Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > S14469 > S23682 > FGC4220 > BY123080

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
9631738-T-C 9794129-T-C IR3_Prx A+
20369262-C-T 18207376-C-T P5_Dst A+
27934250-T-C 25788103-T-C P1_Y2 A+
6238633-A-G 6370592-A-G IR3_Dst A+
4596332-C-T 4728291-C-T A+
56833605-C-A A*
26028151-A-G 23882004-A-G P1_Y1 A*
19638474-G-C 17526594-G-C P5_Prx A*
20017465-C-A 17905585-C-A P5_Prx A*
20026257-G-C 17914377-G-C P5_Prx A*
16122972-G-A 14011092-G-A P8_Prx A*
20717012-C-T 18555126-C-T P4_Prx A*
19810518-G-A 17698638-G-A P5_Prx A*
56831610-C-G A*
24314618-A-G 22168471-A-G P3_t1 A*
22313996-G-A 20152110-G-A DYZ19 A*
26117416-G-A 23971269-G-A P1_Y1 A*
26234943-G-A 24088796-G-A P1_Y1 A*
26456063-T-C 24309916-T-C P1_Y1 A*
26411246-C-T 24265099-C-T P1_Y1 A*
26482495-G-A 24336348-G-A P1_Y1 A*
5381320-C-T 5513279-C-T A*
13687230-G-T 11531554-G-T A*
3522891-T-C 3654850-T-C A*
7582667-T-C 7714626-T-C FT101110 YY+
8191231-TG-T 8323190-TG-T +
8457878-C-T 8589837-C-T FT40813 YY+
8486650-G-A 8618609-G-A FT101310 YY+
8645443-A-C 8777402-A-C FT101348 YY+
19469881-C-A 17358001-C-A FT102770 YY+
9876533-C-A 10038924-C-A FT41185 YY+
21451914-T-A 19290028-T-A BY133003 YY+
21307630-G-T 19145744-G-T FT102851 YY+
28561097-G-T 26414950-G-T FT103402 +
14816706-C-T 12704777-C-T FT101774 YY+
14589009-C-T 12477209-C-T FT41663 YY+
14608739-C-T 12496941-C-T FT101732 YY+
21696669-C-T 19534783-C-T FT102944 YY+
15004529-C-T 12892614-C-T FT41813 YY+
15993064-G-A 13881184-G-A YY+
28782658-A-G 26636511-A-G +
16483869-A-G 14371989-A-G FT102105 YY+
16582782-C-T 14470902-C-T FT102124 YY+
16585115-C-G 14473235-C-G FT102125 YY+
16763489-C-A 14651609-C-A FT42408 YY+
16790095-G-A 14678215-G-A FT42416 YY+
17272632-A-G 15160752-A-G FT102262 YY+
17412104-C-A 15300224-C-A FT102311 YY+
19031443-T-C 16919563-T-C FT102654 YY+
21507813-C-A 19345927-C-A FT102908 YY+
21733979-A-T 19572093-A-T FT102952 YY+
5537475-C-T 5669434-C-T FT100699 +
24443490-G-A 22297343-G-A BY182374 Y+
9524391-T-C 9686782-T-C FT41136 +
23552852-C-T 21390966-C-T BY189555 YY+
2653551-C-A 2785510-C-A Y+
23207269-T-A 21045383-T-A FT103230 Y+
4035096-T-C 4167055-T-C FT100226 +
4115029-C-T 4246988-C-T FT100251 +
4462228-T-C 4594187-T-C FT100363 +
22684199-T-A 20522313-T-A FT103095 YY+
5442055-G-A 5574014-G-A FT39606 +
4553188-A-G 4685147-A-G FT39118 +
6025319-C-A 6157278-C-A FT100831 +
7049265-C-A 7181224-C-A FT101007 YY+
6900757-G-A 7032716-G-A FT40276 YY+
5670981-C-T 5802940-C-T FT39753 +
22445525-T-C 20283639-T-C DYZ19 +
21750659-C-G 19588773-C-G FT31290 YY+
6005913-G-C 6137872-G-C FT100827 +
10753429-G-GCATTC *
18914164-G-GTA 16802284-G-GTA 8×TA*
3480859-C-T 3612818-C-T *
6588021-A-G 6719980-A-G *
13267807-C-T 11112131-C-T *
7133086-AAACAAC-A 7265045-AAACAAC-A 11×AAC*
4706755-C-T 4838714-C-T FT39207 *
11643146-C-G *
10676684-ACT-A *
23096841-A-G 20934955-A-G **
20543124-A-C 18381238-A-C P5_Dst **
24298143-C-A 22151996-C-A P3_t1 **
28808520-G-T 26662373-G-T **
25982179-A-T 23836032-A-T P1_Y1 **
26116558-G-T 23970411-G-T P1_Y1 **
19908136-C-A 17796256-C-A P5_Prx **
20754434-T-A 18592548-T-A P4_Prx **
19811403-T-C 17699523-T-C P5_Prx **
19642958-T-G 17531078-T-G BY31281 P5_Prx **
19789584-T-C 17677704-T-C P5_Prx **
6264497-T-G 6396456-T-G IR3_Dst **
28544777-G-A 26398630-G-A **
19630673-A-C 17518793-A-C P5_Prx **
3561500-C-CA 3693459-C-CA 25×A**
13487428-C-T 11331752-C-T **
24637484-GT-G 22491337-GT-G P3_t2 **
6213428-T-G 6345387-T-G IR3_Dst **
27572556-TG-T 25426409-TG-T P1_Y2 **
9700889-G-T 9863280-G-T IR3_Prx **
20631799-G-T 18469913-G-T P4_Prx **
3370628-A-T 3502587-A-T **
19713199-T-G 17601319-T-G P5_Prx **
3804191-C-T 3936150-C-T **
5365434-C-T 5497393-C-T **
13515087-G-A 11359411-G-A **
3279606-T-C 3411565-T-C Z11347 **
7536042-CAAAAAAA-C 7668001-CAAAAAAA-C 28×A**
7536112-G-A 7668071-G-A **
19629005-T-G 17517125-T-G P5_Prx **
18323991-G-T 16212111-G-T P6_Prx **
17779378-T-C 15667498-T-C **
13487384-G-C 11331708-G-C **
6494854-C-A 6626813-C-A **
15305885-TAATAG-T,TAG 13193987-TAATAG-T,TAG ***
28813077-A-T 26666930-A-T ***
28812959-GA-GT,T 26666812-GA-GT,T ***
28812902-G-A,GTT 26666755-G-A,GTT ***
24510701-T-TA 22364554-T-TA 10×A***
27593240-T-A 25447093-T-A P1_Y2 ***
3812718-C-CAA 3944677-C-CAA 17×A***
22301728-T-A 20139842-T-A DYZ19 ***
16977115-G-A 14865235-G-A ***
15576787-T-C 13464907-T-C ***
13476664-A-G 11320988-A-G ***
13408468-TG-T 11252792-TG-T ***
10846811-C-A ***
3443764-TTTATTATTA-T 3575723-TTTATTATTA-T 12×TTA***
28748570-C-T 26602423-C-T FGC34517 ***
21668680-T-G 19506794-T-G ***
7387396-ATTTT-A,ATTT 7519355-ATTTT-A,ATTT 22×T***
5960696-ATT-A,ATTT 6092655-ATT-A,ATTT 30×T***
3057258-A-G 3189217-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)

Kit: N498081504883994130338328497
Used in age calculations1504883994130338328497
Counts of SNPs3130
Variant counts last updated 2020-05-27 02:34:33.

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