Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z41150 > Z49 > Z142/S211 > Z51 > Z50 > BY158668 > 20893039-T-C > BY33655

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 STR1kG
13883722-A-G 11763016-A-G Y+
13558845-C-T 11403169-C-T +
13964485-T-C 11843779-T-C M9684 Y+
13883690-T-G 11762984-T-G Y+
13720247-G-A 11564571-G-A +
13641473-C-T 11485797-C-T +
13641461-G-A 11485785-G-A FT219177 +
13621471-C-A 11465795-C-A +
13611755-C-T 11456079-C-T +
13611754-T-C 11456078-T-C +
13611716-T-G 11456040-T-G +
13611592-G-A 11455916-G-A +
13602115-C-T 11446439-C-T +
13422535-A-C 11266859-A-C +
14743181-T-A 12631249-T-A Y+
13422505-A-ATG 11266829-A-ATG +
13414546-C-A 11258870-C-A +
13414538-C-T 11258862-C-T +
13379846-T-A 11224170-T-A +
13349184-T-C 11193508-T-C +
13294211-C-T 11138535-C-T +
13291272-T-C 11135596-T-C FGC43579 +
13260024-C-T 11104348-C-T +
13222622-G-A 11066946-G-A +
13127675-A-T 10617161-A-T Z25259 +
10069359-C-A 10231750-C-A +
14286784-C-CTTTTTT 12166078-C-CTTTTTT 22×T+
15279232-A-G 13167331-A-G YY+
10069319-T-A 10231710-T-A +
22628170-C-T 20466284-C-T FT302665 Y+
59001389-AAAG-A 56855242-AAAG-A +
28580387-T-G 26434240-T-G ZS7733 +
28523360-A-C 26377213-A-C +
24466748-C-A 22320601-C-A ZP8Z8191 ZP8 Y+
24127064-A-G 21980917-A-G P3_b1 +
24126674-T-C 21980527-T-C FGC473 P3_b1 +
23544844-TTC-T 21382958-TTC-T +
23218630-G-GGAAA 21056744-G-GGAAA +
22961993-G-T 20800107-G-T YY+
22902108-C-A 20740222-C-A YY17×A+
22902106-T-A 20740220-T-A YY+
22156239-T-G 19994353-T-G YY+
15279261-T-G 13167360-T-G YY+
22145225-C-G 19983339-C-G FT302597 YY+
22133841-A-G 19971955-A-G FT302590 YY+
21477809-GAAAA-G 19315923-GAAAA-G +
21464556-G-A 19302670-G-A YY+
21464232-G-GAAAC 19302346-G-GAAAC +
20516480-G-A 18354594-G-A BY212189 P5_Dst +
19407604-GTC-G 17295724-GTC-G +
19407597-G-T 17295717-G-T YY+
18230822-G-T 16118942-G-T +
17385413-T-A 15273533-T-A YY+
16344768-A-C 14232888-A-C YY+
10069332-T-C 10231723-T-C +
10035107-C-A 10197498-C-A FT303186 +
13456086-TTCCTA-T 11300410-TTCCTA-T +
16242851-T-G 14130971-T-G CTS5384 YY+
23545599-G-C 21383713-G-C FT302929 YY+
23144056-G-A 20982170-G-A CTS11509 YY+
22857437-C-T 20695551-C-T FT302739 Y+
22545286-G-A 20383400-G-A Y+
21264210-G-C 19102324-G-C FT302280 YY+
19448757-C-G 17336877-C-G CTS10423 YY+
19014998-A-T 16903118-A-T Y+
18160832-A-G 16048952-A-G FTA9344 YY+
17732813-C-A 15620933-C-A CTS7906 Y+
17359229-T-C 15247349-T-C FT301607 YY+
17039073-G-A 14927193-G-A FT301532 YY+
15776799-G-C 13664919-G-C CTS4706 YY+
24408642-G-A 22262495-G-A FTA6305 +
14165083-G-T 12044377-G-T Y+
9848856-C-G 10011247-C-G FT300675 YY+
7249327-T-C 7381286-T-C M11066 YY+
6844686-A-G 6976645-A-G FT300002 YY+
23534015-G-A 21372129-G-A BY22819 YY+
15612157-T-C 13500277-T-C PF7273PF7273 YY+
14213757-G-A 12093051-G-A M10638 YY13×AGAA+
22353496-A-G 20191610-A-G DYZ19 +
22271525-C-T 20109639-C-T FGC20814FGC20814 DYZ19 +
58861966-A-C 56728905-T-G +
27378214-A-T 25232067-A-T P1_g3 +
24389778-C-T 22243631-C-T FT303026 Y+
2987545-A-G 3119504-A-G +
10000888-G-A 10163279-G-A Z17019 Y+
5539324-G-A 5671283-G-A +
9740088-C-G 9902479-C-G FT328204 IR3_Prx +
8398857-AG-A 8530816-AG-A +
7249339-T-C 7381298-T-C M11069 YY+
7249337-T-C 7381296-T-C M11068 YY+
6698865-G-T 6830824-G-T YY+
6684200-G-GAA 6816159-G-GAA +
6048371-T-TTG 6180330-T-TTG 12×TG+
6006220-G-A 6138179-G-A Z27788 +
5966753-A-C 6098712-A-C +
5716930-C-T 5848889-C-T FT324860 +
5539342-T-A 5671301-T-A +
5486420-G-A 5618379-G-A +
3194266-A-T 3326225-A-T +
5400550-T-C 5532509-T-C +
5350058-T-TTTTA 5482017-T-TTTTA +
5227087-C-A 5359046-C-A 21×A+
4870173-C-T 5002132-C-T Z5135 +
4525721-C-A 4657680-C-A +
4510382-A-T 4642341-A-T +
4468316-C-A 4600275-C-A FT74871 12×A+
4316122-T-C 4448081-T-C K66 +
3829517-T-C 3961476-T-C +
3755416-C-T 3887375-C-T +
3476406-G-A 3608365-G-A FT317386 +
3403258-ATCC-A 3535217-ATCC-A +
59003005-GAAA-G 56856858-GAAA-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.

Mutation Notes:

Manual16113387-C-A14001507-C-A2C 2A
Manual9162514-A-C9324905-A-C2C. Although the reads don't seem to match the reference sequence very well to the right of 9162514 (hg19).
Manual9162590-A-G9324981-A-G5G. This region doesn't match the reference sequence very well. Could be part of a bigger change.
Manual21486445-ATT-A19324559-ATT-AThree reads cover the deletion and all three are positive.

Big Tree Main Page