1k Genomes

1kG: HG01066
MDKA Birth: Puerto Rico
Puerto Rican in Puerto Rico

Tree Position

R-M269 > L23 > L51 > Z2118 > ~18571755-G-A > S1161 > S1141 > A613 > BY11299 > 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
HG01066		Manual
Edits
22297945-G-T 20136059-G-T DYZ19 +
14392171-G-A 12271467-G-A YY16×A+
22362305-C-A 20200419-C-A DYZ19 +
15505494-CTA-C 13393614-CTA-C +
13705198-T-A 11549522-T-A BY1007 +
13845581-GAATCA-G 11724875-GAATCA-G +
22299833-G-A 20137947-G-A BY24436 DYZ19 +
17794200-TTCTTTC-T 15682320-TTCTTTC-T +
28802844-G-A 26656697-G-A +
13705224-T-A 11549548-T-A BY25122 +
14286775-G-A 12166069-G-A YY+
28803783-T-G 26657636-T-G BY18 +
28802844-G-GAGCGA 26656697-G-GAGCGA +
27637479-C-T 25491332-C-T P1_Y2 +
58829066-T-A 56761805-A-T +
18016494-C-A 15904614-C-A BY178297A18541 A18494 P7_Dst Y+
13455059-G-GCATTC 11299383-G-GCATTC 9×CATTC+
13618495-G-A 11462819-G-A +
13618508-T-A 11462832-T-A +
24600382-C-T 22454235-C-T BY23042 P3_t2 +
17477484-G-A 15365604-G-A YY14×A+
3580631-C-G 3712590-C-G +
2940096-G-A 3072055-G-A +
13529856-G-T 11374180-G-T +
5941845-T-C 6073804-T-C +
13240346-C-T 11084670-C-T +
13387250-A-G 11231574-A-G +
2842003-C-T 2973962-C-T YY14×T+
13222655-C-G 11066979-C-G +
13440350-A-C 11284674-A-C +
9030495-G-A 9192886-G-A BY77520 Y+
13255859-C-T 11100183-C-T +
3436225-T-G 3568184-T-G L707 +
13747513-A-T 11591837-A-T +
9231660-G-A 9394051-G-A Y+
13705196-T-G 11549520-T-G +
3037295-T-C 3169254-T-C +
19447050-T-G 17335170-T-G YY+
13294580-T-G 11138904-T-G +
2750717-T-G 2882676-T-G YY+
2871415-G-T 3003374-G-T YY+
3229146-G-T 3361105-G-T +
3239997-C-A 3371956-C-A +
3292652-T-A 3424611-T-A +
3349274-T-A 3481233-T-A +
3434288-CT-C 3566247-CT-C +
3554056-C-CAA 3686015-C-CAA +
3557529-A-G 3689488-A-G +
3557537-G-C 3689496-G-C +
3568313-G-A 3700272-G-A +
3640987-TTTTCCTTTCC-T 3772946-TTTTCCTTTCC-T 11×TTTCC+
3653551-T-C 3785510-T-C +
3829722-C-T 3961681-C-T FT318630 +
3878659-A-AAG 4010618-A-AAG +
4498179-A-ATTTT 4630138-A-ATTTT 23×T+
4704840-CAATT-C 4836799-CAATT-C +
4764721-TTA-T 4896680-TTA-T 9×TA+
4997551-G-GAGAGAGAT 5129510-G-GAGAGAGAT +
5039911-A-G 5171870-A-G +
5400468-C-CTT 5532427-C-CTT 19×T+
5974086-T-A 6106045-T-A +
6006482-A-T 6138441-A-T +
6231276-CAA-C 6363235-CAA-C IR3_Dst +
6401516-T-C 6533475-T-C +
6447774-G-T 6579733-G-T 16×T+
6734680-C-T 6866639-C-T BY169130 YY21×T+
6998020-G-C 7129979-G-C YY+
8550862-G-A 8682821-G-A S11626 YY+
8747695-ATGAG-A 8879654-ATGAG-A +
8823297-G-T 8955256-G-T M3835 YY+
8835665-C-A 8967624-C-A S11994 YY+
8901990-TC-T 9033949-TC-T +
9030498-A-G 9192889-A-G Y+
9075188-C-CTTT 9237579-C-CTTT 20×T+
9825002-CAT-C 9987393-CAT-C +
10006625-A-C 10169016-A-C Y+
13215171-T-G 11059495-T-G +
13242652-T-G 11086976-T-G +
13274621-C-G 11118945-C-G +
13289001-T-C 11133325-T-C +
13294295-TGAG-T 11138619-TGAG-T +
13363219-C-T 11207543-C-T +
13389065-CTTAGAGTGAGACT-C 11233389-CTTAGAGTGAGACT-C +
13399230-G-A 11243554-G-A +
13445382-A-G 11289706-A-G +
13470538-G-A 11314862-G-A +
13473486-C-T 11317810-C-T +
13476642-C-G 11320966-C-G +
13506676-T-TAA 11351000-T-TAA +
13508623-C-G 11352947-C-G +
13529859-G-A 11374183-G-A +
13538672-A-C 11382996-A-C +
13611988-G-T 11456312-G-T 19×T+
13618226-T-G 11462550-T-G +
13618863-A-C 11463187-A-C +
13620939-G-T 11465263-G-T +
