1k Genomes

1kG: HG04198
MDKA Birth: United Kingdom
Indian Telugu in the UK

Tree Position

A0-T-YP2191 > P305[A1] > A1b > BT/A1b2 > M168/PF1416[CT] > P143[CF] > M89/PF2746[F] > F1329/M3658[GHI > F929[HIJK] > L901/M2939[H] > 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
HG04198
22484559-T-G 20322673-T-G Y125244FT460453 DYZ19 +
2854213-T-A 2986172-T-A FT303267 YY+
3007987-T-C 3139946-T-C FT315725 +
3166079-C-T 3298038-C-T FT316289 +
3178824-C-T 3310783-C-T FT316328 +
3299801-C-T 3431760-C-T FT316756 +
3646814-G-A 3778773-G-A FT318002 +
3688257-A-G 3820216-A-G FT318140 +
3804433-A-T 3936392-A-T FT318542 +
3811551-C-T 3943510-C-T FT318562 +
4168142-A-G 4300101-A-G FT135917 +
4455880-A-G 4587839-A-G FT320702 +
4606607-A-G 4738566-A-G FT321187 +
5081002-G-A 5212961-G-A FT322651 +
5250965-G-A 5382924-G-A FT323249 +
5490336-T-C 5622295-T-C FT324075 +
5728106-G-A 5860065-G-A FT324902 +
5739063-T-G 5871022-T-G +
5843927-A-C 5975886-A-C FT325249 +
6009919-G-T 6141878-G-T FT325847 +
6036573-A-G 6168532-A-G FT325929 +
6039123-C-T 6171082-C-T FT325938 +
6479257-G-A 6611216-G-A FT326689 +
6624692-G-A 6756651-G-A FT303285 Y+
6705381-C-G 6837340-C-G FT303306 YY+
7031239-T-G 7163198-T-G FT303416 Y+
7127231-G-A 7259190-G-A FT195494 YY+
7194488-G-A 7326447-G-A YY+
7327464-G-A 7459423-G-A FT303520 YY+
7389396-C-T 7521355-C-T Y27302 YY+
7931938-G-A 8063897-G-A FT303703 YY+
8064493-G-T 8196452-G-T FT303761 Y+
8139257-C-G 8271216-C-G FT303783 YY+
8148784-G-A 8280743-G-A FT303787 YY+
8211461-A-C 8343420-A-C FT303822 YY+
8235264-A-T 8367223-A-T FT303834 YY+
8322464-C-A 8454423-C-A Y+
8606185-T-C 8738144-T-C FT303947 YY+
8739589-G-A 8871548-G-A FT304014 Y+
8905693-T-C 9037652-T-C FT304058 +
9034891-C-T 9197282-C-T FGC7986 Y+
9438213-C-T 9600604-C-T FT304132 YY+
9803115-G-A 9965506-G-A FGC16207 Y+
9922759-A-G 10085150-A-G Y+
10059223-G-T 10221614-G-T +
13314630-C-T 11158954-C-T +
13431997-A-G 11276321-A-G +
13504496-C-T 11348820-C-T +
13504788-T-C 11349112-T-C +
13509847-C-T 11354171-C-T +
13543490-C-T 11387814-C-T +
13554382-G-A 11398706-G-A +
13563969-T-A 11408293-T-A +
13618449-G-T 11462773-G-T +
13642641-T-A 11486965-T-A +
13827842-G-A 11707136-G-A FT328570 +
13874488-T-C 11753782-T-C Y27356 Y+
13906163-C-A 11785457-C-A FT304183 Y+
14004425-T-C 11883719-T-C FT304247 YY+
14231118-G-A 12110412-G-A FT304352 YY+
14269244-G-T 12148538-G-T FT304365 Y+
14279646-A-G 12158940-A-G FT304374 Y+
14301779-A-G 12181073-A-G FT304381 YY+
14458917-G-A 12338190-G-A FT274004 YY+
14531779-C-A 12419980-C-A FT304489 Y+
14565729-T-A 12453929-T-A FT304496 Y+
14585333-G-C 12473533-G-C FT304503 Y+
14671921-A-G 12559987-A-G FT304528 Y+
14789703-A-T 12677774-A-T FT304565 YY+
14803976-A-G 12692047-A-G FT304571 YY+
15147269-T-A 13035356-T-A FT304665 Y+
15149519-A-T 13037606-A-T FT304666 Y+
15317290-A-C 13205396-A-C FT304718 YY+
