Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > DF21/S192 > S5488 > Z16294 > BY11121 > Z16281 > A14023

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	STR	FTDNA 454093
2783091-C-A	2915050-C-A		FGC63588		Y	Y		+
2784750-G-C	2916709-G-C		FGC63589		Y	Y		+
6787176-G-A	6919135-G-A		BY14547 FGC63590		Y	Y		+
7721167-C-A	7853126-C-A		FGC63591		Y	Y		+
7739131-T-C	7871090-T-C		BY14548 FGC63592		Y	Y		+
7979383-C-T	8111342-C-T		BY14549 FGC63593		Y	Y		+
8169533-G-T	8301492-G-T		BY14550 FGC63594		Y	Y		+
8428703-T-A	8560662-T-A		BY14551 FGC63595		Y	Y		+
8580058-T-C	8712017-T-C		BY14552 FGC63596		Y	Y		+
8887985-C-T	9019944-C-T		BY14553 FGC63597			Y		+
9434936-G-C	9597327-G-C		FGC63598		Y	Y		+
13844275-G-T	11723569-G-T		BY14554 FGC63600					+
14817911-C-T	12705982-C-T		BY14555 FGC63602		Y	Y		+
15261453-C-G	13149537-C-G		BY14556 FGC63603		Y	Y		+
15391972-T-C	13280092-T-C		BY14557 FGC63604		Y	Y		+
15752554-A-T	13640674-A-T		BY14558 FGC63605		Y	Y		+
16582848-T-A	14470968-T-A		BY14559 FGC63606		Y	Y		+
16806781-C-A	14694901-C-A		BY14560 FGC63607		Y	Y		+
17194910-T-G	15083030-T-G		BY14561 FGC63608		Y	Y		+
17206225-C-T	15094345-C-T		BY14562 FGC63609		Y	Y		+
17686406-G-C	15574526-G-C		BY14563 FGC63610		Y	Y		+
18760630-G-T	16648750-G-T		FGC63611		Y	Y		+
21131568-T-C	18969682-T-C		BY14564 FGC63613		Y	Y		+
21292123-A-C	19130237-A-C		BY14565 FGC63614		Y	Y		+
21688330-G-A	19526444-G-A		BY14566 FGC63615		Y	Y		+
21723793-A-C	19561907-A-C		BY14567 FGC63616		Y	Y		+
21841596-G-A	19679710-G-A		BY14568 FGC63617		Y			+
22270733-T-A	20108847-T-A		BY14569 FGC63618	DYZ19				+
22439828-G-T	20277942-G-T		BY218680	DYZ19				+
22470101-G-C	20308215-G-C		BY14570 FGC63619	DYZ19				+
22470854-G-C	20308968-G-C	FTA19354	FGC63620 BY43954	DYZ19				+
22679474-A-G	20517588-A-G		FGC63621		Y	Y		+
4374593-A-G	4506552-A-G		BY58134					**
9937466-TG-T	10099857-TG-T							**
19966688-AAAGAAGAAGAAG-A,AAAG	17854808-AAAGAAGAAGAAG-A,AAAG			P5_Prx			26×AAG	***
21152835-G-A	18990949-G-A							***
13826366-T-G	11705660-T-G		FTA52579					***
9997026-A-G	10159417-A-G							***
13483199-G-T	11327523-G-T							***
13735407-A-C	11579731-A-C							***
13858249-C-A,G	11737543-C-A,G							***
18308777-C-A	16196897-C-A			P6_Prx				***
19952898-C-T	17841018-C-T			P5_Prx				***
21153016-A-AT,T	18991130-A-AT,T							***
22453827-G-C	20291941-G-C			DYZ19				***
24289436-A-T	22143289-A-T			P3_t1				***
25126083-T-C	22979936-T-C			g1				***
25150253-T-C	23004106-T-C			g1				***
25261194-T-C	23115047-T-C			P2_r1				***
26603665-C-G	24457518-C-G			P1_g2				***

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.