13621525-T-G 11465849-T-G +
14022715-T-G 11902009-T-G YY+
14552135-A-C 12440336-A-C YY+
14926335-C-G 12814400-C-G YY+
15231011-A-C 13119097-A-C Y+
15276877-T-C 13164966-T-C YY+
15566839-AG-A 13454959-AG-A +
15608289-G-T 13496409-G-T YY+
15967483-G-T 13855603-G-T YY+
16215905-C-T 14104025-C-T FTB21439 Y+
16277219-A-C 14165339-A-C YY+
16467955-G-T 14356075-G-T Y+
16564393-T-TAGAC 14452513-T-TAGAC 4×AGAC+
17145245-G-T 15033365-G-T YY+
17276551-T-C 15164671-T-C M12078 Y+
17662175-A-G 15550295-A-G YY+
17668513-T-TTTTTG 15556633-T-TTTTTG 7×TTTG+
17713850-C-CTTT 15601970-C-CTTT 23×T+
17793863-T-TATCA 15681983-T-TATCA +
17948277-A-C 15836397-A-C YY+
17998267-C-G 15886387-C-G P7_Gap Y+
17998578-G-C 15886698-G-C P7_Gap Y+
18412865-G-A 16300985-G-A FTB29587 P6_Gap +
18872278-CTTT-C 16760398-CTTT-C +
18872279-TTTC-T 16760399-TTTC-T +
18923360-TGG-T 16811480-TGG-T +
19372327-T-TAGAC 17260447-T-TAGAC +
21772948-C-A 19611062-C-A YY+
21853675-C-CAA 19691789-C-CAA +
22245793-C-A 20083907-C-A DYZ19 +
22259633-C-T 20097747-C-T S3078 DYZ19 +
22269114-T-C 20107228-T-C DYZ19 +
22269120-G-A 20107234-G-A DYZ19 +
22297923-T-A 20136037-T-A DYZ19 +
22297926-C-G 20136040-C-G BY216606 DYZ19 +
22366324-G-C 20204438-G-C DYZ19 +
22792261-C-A 20630375-C-A YY+
23123237-C-CA 20961351-C-CA 9×A+
24929437-CAT-C 22783290-CAT-C g1 +
27055691-CA-C 24909544-CA-C P1_r4 +
28385952-C-T 26239805-C-T P1_gr2 +
28385966-C-T 26239819-C-T P1_gr2 +
28709570-T-C 26563423-T-C +
28711307-T-TG 26565160-T-TG +
28726259-A-G 26580112-A-G Y+
28814708-T-A 26668561-T-A +
58895258-T-C 56695613-A-G +
59013901-A-AAG 56867754-A-AAG +
3024645-G-A 3156604-G-A FGC9662 +
3108773-C-T 3240732-C-T Z897 +
3153434-A-C 3285393-A-C FT316249 +
3634999-A-C 3766958-A-C +
4005071-G-T 4137030-G-T +
4438800-A-G 4570759-A-G +
4438805-T-C 4570764-T-C +
4669408-A-G 4801367-A-G +
4850376-C-T 4982335-C-T FT223456 +
4936897-C-T 5068856-C-T TY4988 FGC1178 +
6037090-A-G 6169049-A-G +
7020475-G-A 7152434-G-A L158CTS799 PF3954 Y+
7384203-C-A 7516162-C-A CTS1401 Y+
8203533-C-A 8335492-C-A YY+
8482425-A-C 8614384-A-C YY+
9127953-G-T 9290344-G-T FT295698 Y+
9423154-AAT-A 9585545-AAT-A +
13304489-T-C 11148813-T-C A14599 +
13529749-T-G 11374073-T-G FGC24549 +
13537537-A-G 11381861-A-G +
13617216-C-T 11461540-C-T +
13919733-A-C 11799027-A-C FT295856 Y+
13971476-G-A 11850770-G-A PF639 Y+
14300581-G-T 12179875-G-T CTS2428 Y+
14509984-G-C 12398189-G-C CTS2834 YY+
15804138-G-A 13692258-G-A CTS4767 Y+
16054475-C-T 13942595-C-T CTS5184 YY+
16379199-C-G 14267319-C-G YY+
16900479-G-T 14788599-G-T YY+
17038332-TC-T 14926452-TC-T +
17754419-G-T 15642539-G-T CTS7938 YY+
18018353-A-G 15906473-A-G Y+
18693289-C-T 16581409-C-T Z10921 V3407 YY+
19100856-T-G 16988976-T-G CTS9851 Y+
19561869-C-T 17449989-C-T Y+
21170653-T-C 19008767-T-C YY+
21274881-C-T 19112995-C-T Y+
21580466-G-A 19418580-G-A FT298546 Y+
22271797-C-T 20109911-C-T FT454357 DYZ19 +
22460435-G-T 20298549-G-T BY27545 DYZ19 +
22483240-G-C 20321354-G-C DYZ19 +
22815525-TA-T 20653639-TA-T +
23082477-T-A 20920591-T-A CTS11362 Y+
23200904-C-T 21039018-C-T CTS11640 Y+
24386538-CTA-C 22240391-CTA-C +
24455364-G-A 22309217-G-A M11011 Y+

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
Manual17324164-G-C15212284-G-C1C
Manual8467345-G-C8599304-G-C1C
Manual9762593-T-C9924984-T-C1C