Tree Position

R-U106/S21 > Z2265 > Z18 > Z372/S375 > S3207 > S5676 > S5681 > S5678 > BY39556

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 102416
13620825-G-A	11465149-G-A		PF4903					**
16605142-C-A	14493262-C-A		CTS6003					**
10062719-G-C	10225110-G-C							**
13132141-C-T	10621627-C-T							**
17540740-C-T	15428860-C-T		CTS7565 M5960 PF4566					**
18229824-C-A	16117944-C-A		PF4035 CTS8830					**
7647357-A-G	7779316-A-G							***
15581983-G-A	13470103-G-A							***
22246669-A-G	20084783-A-G		FGC465	DYZ19				***
22369541-A-C	20207655-A-C			DYZ19				***
23714362-C-G	21552476-C-G		E739					***
28755152-C-T	26609005-C-T		CTS12937					***
9350090-C-T	9512481-C-T		FGC46095					***
8032311-G-A	8164270-G-A		Z526 FGC3945					***
22024891-CA-C	19863005-CA-C							***
6955868-A-C	7087827-A-C		PF6153 F886					***
13848122-T-C	11727416-T-C		PF1619					***
8222299-T-C	8354258-T-C		L403 FGC1573					***
8590752-C-T	8722711-C-T		PF3526 P127					***
14144593-A-G	12023887-A-G		PF3536 P129					***
15277466-G-A	13165555-G-A		YSC0001275 PF4543 CTS3936					***
16839810-C-T	14727930-C-T		FGC1575 CTS6349					***
16966024-T-C	14854144-T-C		FGC1577 F2345					***
17200869-G-A	15088989-G-A		FGC1565 CTS6932					***
18567169-T-G	16455289-T-G		PF4577 CTS8938					***
21329083-T-C	19167197-T-C		YSC0001314 PF4592 F3176					***
23088142-T-C	20926256-T-C		YSC0000236 PF4616 L778					***
9983963-CA-T	10146354-CA-T							***
15055079-A-T	12943170-A-T		Y1885 FGC1581 CTS3597					***
6826507-A-AG	6958466-A-AG							***
9895438-G-A	10057829-G-A		BY47563					***
14393681-C-A	12272977-C-A		CTS2622 Z1827					***
16535337-C-T	14423457-C-T		Z601 AM01365					***
19449428-GAAAAAAA-G	17337548-GAAAAAAA-G						23×A	***
10006933-C-G	10169324-C-G							***
8878325-A-C	9010284-A-C		BY76565					***
14173493-C-T	12052787-C-T		Y66089					***
16851946-C-T	14740066-C-T		BY110578					***
18716802-A-C	16604922-A-C		BY123369					***
22217456-T-G	20055570-T-G			DYZ19				***
22278969-T-C	20117083-T-C			DYZ19				***
23054731-C-A	20892845-C-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.