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)	Blocks	Names	Region	McDonald BED	combBED	STR	1kG HG00103	Manual Edits
13845538-G-A	11724832-G-A							+
15353851-G-T	13241970-G-T		CTS4044		Y	Y		+
13931739-C-T	11811033-C-T				Y		22×T	+
14101407-C-T	11980701-C-T		CTS1863		Y	Y		+
14729321-A-T	12617389-A-T				Y	Y		+
14760882-C-T	12648951-C-T				Y			+
14848351-G-A	12736417-G-A		CTS3340		Y	Y		+
15047302-TG-T	12935393-TG-T							+
15123165-C-A	13011252-C-A				Y	Y		+
15554944-G-A	13443064-G-A				Y	Y		+
13873187-G-T	11752481-G-T				Y			+
15737506-A-C	13625626-A-C				Y	Y		+
16242401-GCT-G	14130521-GCT-G							+
16248072-A-C	14136192-A-C				Y	Y		+
16257958-T-C	14146078-T-C				Y	Y		+
16710922-A-G	14599042-A-G				Y	Y		+
16729170-A-T	14617290-A-T		M12048		Y	Y		+
16729171-CGTT-C	14617291-CGTT-C							+
13931735-C-T	11811029-C-T				Y			+
13840815-C-G	11720109-C-G		Y133466				9×GAATG	+
16813105-ACG-A	14701225-ACG-A							+
13500003-C-T	11344327-C-T							+
13267454-G-A	11111778-G-A							+
13273818-A-G	11118142-A-G							+
13305685-G-A	11150009-G-A							+
13307070-G-T	11151394-G-T							+
13379781-G-A	11224105-G-A							+
13382987-C-T	11227311-C-T							+
13411536-G-T	11255860-G-T							+
13500074-C-A	11344398-C-A							+
13691813-A-AATGGC	11536137-A-AATGGC							+
13500077-C-G	11344401-C-G							+
13508867-T-C	11353191-T-C							+
13621171-G-C	11465495-G-C							+
13636131-A-G	11480455-A-G							+
13636145-C-T	11480469-C-T							+
13691802-G-GAATGC	11536126-G-GAATGC							+
13691811-G-GGAATT	11536135-G-GGAATT							+
16786235-TC-T	14674355-TC-T							+
17322927-G-A	15211047-G-A		Y1090		Y	Y		+
10091676-G-GAATT	10254067-G-GAATT							+
28522394-TG-T	26376247-TG-T							+
23584011-C-T	21422125-C-T				Y	Y		+
23901432-N-G	21739546-N-G							+
24386328-T-C	22240181-T-C							+
24480646-A-T	22334499-A-T					Y		+
26508182-C-T	24362035-C-T		FGC8528	P1_Y1				+
28485487-C-T	26339340-C-T							+
28490934-G-A	26344787-G-A							+
28571435-CTT-C	26425288-CTT-C							+
23479934-A-T	21318048-A-T		BY145589		Y	Y		+
28571474-C-T	26425327-C-T							+
28595390-C-G	26449243-C-G		CTS12491					+
28595406-A-G	26449259-A-G		CTS12492					+
28595450-C-A	26449303-C-A		CTS12493					+
28595452-A-G	26449305-A-G		CTS12494					+
28726834-C-T	26580687-C-T					Y		+
28802738-G-C	26656591-G-C							+
23541400-G-A	21379514-G-A				Y	Y		+
23128622-C-T	20966736-C-T		CTS11477		Y	Y		+
17872656-TG-T	15760776-TG-T							+
21170326-T-G	19008440-T-G				Y	Y		+
17923152-C-T	15811272-C-T				Y	Y		+
19387017-A-ATGTAT	17275137-A-ATGTAT							+
20803192-G-C	18641306-G-C			P4_Gap				+
21012234-A-T	18850348-A-T			P4_Dst	Y			+
21089752-T-C	18927866-T-C				Y	Y		+
21146297-C-A	18984411-C-A				Y	Y		+
21170322-T-G	19008436-T-G				Y	Y		+
21170346-C-T	19008460-C-T				Y	Y		+
23112705-C-G	20950819-C-G		CTS11438		Y	Y		+
21459021-C-A	19297135-C-A				Y			+
21502775-G-T	19340889-G-T				Y			+
21662606-A-G	19500720-A-G				Y	Y		+
21908671-C-T	19746785-C-T				Y	Y		+
22325240-C-G	20163354-C-G			DYZ19				+
22458007-T-A	20296121-T-A			DYZ19				+
22981818-G-A	20819932-G-A				Y			+
23106031-A-T	20944145-A-T				Y			+
13256166-C-T	11100490-C-T							+
9997062-C-A	10159453-C-A		F10492		Y			+
28571558-C-G	26425411-C-G		CTS12306					+
3272097-C-T	3404056-C-T							+
23507296-C-G	21345410-C-G				Y	Y		+
5354745-TACAC-T	5486704-TACAC-T							+
8445984-CC-GAAA	8577943-CC-GAAA	CTS750							+
13339812-G-A	11184136-G-A							+
2664162-C-T	2796121-C-T				Y	Y		+
2718877-C-T	2850836-C-T				Y	Y		+
3147666-C-T	3279625-C-T		Z8497					+
3342287-A-T	3474246-A-T						10×T	+
21889540-A-G	19727654-A-G				Y	Y		+
3342316-A-C	3474275-A-C							+
3554057-C-A	3686016-C-A						8×A	+
3554062-A-G	3686021-A-G							+
3554125-C-G	3686084-C-G							+
3604675-T-G	3736634-T-G							+
3830334-C-A	3962293-C-A						9×A	+
3830343-A-C	3962302-A-C		FGC7560					+
23061176-C-A	20899290-C-A				Y	Y		+
18846444-G-A	16734564-G-A		CTS9358		Y			+
4123990-C-A	4255949-C-A							+
28491035-T-C	26344888-T-C							+
28571522-G-A	26425375-G-A		CTS12305					+
28755163-C-T	26609016-C-T		CTS12938			Y		+
22715167-AG-A	20553281-AG-A							+
28630057-T-C	26483910-T-C		CTS12593					+
2898521-C-G	3030480-C-G				Y			+
2898533-G-T	3030492-G-T				Y			+
7218538-GAC-CAG	7350497-GAC-CAG							+
14737352-C-T	12625420-C-T				Y			+
15654923-A-G	13543043-A-G				Y	Y		+
28490956-C-T	26344809-C-T		CTS12136					+
2702974-A-AGTTTTTTTTTTTT	2834933-A-AGTTTTTTTTTTTT							+
19452278-A-T	17340398-A-T		CTS10428		Y	Y		+
19452295-G-T	17340415-G-T		CTS10429		Y	Y		+
2659133-T-G	2791092-T-G		CTS9 S3199		Y	Y		+
2803921-T-C	2935880-T-C		CTS197 S3200		Y	Y		+
7996735-C-T	8128694-C-T		B53		Y	Y		+
14366294-A-T	12245589-A-T		CTS2563		Y	Y		+
3902277-A-AT	4034236-A-AT							+
4152013-C-A	4283972-C-A							+
8971407-C-T	9133798-C-T							+
7774813-T-G	7906772-T-G				Y	Y		+
6438063-T-A	6570022-T-A							+
6992927-C-T	7124886-C-T		BY62773		Y	Y		+
7105122-C-A	7237081-C-A				Y	Y		+
7218477-G-C	7350436-G-C				Y	Y		+
7218538-G-C	7350497-G-C		BY184446		Y	Y		+
7218540-C-G	7350499-C-G				Y	Y		+
7581573-T-C	7713532-T-C		Z40735		Y	Y		+
8085460-G-A	8217419-G-A				Y	Y		+
6042023-A-T	6173982-A-T							+
8359497-A-G	8491456-A-G				Y	Y		+
8369847-G-A	8501806-G-A				Y			+
8467454-G-A	8599413-G-A		Z20313		Y	Y		+
8505964-G-A	8637923-G-A				Y	Y		+
8616588-C-T	8748547-C-T				Y	Y		+
8696020-G-T	8827979-G-T				Y	Y		+
8730021-G-A	8861980-G-A				Y	Y		+
6075821-C-T	6207780-C-T		Z3804					+
6042007-T-A	6173966-T-A						18×A	+
4165240-C-T	4297199-C-T							+
5495433-TG-T	5627392-TG-T							+
4293806-A-G	4425765-A-G							+
4571872-G-A	4703831-G-A							+
4580751-C-T	4712710-C-T							+
4640648-A-C	4772607-A-C							+
4742852-T-A	4874811-T-A							+
5092265-T-C	5224224-T-C							+
5254263-G-A	5386222-G-A		FGC29365					+
5495454-T-G	5627413-T-G							+
6013651-A-T	6145610-A-T							+
5512992-T-C	5644951-T-C							+
5539342-T-A	5671301-T-A							+
5754647-A-T	5886606-A-T							+
5768635-A-G	5900594-A-G							+
5831298-G-A	5963257-G-A							+
5964425-T-C	6096384-T-C							+
6006838-G-T	6138797-G-T							+
6006845-C-T	6138804-C-T							+
58985194-C-A	56839047-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.

