Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > FGC11134 > FGC12055 > A353 > S3675 > Y16012

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
58837247-T-C 56753624-A-G +
13399359-C-T 11243683-C-T +
13255975-A-G 11100299-A-G +
13259580-G-A 11103904-G-A +
13259643-T-C 11103967-T-C +
13265855-C-T 11110179-C-T +
13271784-AAAAC-A 11116108-AAAAC-A +
13279495-C-G 11123819-C-G +
13287415-C-G 11131739-C-G +
13290548-C-T 11134872-C-T +
13311989-G-A 11156313-G-A +
13339788-C-T 11184112-C-T +
13351208-T-A 11195532-T-A +
13398996-T-C 11243320-T-C +
13402099-T-G 11246423-T-G +
13206798-A-AAG 11051122-A-AAG +
13435909-A-G 11280233-A-G +
13445647-C-T 11289971-C-T ZS200 +
13451550-A-ACTGCC 11295874-A-ACTGCC +
13457955-C-G 11302279-C-G +
13478556-T-G 11322880-T-G +
13503307-AGAAGTAG-A 11347631-AGAAGTAG-A +
13506676-T-TAA 11351000-T-TAA +
13518961-G-A 11363285-G-A +
13519382-A-C 11363706-A-C +
13572807-G-A 11417131-G-A +
13242795-C-G 11087119-C-G +
13206783-T-TAA 11051107-T-TAA +
13640567-A-T 11484891-A-T +
6909168-C-A 7041127-C-A M8148 YY+
5253238-A-G 5385197-A-G +
5305681-A-C 5437640-A-C FT323475 +
5353441-G-A 5485400-G-A FT323628 +
5507709-T-G 5639668-T-G +
5508057-A-T 5640016-A-T +
5846180-G-GAAAA 5978139-G-GAAAA 39×A+
6003909-A-C 6135868-A-C +
6566077-C-T 6698036-C-T +
6597368-A-AC 6729327-A-AC +
6597965-A-G 6729924-A-G +
6616381-G-A 6748340-G-A FT326998 +
6630511-TC-T 6762470-TC-T +
7197567-TGTA-T 7329526-TGTA-T +
10077334-T-C 10239725-T-C +
7601007-G-GA 7732966-G-GA +
7688651-A-C 7820610-A-C YY+
8367622-CA-C 8499581-CA-C +
8407600-C-CT 8539559-C-CT +
8566852-T-TG 8698811-T-TG +
8725796-CAA-C 8857755-CAA-C +
9157091-C-T 9319482-C-T FT295708 +
9429496-AAAG-A 9591887-AAAG-A +
9854215-TTG-T 10016606-TTG-T +
9958668-G-A 10121059-G-A BY18201FGC17916 Y+
10020656-C-T 10183047-C-T Y+
13611988-G-T 11456312-G-T 19×T+
13640577-A-G 11484901-A-G +
5178061-GCA-G 5310020-GCA-G +
22269114-T-C 20107228-T-C DYZ19 +
18763904-CGT-C 16652024-CGT-C +
18855776-T-G 16743896-T-G YY+
19126461-ATGT-A 17014581-ATGT-A +
19231319-C-CTTT 17119439-C-CTTT 24×T+
19409413-AC-A 17297533-AC-A +
20243597-T-C 18081711-T-C P5_Dst +
20659075-A-G 18497189-A-G P4_Prx +
21233755-G-C 19071869-G-C YY+
21523471-A-C 19361585-A-C Y+
21870887-T-G 19709001-T-G YY+
21979616-TA-T 19817730-TA-T +
22009617-G-A 19847731-G-A YY+
22269120-G-A 20107234-G-A DYZ19 +
17895823-C-T 15783943-C-T YY+
22294790-G-T 20132904-G-T DYZ19 +
23106176-A-C 20944290-A-C Y+
23161972-T-G 21000086-T-G Y+
23321854-T-G 21159968-T-G M4934 YY+
24413807-TTC-T 22267660-TTC-T +
24470935-A-C 22324788-A-C Y+
28571219-T-G 26425072-T-G +
28780461-G-A 26634314-G-A +
28802591-G-T 26656444-G-T +
28818222-G-GAATGT 26672075-G-GAATGT +
58861967-T-A 56728904-A-T +
