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 HG02436
22962402-C-T	20800516-C-T				Y	Y		+
59033093-T-C	56886946-T-C							+
9654341-A-AGAT	9816732-A-AGAT			IR3_Prx				+
3152180-A-G	3284139-A-G		BY41572					+
14170816-C-A	12050110-C-A				Y	Y	15×A	+
8498889-TTG-T	8630848-TTG-T							+
17836401-T-G	15724521-T-G		CTS8102		Y			+
9985414-C-CT	10147805-C-CT							+
14604589-TC-T	12492791-TC-T							+
3161695-A-G	3293654-A-G		BY11553					+
18964263-G-A	16852383-G-A				Y	Y		+
9857394-G-GA	10019785-G-GA						8×A	+
13503733-C-T	11348057-C-T							+
21894650-T-A	19732764-T-A				Y	Y		+
17804172-G-A	15692292-G-A	S3781	CTS8035 S3786		Y	Y		+
13503964-T-C	11348288-T-C							+
13503969-A-C	11348293-A-C							+
7758719-G-T	7890678-G-T				Y			+
22970326-A-T	20808440-A-T				Y	Y		+
14696029-G-A	12584095-G-A				Y	Y		+
22970334-C-T	20808448-C-T				Y	Y		+
22976322-A-C	20814436-A-C		M9371		Y	Y		+
14776960-T-G	12665029-T-G				Y	Y		+
2718877-C-T	2850836-C-T				Y	Y		+
3039840-T-C	3171799-T-C							+
3086855-A-G	3218814-A-G							+
3146745-T-C	3278704-T-C							+
3161701-T-G	3293660-T-G							+
3171862-T-A	3303821-T-A							+
3444239-G-C	3576198-G-C							+
3444392-T-C	3576351-T-C							+
3511100-T-C	3643059-T-C							+
3542532-C-T	3674491-C-T		FTB50829					+
3545949-T-C	3677908-T-C		FTA2849					+
3586633-T-C	3718592-T-C							+
3628735-AG-A	3760694-AG-A							+
3696248-A-G	3828207-A-G							+
3701685-C-T	3833644-C-T							+
3827144-G-A	3959103-G-A							+
3850621-C-A	3982580-C-A		FGC1588					+
3875652-A-G	4007611-A-G							+
3916097-C-A	4048056-C-A		FGC3548					+
4114449-GAC-G	4246408-GAC-G							+
4234761-G-A	4366720-G-A							+
4456600-C-T	4588559-C-T							+
4755444-C-T	4887403-C-T		S8945					+
4755616-A-T	4887575-A-T							+
4819600-T-G	4951559-T-G							+
4953848-G-GTGTT	5085807-G-GTGTT							+
4964911-T-A	5096870-T-A							+
4986981-C-T	5118940-C-T							+
5035557-ATT-A	5167516-ATT-A							+
5150815-A-G	5282774-A-G							+
5525823-A-G	5657782-A-G							+
5630797-T-C	5762756-T-C							+
5770338-C-CTTT	5902297-C-CTTT						25×T	+
5786634-C-A	5918593-C-A							+
5906857-GCA-G	6038816-GCA-G							+
5998402-A-G	6130361-A-G							+
6024535-CTT-C	6156494-CTT-C							+
6040848-C-A	6172807-C-A							+
6091007-G-T	6222966-G-T							+
6108936-G-T	6240895-G-T							+
6401812-C-T	6533771-C-T							+
6517668-A-G	6649627-A-G							+
6684205-C-CAAAA	6816164-C-CAAAA						31×A	+
6776551-G-T	6908510-G-T		M12028		Y	Y		+
6776566-G-T	6908525-G-T				Y	Y		+
6858564-T-G	6990523-T-G				Y	Y		+
6931809-C-T	7063768-C-T		L448 S200		Y	Y		+
6934599-G-T	7066558-G-T	S2555	S2498		Y	Y		+
7032355-TG-T	7164314-TG-T							+
