Big Tree: Person Data

Tree Position

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)	Names	Region	McDonald BED	combBED	1kG HG00181
3287711-G-A	3419670-G-A	Z18340				+
3422900-C-T	3554859-C-T	ZS2681				+
3481521-A-C	3613480-A-C	FT15328				+
3564730-G-A	3696689-G-A	ZS250				+
3984395-A-G	4116354-A-G	ZS2682				+
4121098-T-C	4253057-T-C	ZS254				+
4574089-C-G	4706048-C-G	Z18341				+
4689237-A-G	4821196-A-G	ZS2683				+
4939235-A-C	5071194-A-C	ZS2684				+
5525222-T-C	5657181-T-C	ZS2686				+
5597013-G-A	5728972-G-A	Z18342				+
5699479-T-C	5831438-T-C	Z18343				+
6032959-C-T	6164918-C-T	ZS2687				+
6190221-G-T	6322180-G-T	ZS2688	IR3_Dst			+
6353596-G-T	6485555-G-T	ZS2689				+
6716702-G-T	6848661-G-T	Y4066 Z18299		Y	Y	+
6858457-G-A	6990416-G-A	ZS2690		Y	Y	+
6932106-A-T	7064065-A-T	L816		Y	Y	+
6932171-G-C	7064130-G-C	L817		Y	Y	+
7112172-T-C	7244131-T-C	Y4090 Z18300		Y	Y	+
7315596-G-A	7447555-G-A	Y4091 Z18301		Y	Y	+
7523230-T-G	7655189-T-G	Y4092 Z18302		Y	Y	+
7936637-A-G	8068596-A-G	ZS2691		Y	Y	+
8073176-G-A	8205135-G-A	Z18345		Y		+
8357649-G-A	8489608-G-A	ZS252		Y	Y	+
8393759-A-G	8525718-A-G	Y4067 Z18303		Y	Y	+
8669042-T-C	8801001-T-C	Z18346		Y		+
8825317-C-T	8957276-C-T	ZS2692		Y		+
8847052-C-T	8979011-C-T	Y4069 Z18305		Y	Y	+
9758788-C-T	9921179-C-T	Y4070 Z18306		Y		+
13397026-G-A	11241350-G-A	ZS2693				+
13482493-G-T	11326817-G-T	ZS2694				+
13806772-G-A	11686066-G-A	Y4071 Z18307				+
13945130-G-A	11824424-G-A	Y4072 Z18308		Y	Y	+
14405428-G-A	12284725-G-A	Y4074 Z18309		Y	Y	+
14628879-T-C	12516947-T-C	S4940		Y	Y	+
14668247-A-C	12556313-A-C	Z18348		Y		+
14794737-C-T	12682808-C-T	Z18349		Y		+
14938482-C-T	12826557-C-T	ZS2696		Y	Y	+
14980067-A-G	12868143-A-G	S4932		Y	Y	+
15086779-C-T	12974869-C-T	ZS2697		Y	Y	+
15465507-G-A	13353627-G-A	S4924		Y	Y	+
15620119-C-G	13508239-C-G	Y4075 ZS251		Y	Y	+
15752320-C-T	13640440-C-T	S4966		Y	Y	+
15855262-C-T	13743382-C-T	ZS2698		Y		+
16010699-C-A	13898819-C-A	Z18350		Y		+
16197875-T-G	14085995-T-G	ZS2699		Y	Y	+
16308123-A-G	14196243-A-G	Y4076 ZS262		Y	Y	+
16364855-G-A	14252975-G-A	S5014		Y	Y	+
16455010-C-T	14343130-C-T	S4926		Y	Y	+
16502002-T-G	14390122-T-G	ZS2700		Y		+
16528614-T-C	14416734-T-C	S4950		Y	Y	+
16566686-G-A	14454806-G-A	Y4080 Z18311		Y	Y	+
16960553-C-A	14848673-C-A	Y4077 ZS261		Y	Y	+
16970191-G-A	14858311-G-A	Y4078 Z18313		Y	Y	+
17058575-A-G	14946695-A-G	S4927		Y		+
17377325-G-C	15265445-G-C	Z18351		Y		+
17498885-G-T	15387005-G-T	Z18352		Y	Y	+
17534100-A-G	15422220-A-G	ZS2702		Y	Y	+
17534330-A-T	15422450-A-T	S4923		Y	Y	+
17660960-T-C	15549080-T-C	S4925		Y	Y	+
17813203-G-A	15701323-G-A	Z18353		Y		+
18149930-A-G	16038050-A-G	S4998		Y	Y	+
18631893-A-T	16520013-A-T	Z18354		Y	Y	+
18872509-G-A	16760629-G-A	S4941		Y	Y	+
18982806-C-A	16870926-C-A	Y4093 ZS259		Y	Y	+
19136821-A-G	17024941-A-G	S4972 L818		Y	Y	+
19165653-A-G	17053773-A-G	Y4082 Z18315		Y		+
19558746-T-C	17446866-T-C	Y4064		Y		+
21356711-C-T	19194825-C-T	Y4065 Z18317		Y	Y	+
21391792-G-A	19229906-G-A	Y4083 Z18319		Y	Y	+
21591788-G-A	19429902-G-A	Y4085 Z18321		Y	Y	+
21612896-A-G	19451010-A-G	Y4086 Z18322		Y	Y	+
21628992-C-T	19467106-C-T	S4944		Y	Y	+
21731783-T-A	19569897-T-A	S4960		Y	Y	+
21770336-C-T	19608450-C-T	ZS2706		Y		+
21971214-A-G	19809328-A-G	Y4087 Z18323		Y	Y	+
22130103-G-T	19968217-G-T	ZS2707		Y	Y	+
22273035-C-G	20111149-C-G	Z18325	DYZ19			+
22280434-A-C	20118548-A-C	Z18326	DYZ19			+
22318766-A-T	20156880-A-T	Z18327	DYZ19			+
22441860-G-T	20279974-G-T	BY45480	DYZ19			+
22472849-T-A	20310963-T-A	Y4097 Z18334	DYZ19			+
22486835-C-T	20324949-C-T	BY26577	DYZ19			+
22962878-T-C	20800992-T-C	ZS2708		Y	Y	+
23141944-G-C	20980058-G-C	Y4088 Z18337		Y	Y	+
23248851-A-G	21086965-A-G	S4985		Y	Y	+
23383273-A-C	21221387-A-C	S4935		Y	Y	+
23444137-G-A	21282251-G-A	ZS2709		Y	Y	+
23497002-T-C	21335116-T-C	S4951		Y	Y	+
28634988-T-C	26488841-T-C	Z18355				+
28809213-A-T	26663066-A-T	ZS2711				+

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.

1k Genomes

Tree Position

Unique Mutations