1k Genomes

1kG: NA12340
MDKA Birth: United States

Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > CTS1751 > Z17966 > Z17969 > Z17967 > BY3227

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
NA12340		Manual
Edits
28571616-G-A 26425469-G-A CTS12307 +
15637191-A-G 13525311-A-G Y+
14681201-A-G 12569267-A-G Z6427 Y+
16242618-C-T 14130738-C-T YY+
13311500-C-A 11155824-C-A +
7622068-T-G 7754027-T-G YY+
2862737-A-T 2994696-A-T FT299932 YY+
7359439-C-A 7491398-C-A FTA9309 YY+
8245700-G-C 8377659-G-C FT300376 YY+
8434650-T-C 8566609-T-C FT300431 YY+
8558954-C-T 8690913-C-T FT300476 YY+
8614901-A-G 8746860-A-G FT300489 YY+
13952097-C-A 11831391-C-A FT300726 Y+
14293749-C-T 12173043-C-T Y66407 YY+
14660121-G-T 12548186-G-T YY+
15194739-G-C 13082825-G-C S3664 CTS3805 YY+
15200427-G-A 13088513-G-A FT301096 YY+
17240035-A-T 15128155-A-T FT301584 YY+
18166376-A-G 16054496-A-G FT301855 YY+
19101851-A-T 16989971-A-T Y+
19244686-C-T 17132806-C-T FT302105 YY+
19341779-A-G 17229899-A-G CTS10243 YY+
21267106-C-T 19105220-C-T Z4057 YY+
21290521-T-C 19128635-T-C FT302293 YY+
21741199-T-C 19579313-T-C FT302465 YY+
22645794-G-T 20483908-G-T FT302669 YY+
22883665-C-A 20721779-C-A FTA9308 Y+
28497515-G-A 26351368-G-A CTS12151 S3663 Y+
28542625-A-C 26396478-A-C FT303091 +
13921465-A-G 11800759-A-G YY+
13587405-T-C 11431729-T-C +
13587406-C-T 11431730-C-T 9×T+
2657940-G-C 2789899-G-C YY+
2810640-A-T 2942599-A-T YY+
2900547-T-C 3032506-T-C Y+
2915001-C-CTCTT 3046960-C-CTCTT +
3186017-A-G 3317976-A-G +
3301818-T-G 3433777-T-G +
3693239-A-G 3825198-A-G +
3741297-C-T 3873256-C-T +
3872973-G-A 4004932-G-A FT318802 +
4177127-T-A 4309086-T-A PF3591 +
4320985-T-C 4452944-T-C +
4536458-T-C 4668417-T-C FT320949 +
4536459-C-A 4668418-C-A FT320950 +
4555653-C-T 4687612-C-T +
4830476-G-A 4962435-G-A FT321838 +
4830627-G-A 4962586-G-A FT321839 +
4839018-TC-T 4970977-TC-T +
4966902-T-G 5098861-T-G +
5248639-C-T 5380598-C-T +
5531055-C-T 5663014-C-T +
6643703-T-G 6775662-T-G YY+
6915795-CAT-C 7047754-CAT-C +
7310413-G-C 7442372-G-C YY+
7551221-T-G 7683180-T-G YY+
7700065-ATC-A 7832024-ATC-A +
7740988-C-A 7872947-C-A YY+
8550861-AG-A 8682820-AG-A +
8823297-G-T 8955256-G-T M3835 YY+
8967665-G-A 9130056-G-A +
9713365-CAG-C 9875756-CAG-C IR3_Prx +
13256070-G-A 11100394-G-A +
13260623-A-G 11104947-A-G +
13292228-C-CT 11136552-C-CT +
13308068-T-G 11152392-T-G +
13346339-A-G 11190663-A-G +
13375838-TG-T 11220162-TG-T +
13389725-A-G 11234049-A-G +
13403524-C-T 11247848-C-T +
13407940-A-G 11252264-A-G +
13411668-A-G 11255992-A-G +
13440887-C-A 11285211-C-A +
13448891-C-CTCCAG 11293215-C-CTCCAG +
13499051-G-A 11343375-G-A +
13515218-T-C 11359542-T-C +
13602115-C-T 11446439-C-T +
