Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z272 > S450 > ZZ40 > S21184 > FGC13557 > A7066 > BY50830

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 STRBigY3
802975
56834498-C-T A*
58976897-C-T 56830750-C-T A*
9932010-A-C 10094401-A-C YA*
16107361-G-A 13995481-G-A P8_Prx A*
16159129-C-T 14047249-C-T P8_Dst A*
19689681-A-C 17577801-A-C P5_Prx A*
19692812-G-A 17580932-G-A P5_Prx A*
19947316-C-T 17835436-C-T P5_Prx A*
20490096-T-G 18328210-T-G P5_Dst A*
28812859-A-G 26666712-A-G A*
28812870-A-T 26666723-A-T A*
56836101-C-T A*
26325626-C-G 24179479-C-G P1_Y1 A*
20249702-C-CA 18087816-C-CA P5_Dst 13×AA*
3999627-A-G 4131586-A-G A*
25986868-A-G 23840721-A-G P1_Y1 A*
26010389-T-C 23864242-T-C P1_Y1 A*
13711877-T-G 11556201-T-G A*
26340254-G-A 24194107-G-A P1_Y1 A*
56831078-A-G A*
25946948-C-T 23800801-C-T P1_Y1 A*
56830958-A-G A*
14201671-C-T 12080965-C-T FT50128 YY+
11653735-T-C +
11645430-A-T +
13682145-A-G 11526469-A-G +
10753956-T-A +
9842040-C-T 10004431-C-T FT49989 YY+
8722708-T-C 8854667-T-C FT49874 YY+
9833170-G-A 9995561-G-A FT49987 YY+
9161969-A-T 9324360-A-T +
3544051-C-G 3676010-C-G FT48806 +
8541901-C-A 8673860-C-A FT49846 YY+
14520783-C-G 12408984-C-G FT50217 YY+
6410260-G-T 6542219-G-T FT49488 +
5572765-C-T 5704724-C-T FT49325 +
3794148-A-G 3926107-A-G FT48871 +
6730333-G-A 6862292-G-A FT49552 Y+
15940510-A-G 13828630-A-G FT50458 YY9×T+
14577802-C-A 12466002-C-A FT50229 YY+
21797639-G-A 19635753-G-A FT51334 YY+
28615963-A-G 26469816-A-G FT51730 +
26078852-T-C 23932705-T-C P1_Y1 +
23866722-C-A 21704836-C-A FT51654 Y+
23801487-A-G 21639601-A-G FT51645 Y+
23249226-C-T 21087340-C-T FT51547 YY+
22617232-G-T 20455346-G-T FT51446 YY15×T+
22616476-A-G 20454590-A-G FT51445 YY+
22474508-T-A 20312622-T-A DYZ19 +
21149510-T-A 18987624-T-A FT51200 YY+
14681953-C-T 12570019-C-T FT50246 Y+
17200249-T-C 15088369-T-C FT50713 YY+
17077444-G-A 14965564-G-A FT50686 YY+
16812038-G-T 14700158-G-T FT50639 YY+
3140095-T-C 3272054-T-C FT48700 +
15605105-A-T 13493225-A-T FT50390 YY+
15544321-T-C 13432441-T-C FT50381 YY+
15277068-A-G 13165157-A-G FT50328 YY+
15248482-A-G 13136568-A-G FT50324 Y+
15226195-G-C 13114281-G-C FT50322 Y+
3254043-A-G 3386002-A-G FT48725 +
6472746-G-A 6604705-G-A FT49504 +
2848760-C-G 2980719-C-G FT48625 YY+
5635215-C-T 5767174-C-T FGC49096 +
14045305-G-A 11924599-G-A BY206579 YY+
23549444-G-A 21387558-G-A BY13132BY13132 YY+
8603396-A-G 8735355-A-G Z229F1343 Z225 S225 V2334 YY+
2832519-A-G 2964478-A-G FT48622 YY+
22730540-C-A 20568654-C-A FT51467 YY+
7628376-G-T 7760335-G-T BY11943BY11944 YY+
2715293-C-T 2847252-C-T FT48599 YY+
28805653-G-T 26659506-G-T *
7611640-T-TAC 7743599-T-TAC 16×AC*
8565334-T-TTTG 8697293-T-TTTG 5×TTG*
22318795-G-T 20156909-G-T DYZ19 *
14848991-C-G 12737057-C-G **
15264696-T-C 13152786-T-C **
3534526-C-CA 3666485-C-CA 15×A**
15909575-G-A 13797695-G-A **
17250010-T-TAA 15138130-T-TAA 13×A**
16882574-G-A 14770694-G-A **
19189669-C-T 17077789-C-T **
19330572-T-TG 17218692-T-TG **
