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	1kG NA18647
13693908-G-T	11538232-G-T		BY88819				+
8890040-C-T	9021999-C-T	Z16506	F1452			Y	+
22982689-G-T	20820803-G-T		CTS11157		Y		+
2696013-C-T	2827972-C-T		F14840		Y	Y	+
2948894-T-A	3080853-T-A		FT315522				+
3103892-T-C	3235851-T-C						+
3240489-C-G	3372448-C-G		FT316548				+
3294522-G-C	3426481-G-C						+
3426377-A-C	3558336-A-C						+
3461085-G-C	3593044-G-C		FT317322				+
3490129-T-A	3622088-T-A						+
3665284-G-A	3797243-G-A						+
3686062-T-C	3818021-T-C		FT318132				+
3691134-G-C	3823093-G-C		FT318155				+
3844721-C-T	3976680-C-T						+
4145665-T-C	4277624-T-C		FT319670				+
4192995-G-T	4324954-G-T						+
4745940-G-A	4877899-G-A						+
4877015-C-T	5008974-C-T						+
5207518-C-T	5339477-C-T						+
5222960-C-T	5354919-C-T						+
5295887-G-A	5427846-G-A		FT323439				+
5482560-C-T	5614519-C-T						+
5540233-C-T	5672192-C-T		FT324247				+
5609035-G-A	5740994-G-A						+
5705201-C-G	5837160-C-G						+
5745460-G-A	5877419-G-A		FT324943				+
5811426-G-A	5943385-G-A						+
5831770-A-G	5963729-A-G		FT325194				+
5918909-A-T	6050868-A-T		FT325497				+
6027117-T-C	6159076-T-C		FT325892				+
6498237-G-A	6630196-G-A						+
6681921-G-A	6813880-G-A		F15247		Y	Y	+
6738573-A-T	6870532-A-T		F819 AMM191 AM00381		Y	Y	+
6810920-C-T	6942879-C-T	BY3503	BY3503 AM00382 AMM192 Y35628		Y	Y	+
7036383-C-T	7168342-C-T		F15541		Y	Y	+
7038378-C-T	7170337-C-T		F15545		Y	Y	+
7070489-C-G	7202448-C-G		F15573		Y	Y	+
7151519-A-G	7283478-A-G		AM00383 AMM193 Z39165 Z39164		Y	Y	+
7513805-G-A	7645764-G-A		Z39166		Y		+
7648468-T-C	7780427-T-C		F16089		Y	Y	+
7704817-T-A	7836776-T-A		Z39167		Y	Y	+
7831353-C-T	7963312-C-T		Z39169		Y	Y	+
7866588-G-A	7998547-G-A		Z39170		Y	Y	+
7910516-G-T	8042475-G-T		F16417		Y	Y	+
8021798-A-G	8153757-A-G		F16562		Y	Y	+
8501449-T-C	8633408-T-C		F1263		Y	Y	+
8676377-G-A	8808336-G-A		F17379		Y	Y	+
8731851-G-A	8863810-G-A		Z39172		Y		+
8752910-T-C	8884869-T-C		Z39173		Y	Y	+
8782363-G-T	8914322-G-T		Z39174		Y	Y	+
8836999-C-T	8968958-C-T		F17528		Y	Y	+
9029974-A-T	9192365-A-T					Y	+
9172314-C-A	9334705-C-A		FGC69642		Y		+
9450730-A-G	9613121-A-G		FT300664		Y	Y	+
10020414-T-G	10182805-T-G				Y		+
10066746-C-G	10229137-C-G		Z39176				+
13127299-A-G	10616785-A-G						+
13394097-C-G	11238421-C-G						+
13437895-T-G	11282219-T-G						+
13438066-C-A	11282390-C-A						+
13540631-G-T	11384955-G-T						+
13639641-G-A	11483965-G-A						+
13677929-G-A	11522253-G-A		BY88098				+