59019548-ACACAAG-A 56873401-ACACAAG-A +
17923789-AGAAG-A 15811909-AGAAG-A +
17737786-C-G 15625906-C-G YY+
13647478-C-A 11491802-C-A +
15259276-TC-T 13147360-TC-T +
13649265-A-G 11493589-A-G +
13805447-G-C 11684741-G-C BY1025 +
13884598-T-A 11763892-T-A Y+
13914244-A-C 11793538-A-C Y+
14067329-A-C 11946623-A-C M3799 YY+
14286784-C-CTTTTTT 12166078-C-CTTTTTT 22×T+
14440391-G-A 12319664-G-A Z25315 Y+
14790440-G-A 12678511-G-A YY+
14875585-TC-T 12763655-TC-T +
14875592-G-GTT 12763662-G-GTT 28×T+
15178315-A-C 13066401-A-C Y+
15209597-G-T 13097683-G-T M12329 YY+
15557031-CT-C 13445151-CT-C +
17721031-A-C 15609151-A-C YY+
15683652-AT-A 13571772-AT-A +
15869829-GGT-G 13757949-GGT-G +
16277219-A-C 14165339-A-C YY+
16463022-G-A 14351142-G-A CTS5736 Y+
16602219-G-T 14490339-G-T M7210 YY+
16710761-ATG-A 14598881-ATG-A +
16809410-ATAGAT-A 14697530-ATAGAT-A +
17074799-G-C 14962919-G-C YY+
17274959-TAGAC-T 15163079-TAGAC-T +
17477483-AG-A 15365603-AG-A +
17683951-C-G 15572071-C-G CTS7818 M4085 Y+
17720084-T-G 15608204-T-G YY+
5253156-G-T 5385115-G-T +
5168673-T-C 5300632-T-C +
16300321-G-T 14188441-G-T YY+
2658789-T-A 2790748-T-A YY13×A+
58891119-T-A 56699752-A-T +
22300858-G-A 20138972-G-A DYZ19 +
22300856-A-T 20138970-A-T DYZ19 +
58843332-C-G 56747539-G-C +
2940096-G-A 3072055-G-A +
26400702-C-T 24254555-C-T P1_Y1 +
6648613-C-T 6780572-C-T YY27×T+
13254529-C-A 11098853-C-A +
15260684-C-CTTTTTT 13148768-C-CTTTTTT 25×T+
15799114-CCCTT-TCCTC 13687234-CCCTT-TCCTC 14×CCTT+
17694609-G-A 15582729-G-A YY14×A+
14358411-AA-GG 12237706-AA-GG +
9040197-G-A 9202588-G-A Z17893 Y+
6859969-C-G 6991928-C-G FT294695 YY+
7000000-C-T 7131959-C-T FT294729 Y+
7080256-C-G 7212215-C-G Y16008 YY+
7748802-G-C 7880761-G-C FT295014 YY+
7901842-T-C 8033801-T-C YY+
8054610-C-G 8186569-C-G FT295152 YY+
8484093-G-A 8616052-G-A FGC37159 YY+
14306431-A-G 12185725-A-G Y+
14786619-G-A 12674689-G-A Y16067 YY+
15132065-A-T 13020152-A-T YY14×T+
16374062-A-C 14262182-A-C FT296833 YY+
16687612-G-A 14575732-G-A CTS6129 S3669 Y+
22294800-G-C 20132914-G-C DYZ19 +
18271891-C-A 16160011-C-A P6_Prx +
17797266-T-C 15685386-T-C CTS8018 Y+
28790987-C-T 26644840-C-T +
28796517-T-G 26650370-T-G +
23563321-TAC-T 21401435-TAC-T 9×AC+
58862300-G-A 56728571-C-T +
17683950-C-T 15572070-C-T CTS7817 M4248 Y+
14172758-T-C 12052052-T-C YY+
58825021-C-A 56765850-G-T +
9195435-G-T 9357826-G-T Y+
19257945-C-A 17146065-C-A BZ1576 YY+
15324344-TG-T 13212462-TG-T +
13302042-C-T 11146366-C-T +
17676029-C-T 15564149-C-T YY15×T+
25200915-G-A 23054768-G-A g1 4×AGAA+
15522280-T-TA 13410400-T-TA 8×A+
22294838-A-G 20132952-A-G DYZ19 +
58864217-T-C 56726654-A-G +
13323478-T-A 11167802-T-A +
58861966-A-C 56728905-T-G +
58916669-G-T 56674202-C-A +
28818194-G-GTGGAA 26672047-G-GTGGAA 5×TGGAA+
