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 HG00096
20105742-TTATC-T	17993862-TTATC-T			P5_Dst			14×TATC	+
28787589-A-G	26641442-A-G							+
58873456-A-G	56717415-T-C							+
13384812-G-A	11229136-G-A		BY15623					+
21807789-G-A	19645903-G-A	L705	Z16411		Y	Y	8×T	+
28571522-G-A	26425375-G-A		CTS12305					+
58837383-G-A	56753488-C-T							+
58880540-G-A	56710331-C-T							+
16344414-T-TTCTTCA	14232534-T-TTCTTCA							+
13456019-GATTCC-G	11300343-GATTCC-G						11×ATTCC	+
10104554-N-T	10266945-N-T							+
10104555-N-A	10266946-N-A							+
10104557-N-A	10266948-N-A							+
58871362-C-A	56719509-G-T							+
58871385-T-C	56719486-A-G							+
58871345-T-C	56719526-A-G							+
13618508-T-A	11462832-T-A							+
28802841-T-C	26656694-T-C							+
13346809-C-T	11191133-C-T							+
24388090-A-ATG	22241943-A-ATG							+
13139021-C-CA	10628507-C-CA							+
13311579-A-G	11155903-A-G							+
58842502-C-T	56748369-G-A							+
5941845-T-C	6073804-T-C							+
6648613-C-T	6780572-C-T				Y	Y	27×T	+
14866163-A-G	12754233-A-G		BY98097		Y	Y		+
19146569-C-T	17034689-C-T				Y	Y	28×T	+
14866140-C-T	12754206-C-T				Y	Y	11×GT	+
15799114-CCCTT-TCCTC	13687234-CCCTT-TCCTC						14×CCTT	+
19146564-C-T	17034684-C-T				Y	Y		+
28698742-GCTT-ACTC	26552595-GCTT-ACTC							+
9847274-A-T	10009665-A-T				Y	Y		+
15023555-A-C	12911643-A-C		S16678 F11578		Y	Y		+
8119489-G-T	8251448-G-T		BY70093		Y	Y	14×T	+
17841374-A-C	15729494-A-C		S20279		Y	Y		+
17479396-C-A	15367516-C-A				Y	Y	13×A	+
22093164-G-T	19931278-G-T		FT306469		Y	Y		+
6860621-A-G	6992580-A-G		Y15 F46		Y	Y		+
6941518-C-T	7073477-C-T		S9647		Y	Y		+
8486164-C-A	8618123-C-A		Z31722		Y	Y		+
9804357-A-G	9966748-A-G				Y			+
17836380-C-G	15724500-C-G				Y			+
18200505-C-A	16088625-C-A				Y	Y		+
21476078-G-A	19314192-G-A		S3682		Y			+
22155320-G-A	19993434-G-A		S3684		Y			+
13222618-AGAGG-A	11066942-AGAGG-A							+
58877533-T-C	56713338-A-G							+
13222637-A-G	11066961-A-G							+
13294189-T-C	11138513-T-C							+
58871191-C-T	56719680-G-A							+
58871199-G-C	56719672-C-G							+
58878324-C-T	56712547-G-A							+
58894426-G-A	56696445-C-T							+
13747514-T-A	11591838-T-A							+
13741945-A-T	11586269-A-T							+
13747547-A-T	11591871-A-T							+
13738513-A-T	11582837-A-T							+
22005442-A-C	19843556-A-C				Y	Y		+
15037755-A-AGC	12925845-A-AGC							+
24425339-G-GCATT	22279192-G-GCATT							+
24425341-A-ATGCG	22279194-A-ATGCG							+
22272934-CTT-C	20111048-CTT-C			DYZ19				+
24447135-G-GAAAA	22300988-G-GAAAA							+
24447150-A-AGAAG	22301003-A-AGAAG						4×AAAG	+
24408989-TG-T	22262842-TG-T							+
13446679-CCATT-C	11291003-CCATT-C							+
24425343-G-GCATT	22279196-G-GCATT							+
13746345-A-C	11590669-A-C							+
13641262-C-T	11485586-C-T							+
13641268-T-C	11485592-T-C							+
59027475-A-AAAAG	56881328-A-AAAAG							+
13141762-GCCATTCCATT-G	10631248-GCCATTCCATT-G						11×CCATT	+
2758861-AGAAGAAG-A	2890820-AGAAGAAG-A							+
2903232-CTCCTTCCTTCCTTCCTTCCTTCCT-C	3035191-CTCCTTCCTTCCTTCCTTCCTTCCT-C						18×TCCT	+
3171959-T-A	3303918-T-A		ZS448					+
3226950-C-T	3358909-C-T							+
3256136-CTAT-C	3388095-CTAT-C							+
3434302-A-T	3566261-A-T							+
3572648-A-G	3704607-A-G							+
3572650-T-C	3704609-T-C							+
3628012-A-T	3759971-A-T						14×T	+
3727485-T-C	3859444-T-C							+
4098684-G-A	4230643-G-A							+