13680680-G-A	11525004-G-A						+
13862860-G-A	11742154-G-A						+
14031222-G-T	11910516-G-T		CTS1716		Y	Y	+
14120404-A-G	11999698-A-G		CTS1914		Y		+
14148812-T-A	12028106-T-A		CTS1995		Y	Y	+
14209895-C-T	12089189-C-T		F18634		Y	Y	+
14215793-T-C	12095087-T-C		F18646		Y	Y	+
14248740-A-G	12128034-A-G		CTS2288 AMM145 AM00335		Y	Y	+
14499529-C-T	12387734-C-T		F19007		Y	Y	+
14653488-C-T	12541553-C-T		CTS3085 AM00336 AMM146		Y	Y	+
14895608-C-G	12783674-C-G		CTS3400 AM00337 AMM147		Y	Y	+
14920529-T-C	12808594-T-C		CTS3433		Y	Y	+
15028310-C-T	12916398-C-T		F19477		Y	Y	+
15041926-T-C	12930016-T-C				Y	Y	+
15060902-A-G	12948994-A-G		AM00338 AMM148 Z39177		Y	Y	+
15221290-T-G	13109376-T-G				Y		+
15347133-G-C	13235252-G-C		AM00339 AMM149 Z39178		Y	Y	+
15465636-T-G	13353756-T-G		F19814		Y	Y	+
15527109-C-T	13415229-C-T		CTS4261		Y	Y	+
15636328-G-T	13524448-G-T				Y		+
15636482-G-C	13524602-G-C				Y		+
15648328-A-T	13536448-A-T		FT301206		Y	Y	+
15652204-G-T	13540324-G-T		CTS4447		Y	Y	+
15653535-G-A	13541655-G-A		AMM150 AM00340 Z39179		Y	Y	+
15657573-G-A	13545693-G-A		CTS4460		Y	Y	+
15716328-T-C	13604448-T-C		CTS4565		Y	Y	+
15893650-G-T	13781770-G-T		FT301277		Y		+
15893651-A-T	13781771-A-T		FT301278		Y		+
16001295-C-G	13889415-C-G		FT301301		Y		+
16322659-A-C	14210779-A-C		FT301363		Y		+
16398802-G-C	14286922-G-C				Y		+
16422255-C-T	14310375-C-T		FT301395		Y		+
16458831-A-G	14346951-A-G		CTS5726 AMM153 AM00343		Y	Y	+
16531020-G-A	14419140-G-A		F20787		Y	Y	+
16540416-T-A	14428536-T-A				Y		+
16660681-C-G	14548801-C-G		CTS6088		Y	Y	+
17403756-G-C	15291876-G-C				Y	Y	+
17445724-G-T	15333844-G-T		CTS7370 AM00345 AMM155		Y	Y	+
17454293-C-T	15342413-C-T				Y		+
17469084-C-T	15357204-C-T		Y31615		Y	Y	+
17568554-C-T	15456674-C-T		SK1589 AM00346 AMM156		Y	Y	+
17602084-C-T	15490204-C-T		CTS7668		Y	Y	+
17659824-T-C	15547944-T-C		CTS7783		Y	Y	+
17693474-G-A	15581594-G-A		AMM157 AM00347 Z39180		Y	Y	+
17792078-T-C	15680198-T-C		F22117		Y	Y	+
17854864-C-T	15742984-C-T		Z39181		Y		+
17937211-C-T	15825331-C-T		F2644 AM00349 AMM159		Y	Y	+
17938128-A-G	15826248-A-G		F22301		Y	Y	+
18007366-C-T	15895486-C-T		MF2386	P7_Gap	Y		+
18155895-T-C	16044015-T-C		FT337942		Y		+
18183108-C-G	16071228-C-G		CTS8756		Y	Y	+
18184981-G-C	16073101-G-C		FT301865		Y		+
18549117-G-A	16437237-G-A		AMM161 AM00351 Z39182		Y		+
18709346-A-G	16597466-A-G		CTS9138 AM00352 AMM162		Y	Y	+
18771712-C-T	16659832-C-T		CTS9243 AM00353 AMM163		Y	Y	+