7076667-T-G	7208626-T-G				Y	Y		+
7217798-C-T	7349757-C-T				Y			+
7392186-ATT-A	7524145-ATT-A							+
7615587-C-A	7747546-C-A				Y	Y		+
7929063-C-T	8061022-C-T		S5875 FGC3519		Y	Y		+
8095477-T-C	8227436-T-C		Y4150 BY13328		Y	Y		+
8103635-T-C	8235594-T-C				Y	Y		+
8103642-A-C	8235601-A-C		ZS8104		Y	Y		+
8379191-CT-C	8511150-CT-C							+
8379196-T-TTCG	8511155-T-TTCG							+
8465926-G-T	8597885-G-T				Y	Y		+
8468113-T-A	8600072-T-A				Y	Y		+
8550861-AG-A	8682820-AG-A							+
8556297-A-C	8688256-A-C				Y	Y		+
8660568-AG-A	8792527-AG-A							+
8740675-GTT-G	8872634-GTT-G						17×T	+
8843003-C-T	8974962-C-T				Y	Y		+
9105217-AG-A	9267608-AG-A							+
9509568-C-T	9671959-C-T							+
9509573-T-A	9671964-T-A							+
9840833-C-T	10003224-C-T		K523		Y	Y		+
9854378-A-T	10016769-A-T				Y	Y		+
9954280-C-A	10116671-C-A				Y			+
10055774-C-A	10218165-C-A						15×A	+
10075945-A-C	10238336-A-C							+
13244468-AG-A	11088792-AG-A							+
13252473-C-T	11096797-C-T							+
13260379-G-A	11104703-G-A							+
13260518-G-A	11104842-G-A							+
13267546-T-A	11111870-T-A							+
13269042-T-C	11113366-T-C							+
13269043-G-A	11113367-G-A							+
13282807-A-G	11127131-A-G							+
13294960-T-C	11139284-T-C							+
13294965-A-G	11139289-A-G							+
13304509-G-A	11148833-G-A							+
13322986-T-TTTC	11167310-T-TTTC							+
13360230-A-G	11204554-A-G							+
13363431-A-G	11207755-A-G							+
13374473-T-C	11218797-T-C		FGC52406					+
13383967-G-A	11228291-G-A							+
13386941-A-G	11231265-A-G							+
13399359-C-T	11243683-C-T							+
13399425-C-T	11243749-C-T							+
13399458-C-G	11243782-C-G							+
13407141-C-T	11251465-C-T						13×T	+
13411484-G-A	11255808-G-A							+
13422222-T-C	11266546-T-C							+
13428544-C-T	11272868-C-T							+
13453187-T-G	11297511-T-G							+
13478842-A-C	11323166-A-C							+
13478854-A-C	11323178-A-C							+
13500741-C-T	11345065-C-T							+
13503705-A-G	11348029-A-G							+
13618264-A-G	11462588-A-G							+
13885856-TC-T	11765150-TC-T							+
13886423-T-TA	11765717-T-TA							+
13886464-A-G	11765758-A-G				Y			+
14008825-T-G	11888119-T-G				Y	Y		+
14071336-A-C	11950630-A-C				Y	Y		+
14356907-TG-T	12236202-TG-T							+
14358408-TG-T	12237703-TG-T							+
14570778-TG-T	12458978-TG-T							+
14642493-A-T	12530562-A-T				Y	Y		+
14667871-C-A	12555937-C-A				Y	Y		+
14698482-C-A	12586548-C-A		FT34429		Y	Y		+
14864692-A-G	12752758-A-G				Y	Y		+
14910888-A-C	12798955-A-C		M1837		Y	Y		+
15049966-T-G	12938057-T-G				Y	Y		+
15424418-T-G	13312538-T-G				Y			+
15542729-T-G	13430849-T-G				Y	Y		+
15637936-A-T	13526056-A-T				Y			+
15659894-A-C	13548014-A-C				Y	Y		+