Mutation Notes:

Kit	POSITION-REF-ALT (hg19)	POSITION-REF-ALT (hg38)	Note
Manual	3436073-T-C	3568032-T-C	5 reads, all C.
Manual	3436043-G-C	3568002-G-C	2 C reads, 1 A read.
Manual	7080571-C-T	7212530-C-T	2 good reads, both T.
Manual	8445984-CC-GAAA	8577943-CC-GAAA	It's an odd situation. I was checking for 8445984-C-A, but that's not what I found. There were two good reads, both showing the CC -> GAAA mutation.
Manual	8647188-G-T	8779147-G-T	One read, a T.
Manual	15713060-A-G	13601180-A-G	Two reads, both G.
Manual	18405442-G-T	16293562-G-T	No coverage.
Manual	21834863-A-T	19672977-A-T	5 reads, all T. This is a nasty junction between an AT repeat and a T repeat.
Manual	22462458-A-C	20300572-A-C	3 reads, all C.
Manual	23882406-T-C	21720520-T-C	No coverage.
Manual	25821433-G-A	23675286-G-A	2 reads, one A and one G. There's also one third read that seems misaligned.
Manual	26144006-G-T	23997859-G-T	One good read, a G. There is also one other misaligned read, that looks to be a poor match, but is a G also.
Manual	27028447-C-A	24882300-C-A	One read, an A.
Manual	8445983-T-TGA	8577942-T-TGA	In the BigY files, I think the mutations here are recorded as 8445983-T-TGA and 8445984-C-A. But I think it is more correctly reported as 8445984-CC-GAAA.
Manual	18090661-C-A	15978781-C-A	1A
Manual	6236579-C-G	6368538-C-G	2G
Manual	17572831-CCT-C	15460951-CCT-C	All 4 reads positive.
Manual	16718688-C-CAT	14606808-C-CAT	5 reads
Manual	22294679-A-T	20132793-A-T	4A 2T
Manual	27990846-G-C	25844699-G-C	2C
Manual	9028082-CT-C	9190473-CT-C	Just two reads coverage, but both carry the deletion.
Manual	22273433-G-C	20111547-G-C	2C

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Tree Position

Unique Mutations

Mutation Notes: