Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > ZZ10 > Z253 > BY4086 > FGC17436 > Z17693 > FGC73657 > FGC59344

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
913827
24295440-T-C 22149293-T-C P3_t1 A+
6341958-G-T 6473917-G-T A2364 A+
13687621-C-A 11531945-C-A A*
56834497-C-G A*
13698492-G-T 11542816-G-T A*
18447651-C-A 16335771-C-A P6_Dst A*
19604154-C-T 17492274-C-T P5_Prx YA*
19662334-T-TA 17550454-T-TA P5_Prx A*
13451636-T-G 11295960-T-G A*
13687214-A-G 11531538-A-G A*
13263170-A-T 11107494-A-T A*
19865641-A-G 17753761-A-G P5_Prx A*
19904763-G-A 17792883-G-A P5_Prx A*
19844017-A-C 17732137-A-C P5_Prx A*
28816742-G-T 26670595-G-T A*
5765446-G-A 5897405-G-A A*
16116240-T-C 14004360-T-C P8_Prx A*
6575284-T-C 6707243-T-C FT307621 +
8520965-C-T 8652924-C-T FT303925 YY+
10992681-T-G FT393206 +
10883030-C-T FT393203 +
9907637-T-C 10070028-T-C FT307712 Y+
9438236-CT-C 9600627-CT-C +
3724197-C-T 3856156-C-T FT113083 +
8875339-G-A 9007298-G-A FT304048 Y+
8198221-C-A 8330180-C-A FT303812 YY+
8212038-T-G 8343997-T-G FT303823 YY+
5581564-T-C 5713523-T-C FT307470 +
8040886-G-C 8172845-G-C FT303750 YY+
7111065-C-T 7243024-C-T FT203855 Y+
6739174-A-C 6871133-A-C FT303321 YY+
3953718-C-G 4085677-C-G FT307175 +
4484980-C-T 4616939-C-T FT11903 +
5087851-A-G 5219810-A-G FT307384 +
5096812-G-A 5228771-G-A FT307388 +
5550723-T-C 5682682-T-C FT307463 +
15810962-G-T 13699082-G-T L69 S163 PF2681 YY19×GT+
14467819-G-C 12347088-G-C FT300940 YY+
13205735-T-G 11050059-T-G FT393204 +
19419672-A-T 17307792-A-T FT306037 YY+
28649902-T-C 26503755-T-C FT307034 Y+
24507682-T-G 22361535-T-G FT307925 +
24383616-A-G 22237469-A-G FT306904 Y+
24001411-A-G 21855264-A-G FT307905 Y+
23539656-C-T 21377770-C-T FT306820 YY+
23396127-A-C 21234241-A-C FT306769 YY+
22228535-C-A 20066649-C-A FT453101 DYZ19 +
22189099-G-T 20027213-G-T FT306501 YY+
22180050-A-G 20018164-A-G FT306496 YY+
22070962-T-C 19909076-T-C FT306457 YY+
19816263-AG-A 17704383-AG-A P5_Prx +
18538228-C-G 16426348-C-G FT305698 Y+
13841291-G-A 11720585-G-A FT307725 +
18192265-G-C 16080385-G-C FT305637 Y+
17792054-C-G 15680174-C-G FT305486 YY+
17790188-T-C 15678308-T-C FT305485 YY+
17444608-C-T 15332728-C-T FT305376 YY+
17299495-A-G 15187615-A-G FT305322 YY+
16845630-G-A 14733750-G-A FT305180 YY+
16424422-G-A 14312542-G-A FT305032 Y+
15852126-T-C 13740246-T-C FT304887 YY+
15659537-C-A 13547657-C-A FT304820 YY+
14795638-C-T 12683709-C-T FT307760 Y+
3190994-C-G 3322953-C-G FT316372 +
14270835-T-G 12150129-T-G FT304367 Y+
3213050-G-A 3345009-G-A FT316455 +
5109746-T-C 5241705-T-C FT307389 +
13667352-G-A 11511676-G-A BY87667 +
22459156-G-A 20297270-G-A BY220258 DYZ19 +
2758890-A-T 2890849-A-T FT303238 YY+
5675344-G-A 5807303-G-A FT162546 +
15714446-G-A 13602566-G-A FT304833 YY+
10684555-G-GTCCATTCCAT *
16842867-ATGTG-A 14730987-ATGTG-A 22×TG*
56846522-C-T *
28807115-C-T 26660968-C-T FT148754BY40553 *
22233909-T-G 20072023-T-G DYZ19 *
14060688-A-G 11939982-A-G **
14754067-CTTTTTTT-C 12642136-CTTTTTTT-C 27×T**
16411245-G-A 14299365-G-A FT392256 **