13812762-G-T 11692056-G-T FT328443 +
13840603-A-G 11719897-A-G FT328654 +
13847229-GACT-G 11726523-GACT-G +
14031750-C-CTTTA 11911044-C-CTTTA 4×TCTT+
14071336-A-C 11950630-A-C YY+
14328042-G-T 12207336-G-T YY+
14850035-G-T 12738101-G-T FT304581 YY+
14881732-GTA-G 12769800-GTA-G +
15226091-G-T 13114177-G-T Y+
15528551-A-C 13416671-A-C YY+
15637206-A-G 13525326-A-G Y+
16070732-G-A 13958852-G-A FT301323 Y+
16242600-GTCTA-G 14130720-GTCTA-G 4×TCTA+
16242608-A-G 14130728-A-G YY+
16432149-C-G 14320269-C-G Z31312 YY+
16435936-G-T 14324056-G-T YY+
16739068-AG-A 14627188-AG-A +
17181316-C-T 15069436-C-T YY+
17270493-T-G 15158613-T-G YY+
17412979-T-G 15301099-T-G YY+
17828121-G-T 15716241-G-T CTS8085 Y+
17860400-C-T 15748520-C-T Y+
17895173-TAA-T 15783293-TAA-T +
18511611-C-T 16399731-C-T P6_Dst +
18688498-T-TA 16576618-T-TA +
18738092-C-T 16626212-C-T YY+
18948677-C-A 16836797-C-A M5755 YY+
19049508-A-ATAT 16937628-A-ATAT +
19390103-A-G 17278223-A-G Y+
19397977-G-T 17286097-G-T M5006 YY+
21742034-C-A 19580148-C-A YY+
21942036-T-G 19780150-T-G Y+
22168010-AGATT-A 20006124-AGATT-A +
22228890-G-T 20067004-G-T DYZ19 +
22271623-C-A 20109737-C-A DYZ19 +
22273028-G-T 20111142-G-T BY52325 DYZ19 +
22465449-C-G 20303563-C-G DYZ19 +
22507467-G-C 20345581-G-C FGC22160 DYZ19 +
22540571-TAC-T 20378685-TAC-T +
22727630-A-C 20565744-A-C M9358 YY+
22981817-AG-A 20819931-AG-A +
22981818-GT-G 20819932-GT-G +
23325055-T-A 21163169-T-A YY+
23435163-G-T 21273277-G-T YY+
23519330-T-C 21357444-T-C Y+
23640751-G-T 21478865-G-T Y+
23782409-T-G 21620523-T-G Y+
23791642-A-C 21629756-A-C Y+
23807600-G-A 21645714-G-A Y+
23878065-T-A 21716179-T-A +
24357114-G-A 22210967-G-A FT332756 +
24432858-C-A 22286711-C-A Y+
24470935-A-C 22324788-A-C Y+
27617573-G-A 25471426-G-A P1_Y2 14×A+
28642807-CAG-C 26496660-CAG-C +
58974887-ATTCC-A 56828740-ATTCC-A +

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
Manual8407602-T-TG8539561-T-TG3 reads, all show the insertion.
Manual7274352-T-C7406311-T-C2 reads, both are C.
Manual7356592-C-G7488551-C-G4 reads, all G.
Manual7356596-T-C7488555-T-C3 reads, all C.
Manual8265951-G-A8397910-G-A2 reads, both A.
Manual17126267-C-T15014387-C-T2T
Manual17757799-G-A15645919-G-AJust one valid read, but it is an A.
Manual21402261-G-T19240375-G-TJust one valid read, but it is a T.
Manual21938654-T-C19776768-T-C2 reads, both C.
Manual22144855-A-G19982969-A-GOne read, but it's a G.
Manual22445303-C-T20283417-C-T6 reads and all are T.
Manual22460463-A-G20298577-A-GAt least two valid reads, and both are G.
Manual24081244-A-G21935097-A-G5 reads. 3 G and 2 A.
Manual24109676-A-T21963529-A-T7 reads total. 1T 6A. One of the A reads may not belong here.
Manual24661527-C-T22515380-C-T4T 1C