Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > DF21/S192 > S5488 > BY518 > S7200 > S6003 > Z16543 > S6000 > FGC43483 > FGC43477 > FGC43478

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
IN54950
28021301-C-T 25875154-C-T P1_Y2 A+
58977496-G-A 56831349-G-A A*
13451271-C-T 11295595-C-T A*
56833463-A-AATTCC A*
10626866-T-C A*
20059005-G-T 17947125-G-T P5_Prx A*
56836153-T-TTCTGC A*
25941074-G-A 23794927-G-A P1_Y1 A*
15339974-G-A 13228092-G-A FT63088 YY+
8709351-C-A 8841310-C-A FT62901 YY+
3659869-A-AG 3791828-A-AG +
7934505-C-G 8066464-C-G FT62836 YY+
22994383-C-T 20832497-C-T FT63590 YY+
2708411-CGAGAGA-C,CGA 2840370-CGAGAGA-C,CGA 23×GA*
4729765-T-C 4861724-T-C **
15495167-C-CAAAAA 13383287-C-CAAAAA 14×A**
7895748-A-G 8027707-A-G **
6625283-T-C 6757242-T-C **
15184812-C-T 13072898-C-T **
13455731-T-C 11300055-T-C **
14685844-A-G 12573910-A-G **
3779060-A-T 3911019-A-T **
13294167-T-G 11138491-T-G **
3031550-A-T 3163509-A-T **
8751038-A-G 8882997-A-G **
3332343-A-G 3464302-A-G **
3792386-C-T 3924345-C-T **
24582837-CAAAA-C 22436690-CAAAA-C P3_t2 17×A**
3755245-T-A 3887204-T-A **
6260319-AC-A 6392278-AC-A IR3_Dst **
21887409-CT-C 19725523-CT-C **
16050944-TTC-T 13939064-TTC-T **
5346065-T-C 5478024-T-C **
13639155-T-A 11483479-T-A **
13639141-G-C 11483465-G-C **
3459506-CTT-C 3591465-CTT-C 14×T**
13639122-G-A 11483446-G-A **
13639125-A-G 11483449-A-G **
13639181-A-C 11483505-A-C **
22151735-A-G 19989849-A-G **
6634204-C-G 6766163-C-G **
21600714-T-C 19438828-T-C **
21277694-G-A 19115808-G-A **
18932643-C-T 16820763-C-T **
18543991-C-CA 16432111-C-CA 8×A**
17549568-A-G 15437688-A-G **
13945591-A-AAT 11824885-A-AAT ***
8153686-G-A 8285645-G-A ***
6954818-A-G 7086777-A-G ***
17230162-TAA-T 15118282-TAA-T 14×A***
28815239-G-A 26669092-G-A ***
7969913-A-C 8101872-A-C ***
16434630-C-T 14322750-C-T ***
22988430-T-C 20826544-T-C ***
8153698-C-G 8285657-C-G ***
16000728-A-G 13888848-A-G ***
21742509-A-G 19580623-A-G ***
21346851-A-G 19184965-A-G ***
16863618-C-A 14751738-C-A ***
13361704-G-A 11206028-G-A ***
13884529-CA-C,CAA 11763823-CA-C,CAA 17×A***
13329965-T-C 11174289-T-C ***
22601068-C-T 20439182-C-T ***
6954805-G-A 7086764-G-A FT8363 ***
19261146-TTTTC-T 17149266-TTTTC-T ***
8153703-G-A 8285662-G-A ***
8153696-T-C 8285655-T-C ***
10653479-A-C ***
13480297-T-A 11324621-T-A ***
13480291-C-G 11324615-C-G ***
6954822-T-A 7086781-T-A ***
14396417-C-CAA 12275713-C-CAA 13×A***
16863628-T-C 14751748-T-C ***
6954807-A-T 7086766-A-T ***
15406939-TA-T,TAA 13295059-TA-T,TAA 20×A***
10625034-G-A ***
56828579-GATTCC-G ***
13462247-C-T 11306571-C-T ***
17092796-A-AT 14980916-A-AT 13×T***
7032333-A-ATT 7164292-A-ATT 22×T***
3482628-A-G 3614587-A-G ***
5535239-T-C 5667198-T-C ***
5528961-T-TA 5660920-T-TA 11×A***
6734680-CTTTTT-C,CTTT 6866639-CTTTTT-C,CTTT 21×T***
2651975-T-A 2783934-T-A ***
6630512-CTTTT-C,CT 6762471-CTTTT-C,CT 15×T***
5384459-A-G 5516418-A-G ***
5267748-T-C 5399707-T-C ***
4480953-T-C 4612912-T-C ***
4382449-CAA-C,CAAA 4514408-CAA-C,CAAA 17×A***
5581941-A-T 5713900-A-T 12×T***
3229154-CAAA-C,CAA 3361113-CAAA-C,CAA 20×A***
15928702-CAAA-C,CAA 13816822-CAAA-C,CAA 19×A***
6052051-T-TA 6184010-T-TA 10×A***
28800097-GAA-G 26653950-GAA-G ***
13206784-CA-C,CAAA 11051108-CA-C,CAAA 14×A***
6954787-A-G 7086746-A-G ***
16863627-C-A 14751747-C-A ***
16382748-TA-T 14270868-TA-T 10×A***
15128139-TAC-T 13016226-TAC-T ***
2729673-TG-T 2861632-TG-T ***
56864017-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: IN549501476888192648588238306
Used in age calculations1476888192648588238306
Counts of SNPs44
Variant counts last updated 2019-08-26 22:48:36.



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