4179019-AT-A	4310978-AT-A							+
4261308-C-T	4393267-C-T							+
4288455-A-C	4420414-A-C							+
4293797-G-T	4425756-G-T							+
4320933-G-A	4452892-G-A							+
4390157-A-T	4522116-A-T							+
4396184-C-T	4528143-C-T							+
4489282-T-A	4621241-T-A							+
4682803-T-C	4814762-T-C		Y1360					+
5043420-C-T	5175379-C-T							+
5215599-C-T	5347558-C-T		FT78366					+
5225316-ATG-A	5357275-ATG-A							+
5268741-G-A	5400700-G-A							+
5503843-C-T	5635802-C-T							+
5691763-C-A	5823722-C-A							+
5702618-AAC-A	5834577-AAC-A							+
5702619-AC-A	5834578-AC-A							+
5962108-TCATA-T	6094067-TCATA-T							+
6454542-A-C	6586501-A-C							+
6769276-C-T	6901235-C-T				Y	Y		+
7025769-A-T	7157728-A-T				Y			+
7033240-C-A	7165199-C-A				Y		15×A	+
7160877-A-C	7292836-A-C				Y	Y		+
7200292-C-T	7332251-C-T				Y			+
7265849-A-G	7397808-A-G				Y	Y		+
7474427-A-G	7606386-A-G			IR1_L				+
7915372-A-C	8047331-A-C				Y	Y		+
8281028-T-C	8412987-T-C				Y	Y		+
8748601-T-A	8880560-T-A				Y	Y		+
8875443-G-T	9007402-G-T					Y		+
9307402-G-GTT	9469793-G-GTT							+
9307403-T-TTC	9469794-T-TTC							+
9650328-T-C	9812719-T-C		BY157660	IR3_Prx				+
9941960-T-G	10104351-T-G				Y			+
10006625-A-C	10169016-A-C				Y			+
10104556-N-G	10266947-N-G							+
10104558-N-T	10266949-N-T							+
10104559-N-C	10266950-N-C							+
10104560-N-G	10266951-N-G							+
13222616-GGAGA-G	11066940-GGAGA-G							+
13255133-G-T	11099457-G-T							+
13260605-TTC-T	11104929-TTC-T							+
13275119-A-G	11119443-A-G							+
13311501-G-A	11155825-G-A							+
13322986-T-TTTC	11167310-T-TTTC							+
13334362-G-C	11178686-G-C							+
13383888-T-G	11228212-T-G							+
13388103-A-G	11232427-A-G							+
13388173-T-C	11232497-T-C							+
13414762-T-A	11259086-T-A							+
13414853-G-A	11259177-G-A							+
13415224-G-A	11259548-G-A							+
13431505-T-C	11275829-T-C							+
13447117-C-T	11291441-C-T							+
13500604-A-T	11344928-A-T							+
13500639-C-T	11344963-C-T							+
13500658-T-A	11344982-T-A							+
13535681-ATG-A	11380005-ATG-A						9×TG	+
13602316-C-G	11446640-C-G							+
13622184-G-T	11466508-G-T							+
13622191-C-T	11466515-C-T							+
13686909-ACACG-A	11531233-ACACG-A							+
13738889-A-G	11583213-A-G							+
13853311-T-A	11732605-T-A		Y29262					+
13859440-G-C	11738734-G-C							+
13931735-C-T	11811029-C-T				Y			+
13931739-C-T	11811033-C-T				Y		22×T	+
13960892-T-C	11840186-T-C				Y			+
14015392-T-G	11894686-T-G				Y			+
14025561-G-GAAAA	11904855-G-GAAAA							+
14063655-G-C	11942949-G-C		CTS1777		Y	Y		+
14102397-C-CTATG	11981691-C-CTATG							+
14537957-T-C	12426158-T-C				Y	Y		+
14881732-GTA-G	12769800-GTA-G							+
14986717-TGCAC-T	12874785-TGC-T							+
15263363-T-TAAA	13151453-T-TAAA							+
15276900-AG-A	13164989-AG-A							+
15305888-T-TAATAG	13193990-T-TAATAG						11×AG	+
15305889-AG-A	13193991-AG-A							+
15329065-C-T	13217183-C-T		CTS4003		Y	Y		+
15379781-C-T	13267901-C-T				Y			+
15557159-ATATT-A	13445279-ATATT-A							+
15882099-AG-A	13770219-AG-A							+
16021881-C-CT	13910001-C-CT							+
16244821-GTGTA-G	14132941-GTGTA-G							+
16406824-G-T	14294944-G-T				Y	Y		+
16406852-TA-T	14294972-TA-T							+
16986067-G-T	14874187-G-T				Y	Y		+
17026006-C-T	14914126-C-T		CTS6639		Y			+
17129928-C-T	15018048-C-T		PH2842		Y	Y		+
17281981-AGAT-A	15170101-AGAT-A							+
