Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > S1026 > A1101 > A1078

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
3684802-C-T 3816761-C-T A+
9698182-G-A 9860573-G-A IR3_Prx A+
5841222-A-G 5973181-A-G A*
6182213-C-T 6314172-C-T IR3_Dst A*
6214330-G-A 6346289-G-A FTB59005 IR3_Dst A*
19776124-C-T 17664244-C-T P5_Prx A*
20053575-G-GT 17941695-G-GT P5_Prx A*
20782009-G-A 18620123-G-A P4_Prx A*
25581907-G-A 23435760-G-A P1_gr1 A*
25866992-G-T 23720845-G-T P1_Y1 A*
25931899-C-T 23785752-C-T P1_Y1 A*
26260269-G-A 24114122-G-A P1_Y1 A*
56829658-C-G A*
56837095-G-A A*
4651374-C-A 4783333-C-A Y32988ZS43 9×A+
19119008-C-T 17007128-C-T Y81307CTS9884 YY+
9645385-G-A 9807776-G-A BY42837 IR3_Prx +
21508536-G-A 19346650-G-A BY19920BY19926 YY+
23141958-T-C 20980072-T-C BY143317 YY+
3150100-G-A 3282059-G-A FT11530 +
3448784-G-GA 3580743-G-GA +
3585684-T-A 3717643-T-A FT11641 +
3778181-G-T 3910140-G-T FT11698 +
5414990-TG-T 5546949-TG-T +
5434762-A-T 5566721-A-T FT12182 +
5673452-A-T 5805411-A-T FT12273 +
6004538-C-A 6136497-C-A FT12362 +
6082467-G-A 6214426-G-A FT152913 +
6620045-A-T 6752004-A-T BY60364 YY+
6633526-A-G 6765485-A-G BY60430 YY+
7853324-C-T 7985283-C-T BY68239 YY+
8076499-A-G 8208458-A-G BY69772 YY+
8152140-T-G 8284099-T-G BY70338 YY+
8194757-A-G 8326716-A-G BY70610 YY+
8691871-AGACATTTG-A 8823830-AGACATTTG-A +
8799277-G-A 8931236-G-A FT201221 YY+
9002082-A-G 9164473-A-G BY77210 Y+
9484902-G-A 9647293-G-A BY79809 +
9809900-A-G 9972291-A-G BY81123 YY+
10787455-A-T FT91704 +
10835256-C-A FT45485 +
10835754-C-G FT45486 +
14315277-C-A 12194571-C-A BY156433 YY+
14380804-GA-G 12260100-GA-G +
14542817-A-C 12431018-A-C BY96395 YY+
15575722-T-A 13463842-T-A FT13195 YY+
16375352-A-G 14263472-A-G BY107352 YY+
16483556-A-G 14371676-A-G BY108121 YY+
17173843-C-G 15061963-C-G BY112813 YY+
17553940-A-T 15442060-A-T BY115662 YY+
17608027-C-A 15496147-C-A FT181148 YY+
18163208-G-T 16051328-G-T BY120512 YY+
18232486-G-C 16120606-G-C BY121036 Y+
18681503-C-A 16569623-C-A BY123084 YY+
18774932-G-A 16663052-G-A BY123801 YY+
19012202-C-T 16900322-C-T YY+
19033852-C-T 16921972-C-T BY125649 YY+
19109469-C-G 16997589-C-G BY126333 YY+
21148083-T-C 18986197-T-C BY130698 YY+
21212359-G-C 19050473-G-C FT13769 YY+
21313307-C-A 19151421-C-A FT13795 YY+
21519847-C-A 19357961-C-A BY55270 YY+
21963602-G-A 19801716-G-A BY136710 YY+
22439926-G-A 20278040-G-A FT219836 DYZ19 +
22470991-G-T 20309105-G-T BY53017 DYZ19 +
22674040-C-A 20512154-C-A BY139944 YY+
22834933-C-A 20673047-C-A BY141154 YY+
23134129-G-A 20972243-G-A BY143245 YY+
23645831-A-G 21483945-A-G BY147031 Y+
23988331-G-T 21842184-G-T BY149056 Y+
28478232-T-A 26332085-T-A FT14200 +
28655978-A-G 26509831-A-G BY150848 +
28737095-G-A 26590948-G-A FT202746 +
28803530-G-A 26657383-G-A BY151703 +
7591-G-T +
26427283-G-A 24281136-G-A BY226795 P1_Y1 *
15698757-G-GACAC 13586877-G-GACAC 24×AC*
6824935-A-T 6956894-A-T YY*
13205369-T-C 11049693-T-C FT219147 **
24241199-G-GTC 22095052-G-GTC P3_b1 **
5201565-C-T 5333524-C-T FT12125 **
7579142-A-G 7711101-A-G BY66019 **
13469303-G-A 11313627-G-A **
14088275-A-T 11967569-A-T **
12373062-C-A FT89269 **
14682433-C-T 12570499-C-T **
20893176-A-G 18731290-A-G P4_Dst **
22467817-C-G 20305931-C-G BY221984 DYZ19 **
28794860-G-A 26648713-G-A FT219173 **
10347-G-T **
35558-T-G **
17718412-GTTTTT-G 15606532-GTTTTT-G 20×T***
21687951-AACACACACAC-A 19526065-AACACACACAC-A 17×AC***
7137260-C-T 7269219-C-T ***
11022113-CTCCATTCCAT-C ***
10776094-C-A,G ***
15940306-CAAAAA-C,CAA 13828426-CAAAAA-C,CAA 24×A***
16881798-TA-T 14769918-TA-T ***
18008664-T-TG 15896784-T-TG P7_Dst ***
18157107-T-C 16045227-T-C FT32648 ***
21608072-A-C 19446186-A-C ***

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.