7016147-CAA-C 7148106-CAA-C 16×A**
17263194-T-A 15151314-T-A **
20966229-A-AG 18804343-A-AG P4_Dst **
20424788-TGAAGGAAGGAAG-T 18262902-TGAAGGAAGGAAG-T P5_Dst 14×GAAG**
18390146-T-C 16278266-T-C FT392521 P6_Gap **
17953887-T-C 15842007-T-C **
23435798-A-G 21273912-A-G **
19155765-C-T 17043885-C-T **
19289642-T-A 17177762-T-A **
13459575-G-A 11303899-G-A FT443902 **
20804948-T-C 18643062-T-C P4_Gap **
20845410-T-TTC 18683524-T-TTC P4_Dst **
21328344-C-A 19166458-C-A **
13745763-G-T 11590087-G-T **
22443860-T-C 20281974-T-C FT393205 DYZ19 **
21656836-GAAATA-G 19494950-GAAATA-G 10×AAATA**
3543166-CAA-C 3675125-CAA-C 14×A**
23831252-CTTTTTTTTT-C 21669366-CTTTTTTTTT-C 26×T**
5261698-CAAAAAAAAAAAAAAAAAAAAAAAAAA-C 5393657-CAAAAAAAAAAAAAAAAAAAAAAAAAA-C 48×A**
5110156-G-A 5242115-G-A FT391275 **
5521397-A-G 5653356-A-G **
21716327-A-AT 19554441-A-AT 9×T**
3872107-C-T 4004066-C-T **
4773898-T-C 4905857-T-C **
23801765-G-A 21639879-G-A **
9853056-AAGAG-A 10015447-AAGAG-A **
3463043-A-G 3595002-A-G FTA21146 **
9948996-AT-A 10111387-AT-A **
16767153-C-CTT 14655273-C-CTT 17×T**
7762095-TA-T 7894054-TA-T 9×A**
58974947-A-G 56828800-A-G ***
6692829-CAAA-C 6824788-CAAA-C 14×A***
15138012-CTTT-C 13026099-CTTT-C 15×T***
24870887-T-TTCTC 22724740-T-TTCTC IR1_R 23×TC***
4437051-G-A 4569010-G-A ***
2732430-C-CT 2864389-C-CT 10×T***
13266221-G-T 11110545-G-T ***
21939992-A-G 19778106-A-G ***
4607417-T-TCCC 4739376-T-TCCC ***
14456868-C-CA 12336141-C-CA 9×A***
17822028-C-CA 15710148-C-CA 8×A***
4437052-T-C 4569011-T-C ***
13945593-T-A 11824887-T-A ***
5421275-A-T 5553234-A-T ***
4473089-G-A 4605048-G-A ***
18157115-C-T 16045235-C-T Y22841 ***
15938078-CAT-C 13826198-CAT-C ***
24461833-C-CAATA 22315686-C-CAATA 9×AATA***
19320338-A-G 17208458-A-G ***
3086544-CAAA-C 3218503-CAAA-C 18×A***
4167657-CAAA-C,CAA 4299616-CAAA-C,CAA 18×A***
15753178-CTTTT-C,CT 13641298-CTTTT-C,CT 20×T***
13459534-C-G 11303858-C-G ***
13459545-C-CGGTTA 11303869-C-CGGTTA ***
13523938-A-G 11368262-A-G ***
15669964-CAAAAAAA-C 13558084-CAAAAAAA-C 18×A***
2805529-CAA-C,CA 2937488-CAA-C,CA 22×A***
28679067-C-T 26532920-C-T ***
9411307-A-T 9573698-A-T ***
3419521-G-GA 3551480-G-GA 10×A***
28812489-C-A 26666342-C-A ***
15499605-A-G 13387725-A-G ***
10663671-C-A ***
5288959-C-A 5420918-C-A FT1144 ***
28812522-A-G 26666375-A-G ***
4794855-CT-C,CTT 4926814-CT-C,CTT 21×T***
8333480-T-TTTC,TTTCTTC 8465439-T-TTTC,TTTCTTC 31×TTC***
4466932-A-T 4598891-A-T ***
28812496-G-A 26666349-G-A ***
23002319-CT-C,CTT 20840433-CT-C,CTT 14×T***
4678058-GTT-G 4810017-GTT-G 15×T***
6780870-CAAAAAAAAA-C 6912829-CAAAAAAAAA-C 26×A***
28613771-CTTTT-C 26467624-CTTTT-C 16×T***
18138196-A-G 16026316-A-G ***
18138293-A-G 16026413-A-G ***
28812533-A-C 26666386-A-C ***
3084832-A-G 3216791-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: 9138271483680193102538251845
Used in age calculations1483680193102538251845
Counts of SNPs3125
Variant counts last updated 2021-04-25 02:38:27.



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