15441769-G-C 13329889-G-C FT304755 YY+
15673603-C-A 13561723-C-A Y+
15813181-C-G 13701301-C-G FT304870 YY+
15819214-C-A 13707334-C-A FT304873 YY+
15861683-A-G 13749803-A-G FT304889 YY+
15994318-T-A 13882438-T-A FT304919 YY+
16320676-G-T 14208796-G-T FT304997 Y+
16325386-C-A 14213506-C-A FT305001 YY+
16453574-G-T 14341694-G-T FT305045 YY+
16956694-T-G 14844814-T-G FT305221 YY+
17052179-C-T 14940299-C-T FT305245 YY+
17063084-C-T 14951204-C-T Y+
17068148-A-C 14956268-A-C FT305254 Y+
17175165-G-A 15063285-G-A FT237097 YY+
17301580-C-T 15189700-C-T FT305324 YY+
17304869-T-C 15192989-T-C YY+
17339780-A-G 15227900-A-G FT305338 YY+
17499771-C-T 15387891-C-T FT305398 Y+
17747237-A-G 15635357-A-G FT305464 YY+
17883080-G-A 15771200-G-A FT305523 YY+
18076865-C-A 15964985-C-A FT305588 YY+
18080226-T-C 15968346-T-C Y+
18154986-T-G 16043106-T-G FT305626 YY+
18167274-T-C 16055394-T-C FT305631 YY+
18167611-A-T 16055731-A-T FT305632 YY+
18193598-C-T 16081718-C-T Y35416 YY+
18386346-G-A 16274466-G-A FT305671 P6_Gap +
18763904-C-A 16652024-C-A FT305773 YY+
18813358-A-G 16701478-A-G FT305793 YY+
18875946-G-A 16764066-G-A FT305813 Y+
18902637-G-A 16790757-G-A FT305819 YY+
19091780-C-T 16979900-C-T Y103603 YY+
19238733-C-A 17126853-C-A FT305968 YY+
19268263-A-C 17156383-A-C FT305984 YY+
19301416-G-C 17189536-G-C FT305997 Y+
19327845-C-T 17215965-C-T Y+
19331822-C-T 17219942-C-T M6765 YY+
19446829-C-G 17334949-C-G FT306044 YY+
19453202-C-T 17341322-C-T FT306049 YY+
21315645-C-G 19153759-C-G FT306209 YY+
21325582-A-G 19163696-A-G FT306214 Y+
21385854-C-A 19223968-C-A FT306239 YY+
21549135-C-T 19387249-C-T Y27363 YY+
21597280-C-A 19435394-C-A FT306327 Y+
21601661-A-G 19439775-A-G FT306329 Y+
21765668-C-A 19603782-C-A FT306373 YY+
21784885-T-A 19622999-T-A FT306380 YY+
21791481-G-A 19629595-G-A FGC7822 Y+
21913943-A-C 19752057-A-C FT306417 Y+
21979546-G-A 19817660-G-A FT229642 YY+
22001129-T-C 19839243-T-C FT306442 Y+
22004703-A-T 19842817-A-T FT306446 YY+
22161642-C-T 19999756-C-T FT306490 YY+
22220348-G-C 20058462-G-C DYZ19 +
22246875-G-A 20084989-G-A DYZ19 +
22484424-T-C 20322538-T-C DYZ19 +
22485132-G-C 20323246-G-C DYZ19 +
22487738-G-C 20325852-G-C DYZ19 +
22490435-G-T 20328549-G-T DYZ19 +
22510316-A-C 20348430-A-C BY34367 DYZ19 +
22628073-C-A 20466187-C-A FT306551 Y+
22975238-C-G 20813352-C-G FT306639 YY+
23022051-T-C 20860165-T-C FT306653 YY+
23030064-T-C 20868178-T-C FT306656 YY+
23087166-C-A 20925280-C-A FT306686 Y+
23143965-T-A 20982079-T-A FT306708 Y+
23229180-C-T 21067294-C-T Y+
23231913-T-A 21070027-T-A FT306731 Y+
23488996-G-T 21327110-G-T FT306802 YY+
23955329-A-G 21809182-A-G FT332673 +
24071889-A-G 21925742-A-G P3_b1 +
28649247-G-A 26503100-G-A Y+
28689725-A-G 26543578-A-G FT307047 +
58986199-A-G 56840052-A-G +

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.