58864177-T-C 56726694-A-G +
58864194-C-A 56726677-G-T +
13529927-C-A 11374251-C-A +
28797882-G-T 26651735-G-T +
8964955-N-G 9096914-N-G +
8660569-G-A 8792528-G-A Y+
22339013-A-C 20177127-A-C DYZ19 +
16897755-T-C 14785875-T-C CTS6443 S3674 YY+
17962728-C-T 15850848-C-T FGC69619 YY+
5012485-G-A 5144444-G-A FT322422 +
3759084-G-T 3891043-G-T +
28790967-T-A 26644820-T-A +
7241839-C-G 7373798-C-G Y+
16290527-C-A 14178647-C-A S18097 YY+
13302961-GCAAAAAAAA-G 11147285-GCAAAAAAAA-G +
14399072-T-TG 12278368-T-TG +
3111100-G-A 3243059-G-A S3383 +
3229565-GTT-G 3361524-GTT-G +
3247284-C-T 3379243-C-T +
3253419-A-G 3385378-A-G +
3508914-A-G 3640873-A-G +
3511785-G-A 3643744-G-A +
3518435-C-T 3650394-C-T FT141527FT141568 +
3845140-T-TGC 3977099-T-TGC 11×G+
22011557-C-CAA 19849671-C-CAA 21×A+
4030299-G-A 4162258-G-A +
4072708-T-C 4204667-T-C Z479 +
4216951-A-C 4348910-A-C FGC24521 +
4269147-C-T 4401106-C-T +
4342013-G-T 4473972-G-T +
4466549-A-C 4598508-A-C +
4491222-C-A 4623181-C-A +
4491242-C-A 4623201-C-A +
4529168-C-A 4661127-C-A +
4779273-C-A 4911232-C-A +
4779974-C-T 4911933-C-T +
4800722-G-T 4932681-G-T FT321763 +
3196582-C-A 3328541-C-A FT316393 +
13139025-CCACT-C 10628511-CCACT-C +
18069759-A-C 15957879-A-C FT297551 YY+
13255216-C-T 11099540-C-T +
18117638-A-C 16005758-A-C CTS8628 S3672 YY+
18813798-A-G 16701918-A-G CTS9303 S3677 YY+
21310296-G-A 19148410-G-A FT298356 YY+
22981690-A-C 20819804-A-C FT299149 Y+
23326304-C-T 21164418-C-T CTS11871 S3673 YY+
23495623-C-T 21333737-C-T YY+
23516997-G-A 21355111-G-A FT299378 Y+
28751805-C-T 26605658-C-T +
13258549-T-C 11102873-T-C +
13268891-CTT-C 11113215-CTT-C 11×T+
13255204-G-A 11099528-G-A +
58839518-G-T 56751353-C-A +
13194516-ATTCC-A 11038840-ATTCC-A +
58896343-T-C 56694528-A-G +
58896303-T-C 56694568-A-G +
58896320-C-A 56694551-G-T +
13747513-A-T 11591837-A-T +
13441590-T-A 11285914-T-A Z11552 +
13441588-A-T 11285912-A-T +
28802693-G-C 26656546-G-C +
13273994-C-T 11118318-C-T +
7601009-ATGT-A 7732968-ATGT-A +
13694756-G-GGAACT 11539080-G-GGAACT +
24425337-A-ATGCG 22279190-A-ATGCG +
24425339-G-GCATT 22279192-G-GCATT +
58977552-ATTCTG-A 56831405-ATTCTG-A +
59021932-T-TTTC 56875785-T-TTTC +

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:

HG0107922229264-C-A20067378-C-AChecked BAM File.
Manual19216573-A-AAAAAC17104693-A-AAAAAC3 reads cover the area and all show the insertion.
Manual15133462-C-T13021549-C-TJust one read, but it does have the mutation.
Manual17032350-A-G14920470-A-G1 good read, 1 poor read, but both G.
Manual18835438-A-G16723558-A-G2 reads, both G.
Manual22445412-G-C20283526-G-C10 reads, all C.
Manual23459153-ATATTTT-A21297267-ATATTTT-A2 reads, both show the deletion.

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