Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF63/S522 > BY592 > CTS5454 > A7810

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
9399271-T-G 9561662-T-G BY53907 YY+
18865140-C-T 16753260-C-T BY24160 YY+
14490821-C-T 12370090-C-T CTS2801 YY+
22602532-C-T 20440646-C-T M1705 YY+
2860863-T-C 2992822-T-C BY56878 YY+
6739882-C-T 6871841-C-T BY60998 YY+
7186099-T-C 7318058-T-C BY63749 YY+
7962527-A-T 8094486-A-T BY69093 YY+
8379899-T-G 8511858-T-G BY72142 YY+
8501537-C-A 8633496-C-A BY209326 YY+
8566453-G-C 8698412-G-C BY74089 YY+
8833907-T-G 8965866-T-G BY76195 YY+
13654958-G-A 11499282-G-A BY87195 +
14170806-C-T 12050100-C-T BY93506 YY+
14534805-C-T 12423006-C-T BY96340 YY+
15257521-C-T 13145605-C-T BY100488 YY+
15975888-G-A 13864008-G-A BY105242 YY+
16392210-C-T 14280330-C-T BY107465 YY+
17939366-T-C 15827486-T-C BY118576 YY+
18903014-G-A 16791134-G-A BY124660 YY+
18994992-C-T 16883112-C-T BY125342 YY+
18996331-C-A 16884451-C-A BY125362 YY+
19279313-C-A 17167433-C-A BY127909 YY+
21889917-T-C 19728031-T-C BY136221 YY+
22088398-A-G 19926512-A-G BY137548 YY+
22128078-G-C 19966192-G-C BY137847 YY+
22718945-C-G 20557059-C-G BY140278 YY+
22787999-A-G 20626113-A-G BY140772 YY+
23489889-C-G 21328003-C-G BY145704 YY+
28727757-C-A 26581610-C-A **
14162311-G-A 12041605-G-A CTS2041 **
3327991-T-C 3459950-T-C BY57555 **
7044187-C-A 7176146-C-A **
23187945-C-T 21026059-C-T BY143656 **
26409278-C-G 24263131-C-G P1_Y1 **
6262892-T-C 6394851-T-C IR3_Dst ***
13713544-A-G 11557868-A-G ***
19828558-C-T 17716678-C-T P5_Prx ***
19853353-A-G 17741473-A-G P5_Prx ***
19896023-T-G 17784143-T-G P5_Prx ***
19911429-G-T 17799549-G-T P5_Prx ***
20774628-C-T 18612742-C-T P4_Prx ***
22222008-G-T 20060122-G-T DYZ19 ***
22240009-A-G 20078123-A-G DYZ19 ***
22252687-G-T 20090801-G-T DYZ19 ***
22254319-G-T 20092433-G-T DYZ19 ***
22255993-T-G 20094107-T-G DYZ19 ***
22261777-G-A 20099891-G-A DYZ19 ***
22277104-G-T 20115218-G-T DYZ19 ***
22277108-T-C 20115222-T-C DYZ19 ***
22289189-C-T 20127303-C-T DYZ19 ***
22290957-T-C 20129071-T-C DYZ19 ***
22310062-C-T 20148176-C-T DYZ19 ***
22424966-T-A 20263080-T-A DYZ19 ***
22425023-C-G 20263137-C-G DYZ19 ***
22429759-G-A 20267873-G-A DYZ19 ***
22431169-C-T 20269283-C-T DYZ19 ***
22436460-G-T 20274574-G-T BY48548 DYZ19 ***
22477808-T-C 20315922-T-C BY223897 DYZ19 ***
22507007-G-T 20345121-G-T BY48668 DYZ19 ***
24264754-C-A 22118607-C-A P3_b1 ***
24329571-G-C 22183424-G-C P3_t1 ***
24839644-A-G 22693497-A-G IR1_R ***
25034897-A-G 22888750-A-G g1 ***
25240369-G-A 23094222-G-A P2_r1 ***
25735188-A-G 23589041-A-G P1_b3 ***
25965862-G-C 23819715-G-C P1_Y1 ***
25966590-G-A 23820443-G-A P1_Y1 ***
26072297-A-C 23926150-A-C P1_Y1 ***
26427525-C-A 24281378-C-A P1_Y1 ***

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.