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	BigY3 96008
20498990-C-T	18337104-C-T			P5_Dst				A+
20816924-C-CA	18655038-C-CA			P4_Gap			22×A	A*
7475612-T-A	7607571-T-A			IR1_L				A*
26133997-C-T	23987850-C-T			P1_Y1				A*
28817409-T-G	26671262-T-G							A*
13687818-A-T	11532142-A-T							A*
28816795-G-A	26670648-G-A							A*
28817347-A-G	26671200-A-G							A*
	56858628-G-T							A*
18280304-G-A	16168424-G-A			P6_Prx				A*
19587171-C-T	17475291-C-T	BY15485		P5_Prx	Y			A*
26084246-G-A	23938099-G-A			P1_Y1				A*
19696433-T-TA	17584553-T-TA			P5_Prx			14×A	A*
25617175-T-TTG	23471028-T-TTG			P1_gr1			19×TG	A*
26351915-C-T	24205768-C-T			P1_Y1				A*
19680787-G-A	17568907-G-A			P5_Prx				A*
16013103-T-G	13901223-T-G				Y			A*
19631612-A-C	17519732-A-C			P5_Prx				A*
14641193-C-T	12529262-T-.		L52 PF6541		Y	Y		+
22157311-A-.	19995425-A-.		P312					+
17844018-C-.	15732138-C-.							+
16751825-A-.	14639945-A-.							+
8502236-A-.	8634195-A-.							+
6912992-G-.	7044951-G-.							+
6753511-A-.	6885470-A-.							+
22739367-C-.	20577481-C-.							+
6032961-G-.	6164920-G-.							+
19418178-C-.	17306298-C-.							+
8829491-C-A	8961450-C-A	DF99/S11987	DF99 S11987 Z6001		Y	Y		+
4404325-G-A	4536284-G-A	Z29643	Z29643					+
2784645-C-G	2916604-C-G	Y31433	Y31433		Y	Y		+
8023548-C-T	8155507-C-T	Y31433	BY15482 Y31434		Y	Y		+
17688792-G-T	15576912-G-T	FGC16982	Y5049 FGC16982		Y	Y		+
17879816-A-G	15767936-A-G	FGC16979	Y5046 FGC16979		Y	Y		+
18883425-A-G	16771545-A-G	Y31433	CTS9423 S4249		Y	Y		+
21783578-A-C	19621692-A-C	S23540	S23540		Y	Y		+
24425801-G-A	22279654-G-A	Y31433	BY15483 Y31435			Y		+
14539162-G-A	12427363-G-A	S23540	S16136		Y	Y		+
4585565-A-G	4717524-A-G	S23540	FGC16988					+
6286963-GCACACA-G	6418922-GCACACA-G	FT67050		IR3_Dst				+
5465148-A-.	5597107-A-.							+
7242725-C-A	7374684-C-A	BY15485	BY183855		Y			+
15375766-G-A	13263886-G-A	BY11781	Y16635		Y	Y		+
4943495-A-G	5075454-A-G		FGC43638					+
	10973221-G-A							+
	10761260-TTTCCATTCCATTCCA-T							+
	10934009-T-G	FGC84729	FGC84729					+
8614401-A-G	8746360-A-G	BY15485	BY15485		Y	Y		+
8906656-G-A	9038615-G-A	BY15485	BY15486					+
9448171-A-G	9610562-A-G	BY15487	BY15487		Y	Y		+
	10766771-G-A	BY15487	FT310232					+
13213911-G-A	11058235-G-A	BY15487	FT310231					+
13485237-G-A	11329561-G-A	BY15485	BY43128					+
13681255-C-A	11525579-C-A	BY15487	BY38505					+
13717027-A-T	11561351-A-T	BY15487	BY38506					+
14114952-C-T	11994246-C-T		FT304304		Y	Y		+
14604773-C-T	12492975-C-T	BY15485	BY43358		Y	Y		+
14696563-G-A	12584629-G-A		BY15488		Y	Y		+
14883725-A-C	12771791-A-C	BY15487	BY15489		Y	Y		+
15346493-T-C	13234612-T-C	BY15485	BY15490		Y	Y		+
15670909-T-C	13559029-T-C	BY15487	BY15484		Y			+
15704942-T-G	13593062-T-G	BY15487	BY15491		Y	Y		+
16337455-A-C	14225575-A-C	BY15485	BY15492		Y	Y		+
17018466-A-C	14906586-A-C	BY15485	BY15493		Y	Y		+
17113039-TA-T	15001159-TA-T	BY15487						+
17225598-T-A	15113718-T-A	BY15485	BY15494		Y	Y		+
18398343-T-C	16286463-T-C	BY15485	BY15495	P6_Gap				+
18645296-C-T	16533416-C-T	BY15485	BY15496		Y	Y		+
18959922-A-G	16848042-A-G	BY15485	BY15497		Y	Y		+
18979358-C-A	16867478-C-A	BY15485	BY15498		Y	Y		+
19232967-A-G	17121087-A-G	BY15485	BY183856		Y	Y		+
19281778-G-A	17169898-G-A		BY15499		Y	Y		+
19482038-G-A	17370158-G-A	BY15485	BY183857		Y	Y		+