17500836-T-G	15388956-T-G		M8509		Y			+
17515601-AG-A	15403721-AG-A							+
17807478-C-T	15695598-C-T		A14348 YFS1251050		Y	Y		+
17836370-C-A	15724490-C-A				Y			+
17946919-G-GTTT	15835039-G-GTTT						24×T	+
18393269-T-TATC	16281389-T-TATC			P6_Gap				+
18653646-T-A	16541766-T-A				Y	Y		+
19049508-A-ATAT	16937628-A-ATAT							+
19202764-AC-A	17090884-AC-A							+
19386785-TA-T	17274905-TA-T							+
19411950-GAA-G	17300070-GAA-G							+
19415501-C-T	17303621-C-T		Y8743 FGC22598		Y	Y		+
20815452-TAC-T	18653566-TAC-T			P4_Gap				+
21058022-A-G	18896136-A-G				Y			+
21146293-G-T	18984407-G-T				Y	Y		+
21170322-T-G	19008436-T-G				Y	Y		+
21170326-T-G	19008440-T-G				Y	Y		+
21170346-C-T	19008460-C-T				Y	Y		+
21248052-A-G	19086166-A-G		Z34577		Y			+
21330646-C-T	19168760-C-T				Y	Y		+
21435381-GT-G	19273495-GT-G							+
21622674-G-T	19460788-G-T		Z5701		Y	Y	9×T	+
22475864-G-A	20313978-G-A		BY223450	DYZ19				+
23208766-A-T	21046880-A-T				Y			+
23364907-C-A	21203021-C-A				Y	Y		+
23829792-G-A	21667906-G-A		M4658			Y		+
23898750-C-T	21736864-C-T							+
24408990-GA-G	22262843-GA-G							+
24600498-TTC-T	22454351-TTC-T			P3_t2				+
24600509-T-C	22454362-T-C			P3_t2				+
24895715-G-T	22749568-G-T			g1				+
27399223-A-G	25253076-A-G			P1_g3				+
27399225-G-A	25253078-G-A			P1_g3				+
27454144-G-C	25307997-G-C			P1_Y2				+
28478036-TATAG-T	26331889-TATAG-T							+
28611428-G-A	26465281-G-A							+
28620602-G-GA	26474455-G-GA							+
28628428-ATATATT-A	26482281-ATATATT-A							+
28628430-ATATT-A	26482283-ATATT-A							+
28628432-ATT-A	26482285-ATT-A							+
28642837-C-G	26496690-C-G		M3959					+
28663199-A-T	26517052-A-T							+
28686464-C-A	26540317-C-A							+
28698846-A-G	26552699-A-G							+
28734730-ACTGAG-A	26588583-ACTGAG-A							+
58873959-T-C	56716912-A-G							+
59001389-AAAG-A	56855242-AAAG-A							+
59009233-C-CCAAA	56863086-C-CCAAA							+
59009240-AAC-A	56863093-AAC-A							+
59009241-AC-A	56863094-AC-A							+
59026874-C-CT	56880727-C-CT							+
59032459-G-A	56886312-G-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	14026048-AAG-A	11905342-AAG-A	2 reads, both show the deletion.
Manual	21859032-C-CA	19697146-C-CA	One read, it has the insertion.
Manual	22069403-T-C	19907517-T-C	One read, a C.
Manual	22121805-G-A	19959919-G-A	No coverage.
Manual	22285033-G-A	20123147-G-A	8 reads. 3 are A, 5 are G.
Manual	22323252-G-A	20161366-G-A	3 reads. 1 A and 2 G.
Manual	17379207-C-T	15267327-C-T	1T
Manual	2991752-C-T	3123711-C-T	2T
Manual	17542453-G-T	15430573-G-T	2 reads, both T.
Manual	13357060-G-A	11201384-G-A	1G 3A
Manual	5790021-T-C	5921980-T-C	4C
Manual	9514974-G-A	9677365-G-A	1A
Manual	5563777-C-CA	5695736-C-CA	Both reads show the insertion.
Manual	16842867-ATGTGTGTGTGTGTGTGTGTG-A	14730987-ATGTGTGTGTGTGTGTGTGTG-A	1 read show the deletion.
Manual	4439911-TGCAGCTTCACTCCTGAGG-T	4571870-TGCAGCTTCACTCCTGAGG-T	Just one read, it's positive.
Manual	22443795-T-A	20281909-T-A	2T 3A
Manual	13675388-G-A	11519712-G-A	1A, but it is at the very end of a read.
Manual	14743395-A-T	12631463-A-T	3T, one of which has poor quality.
Manual	23817310-A-T	21655424-A-T	Both reads positive.
Manual	23817307-C-CT	21655421-C-CT	Both reads positive.
Manual	4997085-T-A	5129044-T-A	1A

1k Genomes

Tree Position

Unique Mutations

Mutation Notes: