Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z41150 > Z49 > Y107974

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
488815
Manual
Edits
15226371-T-A 13114457-T-A Z16219 Y+
2682182-T-G 2814141-T-G Y81195 YY+
2887522-A-G 3019481-A-G Y81710 YY+
7219734-G-A 7351693-G-A Y83635 YY+
7435231-G-A 7567190-G-A Y84147 Y+
7567779-G-T 7699738-G-T YY+
7693906-A-G 7825865-A-G Y84691 YY+
8635004-A-G 8766963-A-G Y87564 YY+
8906618-C-T 9038577-C-T Y88358 +
8996397-C-G 9158788-C-G BY46729 Y+
9787741-G-A 9950132-G-A Y89198 Y+
13810481-A-G 11689775-A-G BY90217 DYZ17 +
14115296-C-G 11994590-C-G Y90352 YY+
14901062-ATTGT-A 12789129-ATTGT-A +
15267708-G-A 13155797-G-A Y93401 YY+
15485164-T-C 13373284-T-C Y93898 YY+
15744161-T-A 13632281-T-A Y94639 YY+
15829749-C-T 13717869-C-T Y94897 YY+
16473486-G-A 14361606-G-A Y96439 YY+
17418670-G-A 15306790-G-A Y99095 YY+
18039754-C-A 15927874-C-A Y101056 YY+
18084366-C-T 15972486-C-T Y101219 YY+
19455211-T-A 17343331-T-A Y104798 YY+
19679120-C-G 17567240-C-G P5_Prx +
21396327-T-A 19234441-T-A Y106343 YY+
22443108-C-T 20281222-C-T BY219220 DYZ19 +
23203116-G-T 21041230-G-T Y110978 Y+
23873434-G-T 21711548-G-T BY148678 Y+
16492532-G-T 14380652-G-T PR5835 **
16429229-T-A 14317349-T-A PR2150 **
17860521-T-G 15748641-T-G Y100414 **
24136210-G-A 21990063-G-A P3_b1 ***
22458034-G-T 20296148-G-T BY200511 DYZ19 ***
22458036-G-C 20296150-G-C DYZ19 ***
22444902-T-G 20283016-T-G DYZ19 ***
22444925-T-A 20283039-T-A DYZ19 ***
22445023-A-T 20283137-A-T BY2018 DYZ19 ***
22457551-C-A 20295665-C-A BY219939 DYZ19 ***
22457552-C-A 20295666-C-A BY219940 DYZ19 ***
22457567-T-A 20295681-T-A DYZ19 ***
22457568-G-T 20295682-G-T DYZ19 ***
58982197-T-A 56836050-T-A ***
22317560-TA-T 20155674-TA-T DYZ19 ***
22479296-C-G 20317410-C-G FT460236 DYZ19 ***
22444984-T-C 20283098-T-C DYZ19 ***
22457523-C-G 20295637-C-G DYZ19 ***
22458906-A-G 20297020-A-G Z6113 DYZ19 ***
13463705-C-T 11308029-C-T Z22744 ***
16960553-C-A 14848673-C-A Y4077 ZS261 ***
13457697-A-G 11302021-A-G ***
58977635-C-T 56831488-C-T ***
58977638-T-C 56831491-T-C ***
28787861-A-T 26641714-A-T ***
6233726-TCACA-T 6365685-TCACA-T IR3_Dst 13×CA***
22317524-GA-G 20155638-GA-G DYZ19 ***
28787860-C-A 26641713-C-A FT461798 ***
58977652-G-A,T 56831505-G-A,T ***
22223622-G-A 20061736-G-A DYZ19 ***
6208688-T-A 6340647-T-A IR3_Dst ***
6283384-C-A 6415343-C-A IR3_Dst ***
9184506-C-T 9346897-C-T ***
13463702-C-A 11308026-C-A ***
13465445-AAG-A 11309769-AAG-A ***
18379967-C-T 16268087-C-T P6_Prx ***
19697353-A-G 17585473-A-G P5_Prx ***
19700059-C-A 17588179-C-A P5_Prx ***
19990861-C-T 17878981-C-T P5_Prx ***
20618205-G-A 18456319-G-A P4_Prx ***
22243200-T-C 20081314-T-C DYZ19 ***
22250666-C-A 20088780-C-A DYZ19 ***
22254484-G-T 20092598-G-T DYZ19 ***
22363163-T-C 20201277-T-C DYZ19 ***
22444282-A-C 20282396-A-C DYZ19 ***
22444980-T-C 20283094-T-C DYZ19 ***
22444982-A-T 20283096-A-T BY219525 DYZ19 ***
22451685-G-A 20289799-G-A DYZ19 ***
22451734-T-A 20289848-T-A DYZ19 ***
22451735-C-T 20289849-C-T DYZ19 ***
22458937-A-T 20297051-A-T DYZ19 ***
24138781-C-T 21992634-C-T P3_b1 ***
24912888-C-T 22766741-C-T g1 ***
24974407-G-C 22828260-G-C g1 ***
25180639-G-A 23034492-G-A g1 ***
25275776-C-T 23129629-C-T P2_r1 ***
25322938-G-A 23176791-G-A P2_r1 ***
58982248-CACTGT-C,CACTCT 56836101-CACTGT-C,CACTCT ***
58982269-A-C 56836122-A-C ***
58990166-T-C 56844019-T-C ***
58990174-G-C 56844027-G-C ***
58990179-A-T 56844032-A-T ***
58990182-T-A 56844035-T-A ***
58990183-C-G 56844036-C-G ***
58990191-A-AG 56844044-A-AG ***
58990196-C-T 56844049-C-T ***
58990201-G-T 56844054-G-T ***
58990234-T-C 56844087-T-C ***
58990237-C-A 56844090-C-A ***
58990249-T-C 56844102-T-C ***
58990262-A-G 56844115-A-G ***
58990265-A-T 56844118-A-T ***

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.

Mutation Notes:

Kit POSITION-REF-ALT (hg19) POSITION-REF-ALT (hg38) Note
Manual21950258-T-C19788372-T-C8C