Tree Position

R-M269 > L23 > Z2103 > Z2106 > Z2108 > Z2110 > Exact position not yet finalized.

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 STR1kG
HG01277
Manual
Edits
13724028-A-G 11568352-A-G +
4462103-T-C 4594062-T-C FT320722 +
3222149-A-C 3354108-A-C FT316486 +
3242167-T-G 3374126-T-G +
3284870-A-G 3416829-A-G +
3619324-T-C 3751283-T-C +
3619627-G-A 3751586-G-A +
3689614-G-T 3821573-G-T FT318149 +
3845042-T-C 3977001-T-C FT38671 +
3922183-G-A 4054142-G-A 16×A+
5018864-T-C 5150823-T-C FT322451 +
2934644-G-A 3066603-G-A +
5261757-A-G 5393716-A-G +
5456955-T-A 5588914-T-A FT323966 +
5610151-G-A 5742110-G-A FT324489 +
6961351-C-T 7093310-C-T CTS699 YY+
6976211-T-C 7108170-T-C FGC82973 Y+
7290782-A-C 7422741-A-C FT294832 YY+
7975105-T-C 8107064-T-C FT295118 YY+
8184862-G-T 8316821-G-T FT295226 YY+
3138037-T-A 3269996-T-A FT316211 +
2888596-C-T 3020555-C-T FT127867 YY+
8289118-G-T 8421077-G-T YY+
21549200-TA-T 19387314-TA-T +
17569226-G-A 15457346-G-A YY25×A+
17721031-A-C 15609151-A-C YY+
18108471-A-T 15996591-A-T M3889 YY+
18846036-AG-A 16734156-AG-A +
19143142-TG-T 17031262-TG-T +
19520866-AG-A 17408986-AG-A +
21170346-C-T 19008460-C-T YY+
21422260-T-G 19260374-T-G YY+
21578519-G-C 19416633-G-C Y76781 Y+
59021932-T-TTC 56875785-T-TTC +
22230730-A-ATTCT 20068844-A-ATTCT DYZ19 +
22258034-C-G 20096148-C-G DYZ19 +
22258043-A-G 20096157-A-G DYZ19 +
22261446-A-G 20099560-A-G DYZ19 +
22261474-T-A 20099588-T-A BY1889 DYZ19 +
22723416-AG-A 20561530-AG-A +
23274683-A-C 21112797-A-C YY+
28554649-C-T 26408502-C-T FT89779 +
28554651-C-G 26408504-C-G +
8229945-G-C 8361904-G-C Y36455 YY+
8529333-C-T 8661292-C-T FT295401 YY+
16779006-A-AG 14667126-A-AG +
19322472-C-A 17210592-C-A FT298027 YY+
17319940-A-G 15208060-A-G YY+
17375332-C-G 15263452-C-G FT297248 Y+
17694608-AG-A 15582728-AG-A +
17718366-A-C 15606486-A-C YY+
17965066-C-T 15853186-C-T CTS8375 Y+
18958077-A-AT 16846197-A-AT +
19045704-TG-T 16933824-TG-T +
19271531-T-A 17159651-T-A YY+
21146044-C-T 18984158-C-T FT298256 YY+
16694915-G-A 14583035-G-A FT296964 YY+
21156805-G-A 18994919-G-A Y+
21171334-G-A 19009448-G-A Y+
22270149-G-A 20108263-G-A DYZ19 +
22464670-T-C 20302784-T-C BY221375 DYZ19 +
22535805-G-C 20373919-G-C Y+
22633880-TAATA-T 20471994-TAATA-T +
23200831-A-G 21038945-A-G FT299263 Y+
23840642-G-A 21678756-G-A Y+
23967062-T-G 21820915-T-G Y+
17268194-C-T 15156314-C-T CTS7070 Y+
16502266-G-A 14390386-G-A FT296883 Y+
8565709-G-A 8697668-G-A FT295416 YY+
13383648-T-A 11227972-T-A +
8642753-A-C 8774712-A-C S11762 YY+
9466157-G-A 9628548-G-A FT327960 +
9954699-T-G 10117090-T-G Y+
9997214-T-C 10159605-T-C Y+
9997250-G-A 10159641-G-A BY82669 Y+
9999432-T-C 10161823-T-C Y+
10019550-C-T 10181941-C-T A20086 Y+
13355014-T-A 11199338-T-A +
13588223-TA-T 11432547-TA-T +
16373365-C-T 14261485-C-T YY+
13620463-T-A 11464787-T-A +
14070511-A-T 11949805-A-T FT295959 YY+
14073771-T-C 11953065-T-C YY+
14419299-G-C 12298574-G-C FT296149 YY+
14736800-T-C 12624868-T-C FT296268 Y+
14744926-T-G 12632995-T-G FT296270 YY+
14888675-C-T 12776741-C-T FT296322 YY+
15733213-T-C 13621333-T-C FT296592 YY+
15772140-A-T 13660260-A-T FT296618 YY+