22707971-T-C	20546085-T-C		BY15501		Y	Y		+
23293367-C-T	21131481-C-T	BY15485	BY15502		Y	Y		+
23485752-T-C	21323866-T-C	BY15487	BY15503		Y	Y		+
23608303-T-C	21446417-T-C		BY15504		Y	Y		+
24401518-G-C	22255371-G-C	BY15487	BY15505			Y		+
26153823-G-C	24007676-G-C	BY15487		P1_Y1				+
18636727-G-A	16524847-G-A		FT202086		Y	Y		+
28582021-G-C	26435874-G-C		FT202721					+
13839536-A-.	11718830-A-.							+
3605699-G-A	3737658-G-A		FT200332					+
3900675-C-G	4032634-C-G		FT200384					+
4797381-A-G	4929340-A-G		FT200573					+
5746411-A-T	5878370-A-T		FT200755					+
5918961-G-A	6050920-G-A		FT200787					+
5955621-T-C	6087580-T-C		FT200796					+
6481340-A-G	6613299-A-G		FT200861					+
13890249-G-A	11769543-G-A		FT126586		Y			+
18411661-C-T	16299781-C-T		FT202072	P6_Gap				+
21269346-T-C	19107460-T-C		FT202294		Y			+
21526094-G-A	19364208-G-A		FT202341		Y			+
28704418-A-G	26558271-A-G		FT202740					+
9787962-C-A	9950353-C-A		FTB14629		Y			+
13336576-T-C	11180900-T-C							+
17115541-T-G	15003661-T-G				Y	Y		+
19104658-G-C	16992778-G-C				Y	Y		+
21346628-G-C	19184742-G-C				Y			+
22661493-A-ATG	20499607-A-ATG						26×TG	*
5170248-GAGGA-G	5302207-GAGGA-G						11×AGGA	*
3249466-TTGTG-T	3381425-TTGTG-T						17×TG	*
	10781676-A-AATTCC							*
3721207-T-C	3853166-T-C	BY15485	BY42622					*
22301884-C-T	20139998-C-T			DYZ19				*
28796049-G-C	26649902-G-C		FT462009					*
3713579-A-G	3845538-A-G							*
5268561-GC-G	5400520-GC-G							*
9587513-CT-C	9749904-CT-C			IR3_Prx				*
5568497-G-A	5700456-G-A		FT83105					**
21940037-CATATATATATATATATATATAT-C	19778151-CATATATATATATATATATATAT-C						22×AT	**
24293019-T-G	22146872-T-G			P3_t1				**
	11651885-CGAATG-C							**
13453306-T-G	11297630-T-G							**
23825772-AAAT-A	21663886-AAAT-A							**
24517283-G-A	22371136-G-A	BY15487	BY15506					**
13453278-C-G	11297602-C-G							**
19377420-A-G	17265540-A-G							**
24291383-A-T	22145236-A-T			P3_t1				**
20448893-G-GGTGTGT	18287007-G-GGTGTGT			P5_Dst				**
19792501-T-C	17680621-T-C			P5_Prx				**
18035665-CTTTTTTTTTTTTT-C	15923785-CTTTTTTTTTTTTT-C						30×T	**
4163583-T-G	4295542-T-G							**
19597206-TTATTA-T	17485326-TTATTA-T			P5_Prx				**
19788333-C-A	17676453-C-A			P5_Prx				**
22548342-C-A	20386456-C-A							**
22882961-C-A	20721075-C-A							**
24291391-A-C	22145244-A-C			P3_t1				**
25592447-T-A	23446300-T-A			P1_gr1				**
26019729-C-A	23873582-C-A			P1_Y1				**
22420062-C-G	20258176-C-G		BY23368	DYZ19				***
17669700-CAT-C	15557820-CAT-C						15×AT	***
20989104-TAC-T	18827218-TAC-T			P4_Dst			25×AC	***
19537901-C-CAA	17426021-C-CAA						17×A	***
4997519-CAG-C	5129478-CAG-C						16×AG	***
9416722-C-A	9579113-C-A							***
15070614-CAAAAAAAA-C	12958705-CAAAAAAAA-C						20×A	***
23792029-C-CTTT	21630143-C-CTTT						15×T	***
13470032-C-A	11314356-C-A							***
13260592-CTT-C,CT	11104916-CTT-C,CT						14×T	***
	10956556-CTCCACTCCAT-C,CTCCATTCCAT							***
6131927-G-C	6263886-G-C							***
8901182-A-T	9033141-A-T							***
13427974-T-C	11272298-T-C							***
13606495-T-A	11450819-T-A							***
17859649-G-A	15747769-G-A							***
21680438-G-A	19518552-G-A							***
23484315-T-A	21322429-T-A							***
23484317-T-A	21322431-T-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.

Davenport

Tree Position

Unique Mutations