Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > DF21/S192 > S5488 > BY12129

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 STRFTDNA
2815666-T-G 2947625-T-G BY56611 YY+
2826972-G-A 2958931-G-A BY56682 YY+
6786036-C-T 6917995-C-T BY61297 YY+
7047019-C-T 7178978-C-T BY62989 YY+
7811587-A-G 7943546-A-G Y21410FGC3946 YY+
7921360-A-C 8053319-A-C BY68770 YY+
8306875-G-A 8438834-G-A BY71561 YY+
8529661-C-T 8661620-C-T BY73708 YY+
14035355-G-A 11914649-G-A BY92486 YY+
14409754-C-T 12289051-C-T BY95558 YY+
14702282-G-T 12590348-G-T BY97162 YY+
15792459-A-T 13680579-A-T BY104170 YY+
15999465-C-T 13887585-C-T BY105408 YY+
16326462-TCCCTCCC-T 14214582-TCCCTCCC-T +
16880107-T-C 14768227-T-C BY110825 YY+
17102702-C-T 14990822-C-T BY112302 YY+
17152814-C-G 15040934-C-G BY112701 YY+
19024774-C-T 16912894-C-T BY125622 YY+
19079970-G-T 16968090-G-T BY126099 YY+
19277396-C-T 17165516-C-T BY127886 YY+
19524298-A-G 17412418-A-G BY129785 YY+
20830988-C-A 18669102-C-A BY212732 P4_Gap +
21372387-G-A 19210501-G-A BY132419 YY+
21400773-G-A 19238887-G-A BY132630 YY+
22105351-G-A 19943465-G-A BY137658 YY+
22180127-T-A 20018241-T-A BY138207 YY+
22238785-A-C 20076899-A-C BY213837 DYZ19 +
22468623-G-A 20306737-G-A BY52973 DYZ19 +
23248012-C-T 21086126-C-T BY144069 YY+
24360230-A-G 22214083-A-G BY149330 +
7840755-C-CA 7972714-C-CA 9×A+
21766119-G-GT 19604233-G-GT +
14082017-CTCTA-C 11961311-CTCTA-C +
6010403-A-C 6142362-A-C PF166 **
22369831-N-A 20207945-N-A DYZ19 **
2668940-A-C 2800899-A-C **
6751568-C-G 6883527-C-G **
15730404-C-A 13618524-C-A **
19022345-C-T 16910465-C-T CTS9682 **
21199053-G-A 19037167-G-A Z3573 **
22216936-G-A 20055050-G-A DYZ19 **
22338921-T-C 20177035-T-C DYZ19 **
22369832-N-T 20207946-N-T DYZ19 **
22369833-N-A 20207947-N-A DYZ19 **
22369834-N-A 20207948-N-A DYZ19 **
22369835-N-G 20207949-N-G DYZ19 **
22461454-A-T 20299568-A-T BY220699 DYZ19 **
27856317-G-A 25710170-G-A BY51860 P1_Y2 **
28708739-C-G 26562592-C-G BY150903 **
22341307-G-A 20179421-G-A DYZ19 ***
6214141-C-T 6346100-C-T IR3_Dst ***
6263332-C-A 6395291-C-A IR3_Dst ***
6649698-G-T 6781657-G-T ***
9356973-C-G 9519364-C-G ***
13726934-G-A 11571258-G-A ***
20746104-T-C 18584218-T-C P4_Prx ***
20800533-A-G 18638647-A-G P4_Prx ***
22227776-C-A 20065890-C-A DYZ19 ***
22233806-A-G 20071920-A-G DYZ19 ***
22283918-A-G 20122032-A-G DYZ19 ***
22289619-G-T 20127733-G-T DYZ19 ***
22294810-A-C 20132924-A-C DYZ19 ***
22303972-G-A 20142086-G-A BY47926 DYZ19 ***
22308898-G-T 20147012-G-T DYZ19 ***
22318406-A-C 20156520-A-C DYZ19 ***
22423005-C-A 20261119-C-A DYZ19 ***
24172160-A-G 22026013-A-G P3_b1 ***
24959392-G-T 22813245-G-T g1 ***
25252567-A-C 23106420-A-C P2_r1 ***
25275738-A-G 23129591-A-G P2_r1 ***
28813982-G-A 26667835-G-A BY152198 ***
7832170-C-CTT 7964129-C-CTT 12×TCTT***
16063243-TTTTC-T,TCTTT 13951363-TTTTC-T,TCTTT 4×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.