17346142-C-T 15234262-C-T M9211 YY18×T+
16779004-T-TA 14667124-T-TA +
19231315-G-T 17119435-G-T YY+
2992426-A-C 3124385-A-C +
28539164-G-A 26393017-G-A M4646 +
28754078-C-T 26607931-C-T CTS12928 +
8493207-A-ATG 8625166-A-ATG 9×TG+
3655089-T-G 3787048-T-G 8×G+
13510943-T-C 11355267-T-C +
58867788-C-A 56723083-G-T +
13811067-AGGAATGGAAT-A 11690361-AGGAATGGAAT-A 11×GGAAT+
59009238-CAAA-C 56863091-CAAA-C +
3015610-A-ACT 3147569-A-ACT +
8184343-T-TGC 8316302-T-TGC +
3045212-T-G 3177171-T-G +
3126862-A-C 3258821-A-C +
3242444-G-C 3374403-G-C +
3374870-AG-A 3506829-AG-A +
3544888-A-AG 3676847-A-AG +
3557390-GTTC-G 3689349-GTTC-G +
3557391-TTC-T 3689350-TTC-T +
3655081-C-G 3787040-C-G +
58894781-G-A 56696090-C-T +
13143959-N-C 10633445-N-C +
4431344-A-G 4563303-A-G FGC7907 +
7311609-C-T 7443568-C-T BY64494 YY+
19231319-C-T 17119439-C-T YY24×T+
58887623-G-A 56703248-C-T +
19231311-C-T 17119431-C-T YY+
13841449-G-A 11720743-G-A FT236410 +
22884954-T-A 20723068-T-A M222M11666 CTS11001 YY+
7120767-C-T 7252726-C-T CTS978 Y+
21477811-AAAAG-A 19315925-AAAAG-A 14×AAAG+
16077579-AGT-A 13965699-AGT-A +
24508205-C-T 22362058-C-T 22×T+
13143958-N-T 10633444-N-T +
15171221-C-T 13059307-C-T Y+
4243208-G-A 4375167-G-A FT319999 +
13852011-CGAATGGAATG-C 11731305-CGAATGGAATG-C 11×GAATG+
58856410-C-T 56734461-G-A +
22268414-C-CT 20106528-C-CT DYZ19 +
22319023-GTA-G 20157137-GTA-G DYZ19 +
3015575-T-TAC 3147534-T-TAC 17×AC+
19411914-AAAAGAAAG-A 17300034-AAAAGAAAG-A 14×AAAG+
13143957-N-C 10633443-N-C +
4334719-G-A 4466678-G-A +
4455063-T-C 4587022-T-C FT872 +
16244790-AGGGT-A 14132910-AGGGT-A +
13723152-A-AGAATG 11567476-A-AGAATG +
9997125-TA-T 10159516-TA-T +
13222419-C-G 11066743-C-G +
13252626-C-T 11096950-C-T +
13255093-G-A 11099417-G-A FT441893 +
13427896-G-T 11272220-G-T +
13500490-T-A 11344814-T-A +
13621001-C-T 11465325-C-T +
13621065-C-G 11465389-C-G +
13723156-T-TGGAAG 11567480-T-TGGAAG +
8575984-T-TTTTG 8707943-T-TTTTG +
13950946-TC-T 11830240-TC-T +
14245236-G-GAAGT 12124530-G-GAAGT +
14245244-G-GAAGT 12124538-G-GAAGT +
14245257-A-AAGGC 12124551-A-AAGGC +
14593468-C-T 12481668-C-T YY+
14954403-G-GT 12842477-G-GT +
15491537-C-CG 13379657-C-CG +
15496762-C-G 13384882-C-G M2191 CTS4228 YY+
15839817-T-G 13727937-T-G YY+
9434404-T-G 9596795-T-G YY+
8407600-C-CT 8539559-C-CT +
4474281-AT-A 4606240-AT-A 9×T+
5493411-A-T 5625370-A-T +
4474293-C-G 4606252-C-G +
4634318-C-G 4766277-C-G FT33350 +
4773474-C-T 4905433-C-T +
4890730-C-A 5022689-C-A FGC81623 +
5017715-T-C 5149674-T-C +
5127225-G-A 5259184-G-A +
5400488-G-T 5532447-G-T +
5400490-C-T 5532449-C-T 9×T+
5619927-T-C 5751886-T-C +
8379148-T-C 8511107-T-C YY+
5620912-G-A 5752871-G-A +
5828483-C-T 5960442-C-T +
6599422-C-G 6731381-C-G +
6808132-T-A 6940091-T-A YY+
6863782-A-C 6995741-A-C YY+
7310596-G-A 7442555-G-A S10104 YY+
7311383-TTTCC-T 7443342-TTTCC-T 6×TTCC+
7774813-T-G 7906772-T-G YY+
8005824-A-G 8137783-A-G Y+
27453943-A-G 25307796-A-G P1_Y2 +

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
Manual21860912-CA-C19699026-CA-C5 reads, all positive.
Manual16050529-T-G13938649-T-G1G



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