 20173241-G-T DYZ19 ***
58967861-G-T 56821714-G-T ***
14888076-C-CTT 12776142-C-CTT 17×T***
22661493-A-ATGTG 20499607-A-ATGTG 26×TG***
56829010-A-T ***
28500808-T-A 26354661-T-A ***
8739154-AAATAAT-A 8871113-AAATAAT-A 13×AAT***
3205858-CAAA-C 3337817-CAAA-C 15×A***
4698301-G-GA 4830260-G-GA 10×A***
3433335-T-C 3565294-T-C ***
3451528-C-T 3583487-C-T ***
5867721-G-A 5999680-G-A ***
5976000-A-C 6107959-A-C ***
6960851-G-GA 7092810-G-GA 9×A***
13347932-TACAC-T,TAC 11192256-TACAC-T,TAC 21×AC***
14426044-A-G 12305319-A-G ***
15893563-C-G 13781683-C-G ***
18846414-AG-A 16734534-AG-A ***
28500807-T-TA 26354660-T-TA ***
56871919-C-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.