Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z258 > Z367/S255 > L20/S144 > Z46420 > BY5690 > FGC56105 > BY2171 > BY5688

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
3895589-A-C 4027548-A-C A*
19754914-C-CTCTT 17643034-C-CTCTT P5_Prx A*
56831812-T-C A*
6110592-A-G 6242551-A-G A*
6271025-A-C 6402984-A-C IR3_Dst A*
6327569-T-A 6459528-T-A IR3_Dst A*
13451111-A-T 11295435-A-T A*
19683908-T-C 17572028-T-C P5_Prx A*
19754929-C-T 17643049-C-T BY47219 P5_Prx A*
20689460-A-C 18527574-A-C P4_Prx A*
20765164-T-C 18603278-T-C P4_Prx A*
25948860-A-G 23802713-A-G P1_Y1 A*
56831785-A-G A*
4134485-A-C 4266444-A-C FT289 +
19479728-T-C 17367848-T-C FGC2741 M12421 YY+
21408781-C-A 19246895-C-A Z34817 Y+
21889822-T-TA 19727936-T-TA 9×A+
3336578-A-G 3468537-A-G +
5938859-T-C 6070818-T-C FT238860 +
6739678-T-C 6871637-T-C FT238970 YY+
7112191-GCTGT-G 7244150-GCTGT-G +
7198381-A-G 7330340-A-G FT239039 YY+
7314563-C-T 7446522-C-T FT239058 YY+
7472181-T-G 7604140-T-G FT239087 IR1_L +
7620209-A-C 7752168-A-C FT239107 YY+
9158364-TG-T 9320755-TG-T +
13225866-G-C 11070190-G-C FT441274 +
14700233-G-A 12588299-G-A FT239615 YY+
15500626-A-G 13388746-A-G FT36980 YY+
15648500-T-A 13536620-T-A FT239766 YY+
16236715-G-A 14124835-G-A FT239836 YY+
16313516-GAGCTCGCC-G 14201636-GAGCTCGCC-G +
19113552-T-C 17001672-T-C FT240320 YY+
19159567-C-A 17047687-C-A FT240328 YY+
20819058-G-A 18657172-G-A BY212588 P4_Gap +
21316922-C-T 19155036-C-T FT240458 YY+
21374350-G-A 19212464-G-A FT240475 YY+
21639837-G-A 19477951-G-A FT240530 YY+
21857549-T-C 19695663-T-C FT240570 YY+
22589423-T-A 20427537-T-A FT240651 YY+
23191543-A-G 21029657-A-G FT240725 Y+
23408741-T-A 21246855-T-A FT240751 YY+
23488085-C-T 21326199-C-T YY+
10892542-TCATTCCATTC-T *
10842500-AATTCCATTCC-A *
10760684-T-TTTCCATTCCA *
5549533-A-C 5681492-A-C *
10671541-A-G *
22275214-G-T 20113328-G-T BY40523 DYZ19 *
13702623-G-C 11546947-G-C BY48177 **
18492480-GA-G 16380600-GA-G P6_Dst 17×A**
7164467-CAAAAA-C 7296426-CAAAAA-C 24×A**
26097955-G-T 23951808-G-T P1_Y1 **
20943477-C-CTCTG 18781591-C-CTCTG P4_Dst 12×TG**
26073086-G-T 23926939-G-T P1_Y1 **
23899401-C-CGG 21737515-C-CGG 17×GT**
26393020-C-T 24246873-C-T P1_Y1 **
13628071-G-A 11472395-G-A **
13873366-A-T 11752660-A-T **
5936162-A-C 6068121-A-C **
21555215-G-A 19393329-G-A **
18095736-A-G 15983856-A-G **
13459140-C-A 11303464-C-A **
3145285-A-G 3277244-A-G **
3432982-A-AGG 3564941-A-AGG **
4848369-T-C 4980328-T-C **
5342426-A-G 5474385-A-G **
13416891-G-A 11261215-G-A **
13453268-C-A 11297592-C-A **
13459161-C-T 11303485-C-T **
13467933-GT-G 11312257-GT-G **
14375011-A-AAG 12254307-A-AAG **
15739310-A-G 13627430-A-G **
19829299-CTTT-C 17717419-CTTT-C P5_Prx 27×T**
21502036-T-C 19340150-T-C **
22438740-A-C 20276854-A-C FT396992 DYZ19 **
22622432-G-A 20460546-G-A **
56756803-C-T **
7195227-CAA-C,CAAA 7327186-CAA-C,CAAA 17×A***
14324894-CTTTTT-C 12204188-CTTTTT-C 26×T***
8888375-CTTT-C 9020334-CTTT-C 25×T***
17064838-G-A 14952958-G-A ***
3080986-T-TA 3212945-T-TA 10×A***
17064841-G-A 14952961-G-A ***
15422964-T-TC 13311084-T-TC ***
5400468-CT-C,CTT 5532427-CT-C,CTT 19×T***
10896442-C-CT,CTTT ***
56828814-C-T ***
17093304-G-GTA 14981424-G-GTA ***
6489371-CAAAA-C 6621330-CAAAA-C 25×A***
4932707-TTGTG-T,TTG 5064666-TTGTG-T,TTG 17×TG***
3612043-A-G 3744002-A-G ***
4791288-A-G 4923247-A-G ***
4982523-ATTTT-A,ATTT 5114482-ATTTT-A,ATTT 23×T***
5572477-T-TC 5704436-T-TC ***
5572478-T-C 5704437-T-C ***
7115207-C-G 7247166-C-G ***
10080030-T-C 10242421-T-C ***
13323518-AT-A,T 11167842-AT-A,T ***
15462498-G-A 13350618-G-A ***
16675938-C-T 14564058-C-T ***
17064836-G-A 14952956-G-A ***
17064837-G-A 14952957-G-A ***
17064843-G-A 14952963-G-A ***
17064847-G-A 14952967-G-A ***
17064848-G-A 14952968-G-A ***
17064849-G-A 14952969-G-A ***
17064850-G-A 14952970-G-A ***
17065393-T-C 14953513-T-C ***
22210896-T-C 20049010-T-C ***
22287318-T-C 20125432-T-C DYZ19 ***
22340848-G-T 20178962-G-T DYZ19 ***

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.