22426225-G-T 20264339-G-T DYZ19 **
20001263-G-T 17889383-G-T P5_Prx **
23063698-TTTTATTTA-T 20901812-TTTTATTTA-T 10×TTTA**
56862513-T-C **
22505584-C-T 20343698-C-T DYZ19 **
22530246-C-T 20368360-C-T **
22640656-A-G 20478770-A-G **
23053049-C-T 20891163-C-T **
23440243-T-A 21278357-T-A **
24667978-T-C 22521831-T-C P3_b2 **
8907675-G-A 9039634-G-A **
28546307-C-G 26400160-C-G **
3331464-T-A 3463423-T-A M222FGC435 **
13688951-G-A 11533275-G-A **
13453250-A-T 11297574-A-T **
13339001-A-T 11183325-A-T **
7450264-A-G 7582223-A-G IR1_L **
3333466-C-T 3465425-C-T **
5097348-CTT-C 5229307-CTT-C 26×T**
7028227-GACA-G 7160186-GACA-G **
4366428-G-C 4498387-G-C **
5179557-C-T 5311516-C-T **
6053016-C-G 6184975-C-G **
5054702-A-G 5186661-A-G **
17153858-G-A 15041978-G-A ***
13463183-TAC-CGT,T 11307507-TAC-CGT,T ***
5945467-CTTTTTTTTT-C,CTT 6077426-CTTTTTTTTT-C,CTT 25×T***
59008687-C-A 56862540-C-A ***
13339029-A-T 11183353-A-T ***
5977072-GTATATA-G 6109031-GTATATA-G 8×TA***
22193105-C-A 20031219-C-A ***
18913092-ATT-A 16801212-ATT-A 14×T***
21555206-G-A 19393320-G-A ***
5220169-T-TC 5352128-T-TC ***
23105648-T-A 20943762-T-A ***
22621854-G-A 20459968-G-A ***
5178062-C-CAAA 5310021-C-CAAA 20×A***
13684797-AAATGGAATGG-A 11529121-AAATGGAATGG-A 9×AATGG***
13545559-T-C 11389883-T-C ***
5155792-C-T 5287751-C-T ***
6047272-GA-G 6179231-GA-G 11×A***
5507738-G-T 5639697-G-T ***
4375325-T-G 4507284-T-G ***
4735231-T-C 4867190-T-C ***
6457484-CTT-C 6589443-CTT-C 17×T***
3925964-A-T 4057923-A-T ***
3925963-A-T 4057922-A-T ***
28812898-A-G 26666751-A-G ***
2708411-C-CGAGAGA 2840370-C-CGAGAGA 23×GA***
28812845-A-T 26666698-A-T ***
6489394-AAACT-A 6621353-AAACT-A ***
8504198-TTGTG-T 8636157-TTGTG-T 19×TG***
13532875-C-CA 11377199-C-CA 13×A***
13339040-C-T 11183364-C-T ***
13414797-A-ATT 11259121-A-ATT 20×T***
13485617-C-A,G 11329941-C-A,G ***
13339027-T-A 11183351-T-A ***
19064627-T-TA 16952747-T-TA 12×A***
22815505-GT-G,GTT 20653619-GT-G,GTT 20×T***
14000036-T-C 11879330-T-C ***
3732952-CTT-C 3864911-CTT-C 14×T***
10744260-T-G ***
4937662-G-GTT 5069621-G-GTT 12×T***
28812878-A-C 26666731-A-C ***
14931614-T-C 12819679-T-C ***
9429480-TAAAA-T,TA 9591871-TAAAA-T,TA 18×A***
28812884-A-G 26666737-A-G ***
6091720-ATTTTTT-A 6223679-ATTTTTT-A 28×T***
10744255-TC-T ***
10744252-C-T ***
6604084-CTTT-C,CTT 6736043-CTTT-C,CTT 17×T***
5931916-CTTTTT-C 6063875-CTTTTT-C 32×T***
10895833-T-G ***
8314146-CTTT-C,CTTTT 8446105-CTTT-C,CTTTT 24×T***
22902108-C-CAA 20740222-C-CAA 17×A***
13480414-G-C 11324738-G-C ***
7381397-CA-C 7513356-CA-C 11×A***
4348378-A-AAT 4480337-A-AAT 8×AT***
17622192-G-A 15510312-G-A ***
3086728-G-A 3218687-G-A ***
13339030-T-G 11183354-T-G ***
13485899-A-G 11330223-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.

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: 8029751491704993456458280022
Used in age calculations1491704993456458280022
Counts of SNPs3229
Variant counts last updated 2019-09-10 00:14:55.



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