18809368-T-C	16697488-T-C		F2852 AM00354 AMM164		Y	Y	+
18889453-T-G	16777573-T-G		F23011		Y	Y	+
18954012-G-C	16842132-G-C		CTS9540 AMM165 AM00355		Y	Y	+
19011621-G-A	16899741-G-A		AM00358 AMM168 Z39184		Y	Y	+
19021779-T-C	16909899-T-C		F23187		Y	Y	+
19059879-C-T	16947999-C-T		F23237		Y	Y	+
19060993-G-T	16949113-G-T		CTS9765		Y	Y	+
19170017-G-A	17058137-G-A		CTS9955		Y		+
19403978-C-T	17292098-C-T		AMM169 AM00359 Z39185		Y	Y	+
19474424-C-A	17362544-C-A		F3063 AM00361 AMM171		Y	Y	+
19481175-G-A	17369295-G-A		CTS10491		Y	Y	+
19527725-C-G	17415845-C-G		CTS10537		Y	Y	+
21068783-A-G	18906897-A-G		AM00363 AMM173 Z39186		Y	Y	+
21147444-G-C	18985558-G-C		AM00364 AMM174 Z39187		Y	Y	+
21159803-T-G	18997917-T-G		F23948		Y	Y	+
21333109-G-T	19171223-G-T				Y	Y	+
21357716-C-A	19195830-C-A		F24208		Y	Y	+
21440810-G-A	19278924-G-A		AMM175 AM00365 Z39188		Y	Y	+
21450288-T-G	19288402-T-G		AMM176 AM00366		Y		+
21460581-T-A	19298695-T-A		F24330		Y	Y	+
21496735-A-G	19334849-A-G		AM00367 AMM177 Z39189		Y		+
21619802-G-A	19457916-G-A		AM00368 AMM178 Z39190		Y	Y	+
21755690-A-G	19593804-A-G		F24660		Y	Y	+
21803281-C-A	19641395-C-A		FT302482		Y		+
21818623-G-A	19656737-G-A		F24728		Y	Y	+
21932468-A-C	19770582-A-C		AM00370 AMM180 Z39191		Y	Y	+
21987139-T-C	19825253-T-C		F24893		Y	Y	+
22114430-T-C	19952544-T-C		AMM181 AM00371 Z39192		Y		+
22222420-A-G	20060534-A-G			DYZ19			+
22246055-C-A	20084169-C-A			DYZ19			+
22258439-T-C	20096553-T-C			DYZ19			+
22259331-A-C	20097445-A-C		Z39193	DYZ19			+
22270840-G-T	20108954-G-T		Z39194	DYZ19			+
22458803-G-A	20296917-G-A		FT457363	DYZ19			+
22459935-C-T	20298049-C-T		FTA47585	DYZ19			+
22487856-G-A	20325970-G-A			DYZ19			+
22649410-C-T	20487524-C-T		F25325		Y	Y	+
22834188-C-A	20672302-C-A		AMM182 AM00372 Z39195		Y	Y	+
22937270-C-T	20775384-C-T		CTS11079 AM00374 AMM184		Y	Y	+
22947075-T-G	20785189-T-G		CTS11090		Y	Y	+
22983315-A-G	20821429-A-G				Y		+
22990582-T-C	20828696-T-C		AM00375 AMM185 Z39196		Y		+
23043710-C-T	20881824-C-T		FT302783		Y	Y	+
23074707-A-T	20912821-A-T		F25765		Y	Y	+
23093279-A-G	20931393-A-G		CTS11394		Y		+
23250514-G-T	21088628-G-T		F25895		Y	Y	+
23456430-G-A	21294544-G-A		AM00377 AMM187 Z39197		Y	Y	+
23472770-A-C	21310884-A-C		AM00378 AMM188 Z39198		Y	Y	+
23573246-T-G	21411360-T-G		F26235		Y	Y	+
23620488-A-G	21458602-A-G		F3495		Y	Y	+
23751006-C-T	21589120-C-T					Y	+
24448831-C-T	22302684-C-T		F3640			Y	+
28524104-G-T	26377957-G-T						+

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