15660923-T-G	13549043-T-G				Y	Y		+
15956886-T-G	13845006-T-G				Y	Y		+
16237238-G-T	14125358-G-T				Y	Y		+
16482281-G-A	14370401-G-A				Y	Y	11×TA	+
16948378-C-T	14836498-C-T				Y	Y		+
16996654-C-T	14884774-C-T				Y		15×T	+
17047877-A-C	14935997-A-C				Y	Y		+
17474923-A-C	15363043-A-C				Y	Y		+
17497181-C-A	15385301-C-A		CTS7469		Y	Y		+
17831207-C-T	15719327-C-T		M5733		Y	Y	17×T	+
17843237-G-C	15731357-G-C				Y	Y		+
18035631-C-T	15923751-C-T				Y	Y		+
18423886-AC-A	16312006-AC-A			P6_Gap				+
18592268-G-T	16480388-G-T		M4979		Y	Y		+
18653646-T-A	16541766-T-A				Y	Y		+
19183350-GA-G	17071470-GA-G							+
19314734-A-T	17202854-A-T				Y	Y		+
19462180-T-C	17350300-T-C		CTS10451 FGC40		Y			+
19853739-C-A	17741859-C-A			P5_Prx			28×A	+
21086160-AC-A	18924274-AC-A							+
21142833-TC-T	18980947-TC-T							+
21230458-T-G	19068572-T-G				Y	Y		+
21409538-C-A	19247652-C-A				Y			+
21554490-TG-T	19392604-TG-T							+
21575158-A-C	19413272-A-C				Y			+
21583017-A-C	19421131-A-C				Y			+
21617775-TC-T	19455889-TC-T							+
21759920-TTG-T	19598034-TTG-T							+
21919421-C-T	19757535-C-T		Z29822		Y	Y		+
22035827-G-A	19873941-G-A		FGC2155 Y6746		Y	Y		+
22165238-C-A	20003352-C-A				Y	Y		+
22469940-C-T	20308054-C-T		BY222326	DYZ19				+
22784216-C-T	20622330-C-T		Y26343 Z42278		Y	Y		+
23136908-G-T	20975022-G-T				Y	Y		+
23364086-GC-G	21202200-GC-G							+
23476059-C-A	21314173-C-A				Y	Y		+
23802155-T-G	21640269-T-G					Y		+
23802160-T-G	21640274-T-G					Y		+
24205509-TGTGC-T	22059362-TGTGC-T			P3_b1				+
24452960-T-G	22306813-T-G					Y		+
24482132-A-C	22335985-A-C							+
25899807-G-A	23753660-G-A			P1_Y1				+
26508204-T-G	24362057-T-G			P1_Y1				+
28545039-G-A	26398892-G-A							+
28545054-G-A	26398907-G-A							+
28613788-G-T	26467641-G-T							+
58974146-A-AATTCC	56827999-A-AATTCC							+
58977091-CACCAT-C	56830944-CACCAT-C							+
58988033-C-T	56841886-C-T							+
59019550-ACAAG-A	56873403-ACAAG-A							+
59024404-A-ACC	56878257-A-ACC							+
59026874-C-CT	56880727-C-CT							+

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	22477719-C-T	20315833-C-T	1C 1T. The C read may be misaligned.
Manual	5356979-T-A	5488938-T-A	3A 1T
Manual	18628121-G-A	16516241-G-A	4A 1G
Manual	7902196-T-A	8034155-T-A	1A
Manual	15929351-T-C	13817471-T-C	1C
Manual	22304007-C-T	20142121-C-T	3C 1T
Manual	15598293-G-A	13486413-G-A	1A
Manual	18138802-A-G	16026922-A-G	2G 1A
Manual	2870977-A-C	3002936-A-C	2C
Manual	17652884-C-T	15541004-C-T	1T
Manual	18117189-C-T	16005309-C-T	1T
Manual	22268632-T-A	20106746-T-A	1A
Manual	23197890-G-A	21036004-G-A	1A

1k Genomes

Tree Position

Unique Mutations

Mutation Notes: