1k Genomes

1kG: HG02088
MDKA Birth: Viet Nam
Kinh in Ho Chi Minh City, Vietnam

Tree Position

A0-T-YP2191 > P305[A1] > A1b > BT/A1b2 > M168/PF1416[CT] > P143[CF] > M89/PF2746[F] > F1329/M3658[GHI > F929[HIJK] > IJK > K > M526[K2] > M2335 > F346[NO] > P191[O] > 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
HG02088
8409796-G-A 8541755-G-A Z17557Z17557 YY+
14872230-G-A 12760300-G-A Y128219 YY+
2652153-T-G 2784112-T-G Y+
2712079-A-G 2844038-A-G F14853 YY+
2727275-T-A 2859234-T-A BY56049 YY+
2740392-A-G 2872351-A-G YY+
3397265-C-T 3529224-C-T FT516 +
3431055-G-A 3563014-G-A FT120365 +
3432738-C-T 3564697-C-T FTB5786 +
3635028-T-C 3766987-T-C +
4124091-T-C 4256050-T-C FT778 +
4607832-C-A 4739791-C-A +
4633443-T-G 4765402-T-G +
4736174-C-T 4868133-C-T +
4830926-T-C 4962885-T-C FT993 +
5132289-C-G 5264248-C-G FT1098 +
5362947-G-A 5494906-G-A FT1170 +
5403787-T-C 5535746-T-C FT1181 +
5419474-A-T 5551433-A-T FT1188 +
5620205-G-A 5752164-G-A FT1251 +
6424766-G-A 6556725-G-A FTA44292 +
6726543-T-A 6858502-T-A FT345033 Y+
6775784-A-C 6907743-A-C F15323 YY+
6933136-T-C 7065095-T-C YY+
6974433-C-T 7106392-C-T BY62667 YY+
7190504-C-T 7322463-C-T F15668 YY+
7235382-T-C 7367341-T-C YY+
7680717-A-G 7812676-A-G F16131 YY+
7772828-G-A 7904787-G-A F16236 YY+
7828061-C-T 7960020-C-T F16299 YY+
7856264-A-C 7988223-A-C F16342 YY+
7890050-G-A 8022009-G-A F16388 YY+
7998073-A-T 8130032-A-T F16534 YY+
8119888-C-T 8251847-C-T FT345547 YY+
8179869-C-A 8311828-C-A BY70486 YY+
8332671-C-T 8464630-C-T F16912 YY+
8480967-C-T 8612926-C-T A4917 V2088 YY+
8555218-C-A 8687177-C-A F17226 YY+
8597567-C-T 8729526-C-T F17285 YY+
8711819-C-G 8843778-C-G YY+
8721725-A-G 8853684-A-G F17423 YY+
8871299-A-G 9003258-A-G F17570 Y+
8979088-A-G 9141479-A-G Y+
9163244-C-T 9325635-C-T +
9172554-C-A 9334945-C-A F4136 Y+
9406191-A-G 9568582-A-G F17849 YY+
9901822-G-A 10064213-G-A PF4440PF4440 Y+
9929927-G-A 10092318-G-A Y+
9959174-T-C 10121565-T-C BY50584 Y+
9978606-C-A 10140997-C-A FT359049 Y+
13237608-A-G 11081932-A-G +
13243280-G-A 11087604-G-A +
13311361-G-C 11155685-G-C BY85083 +
13471405-G-A 11315729-G-A BY85862 +
13471406-G-A 11315730-G-A BY85863 +
13484248-T-C 11328572-T-C +
13523266-C-T 11367590-C-T +
13646427-G-A 11490751-G-A BY86892 +
13671209-T-C 11515533-T-C +
13694184-A-T 11538508-A-T +
13810304-G-T 11689598-G-T BY90210 +
13839360-G-A 11718654-G-A BY156355 +
13869580-G-T 11748874-G-T +
13908324-C-A 11787618-C-A FT1724 YY+
13998258-G-A 11877552-G-A YY+
14006996-T-C 11886290-T-C BY92281 Y+
14039312-T-C 11918606-T-C Y30401 YY+
14173315-G-T 12052609-G-T F18573 YY+
14258409-T-C 12137703-T-C Y+
14280783-A-T 12160077-A-T F18738 YY+
14295542-G-T 12174836-G-T FT1794 YY+
14371404-A-G 12250700-A-G Y+
14385201-C-G 12264497-C-G FT346301 Y+
14496439-T-G 12384644-T-G YY+
15149794-C-G 13037881-C-G FT346548 Y+
15155439-A-G 13043526-A-G YY+
15181602-A-G 13069688-A-G FT1858 YY+
15789898-G-C 13678018-G-C FT346752 Y+
15872732-C-A 13760852-C-A F20231 YY+
16245456-T-C 14133576-T-C FT346890 Y+
16874384-A-G 14762504-A-G FT1965 YY+
16936701-C-T 14824821-C-T F21224 YY+
17082297-A-G 14970417-A-G BY112192 YY+
17121830-T-C 15009950-T-C FT347246 YY+
17248594-G-T 15136714-G-T FT1996 Y+
17256460-G-T 15144580-G-T F21539 YY+
17297276-T-C 15185396-T-C YY+
17365823-C-T 15253943-C-T F21680 YY+
17420429-G-A 15308549-G-A BY205279 YY+
17439290-A-G 15327410-A-G F21776 YY+
17536197-C-T 15424317-C-T F21869 YY+
17656337-T-C 15544457-T-C F21985 YY+
17739413-G-A 15627533-G-A F22060 YY+
17803670-G-A 15691790-G-A F22141 YY+
17903598-C-T 15791718-C-T F22256 YY+
18028364-T-C 15916484-T-C Y+
18111097-T-G 15999217-T-G F22471 YY+
18123047-A-C 16011167-A-C F22483 YY+
18162257-G-T 16050377-G-T F22516 YY+
18677902-G-C 16566022-G-C F22794 YY+
18754476-A-G 16642596-A-G YY+
18899304-A-G 16787424-A-G F23032 YY+
18918868-C-T 16806988-C-T BY124805 YY+
18960675-G-T 16848795-G-T F23117 YY+
19095511-T-C 16983631-T-C F23307 BY20266 YY+
19123537-G-C 17011657-G-C BY126502 YY+
19292074-G-A 17180194-G-A BY128020 YY+
19336855-T-C 17224975-T-C YY+
19398893-G-A 17287013-G-A F23636 YY+
19420289-T-C 17308409-T-C F23669 YY+
19420774-A-G 17308894-A-G F23670 YY+
19532576-A-G 17420696-A-G FT2136 YY+
21093258-G-T 18931372-G-T F23880 YY+
21145101-G-A 18983215-G-A F23941 YY+
21205779-G-C 19043893-G-C F23999 YY+
21329140-G-T 19167254-G-T YY+
21380737-T-A 19218851-T-A FT348323 Y+
21457071-G-A 19295185-G-A F24322 YY+
21458153-A-G 19296267-A-G FT348347 Y+
21577661-A-G 19415775-A-G Y+
21645640-T-G 19483754-T-G F24540 YY+
21667719-T-G 19505833-T-G F24566 YY+
21681433-C-T 19519547-C-T FT348421 Y+
21778282-C-A 19616396-C-A F24683 YY+
21916201-C-G 19754315-C-G F24826 YY+
22055766-G-A 19893880-G-A F24975 YY+
22147376-T-A 19985490-T-A F25072 YY+
22193236-T-C 20031350-T-C Y+
22277282-G-C 20115396-G-C BY215732 DYZ19 +
22288276-A-C 20126390-A-C DYZ19 +
22298816-G-A 20136930-G-A DYZ19 +
22419852-T-A 20257966-T-A DYZ19 +
22419870-G-A 20257984-G-A DYZ19 +
22444430-T-C 20282544-T-C BY219398 DYZ19 +
22463828-C-G 20301942-C-G BY221204 DYZ19 +
22471838-T-A 20309952-T-A BY222664 DYZ19 +
22539630-C-A 20377744-C-A Y+
22732360-C-A 20570474-C-A F25404 YY+
23030803-C-G 20868917-C-G F25708 YY+
23102313-T-A 20940427-T-A Y+
23126615-T-C 20964729-T-C FT2262 Y+
23146800-G-T 20984914-G-T BY143345 YY+
23213125-T-C 21051239-T-C Y+
23288397-C-G 21126511-C-G FT348931 Y+
23336904-C-T 21175018-C-T Y29821 YY+
23472542-G-A 21310656-G-A BY145529 YY+
23523084-T-G 21361198-T-G F26164 YY+
23819563-A-G 21657677-A-G F26416 Y+
24414474-T-A 22268327-T-A Y+
28542653-T-C 26396506-T-C FT349208 +

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.