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
HG01625
Manual
Edits
13883722-A-G 11763016-A-G Y+
13456086-TTCCTA-T 11300410-TTCCTA-T +
27378214-A-T 25232067-A-T P1_g3 +
58861966-A-C 56728905-T-G +
22271525-C-T 20109639-C-T FGC20814FGC20814 DYZ19 +
22353496-A-G 20191610-A-G DYZ19 +
14213757-G-A 12093051-G-A M10638 YY13×AGAA+
15612157-T-C 13500277-T-C PF7273PF7273 YY+
23534015-G-A 21372129-G-A BY22819 YY+
6844686-A-G 6976645-A-G FT300002 YY+
7249327-T-C 7381286-T-C M11066 YY+
9848856-C-G 10011247-C-G FT300675 YY+
14165083-G-T 12044377-G-T Y+
15776799-G-C 13664919-G-C CTS4706 YY+
16242851-T-G 14130971-T-G CTS5384 YY+
17039073-G-A 14927193-G-A FT301532 YY+
17359229-T-C 15247349-T-C FT301607 YY+
17732813-C-A 15620933-C-A CTS7906 Y+
18160832-A-G 16048952-A-G FTA9344 YY+
19014998-A-T 16903118-A-T Y+
19448757-C-G 17336877-C-G CTS10423 YY+
21264210-G-C 19102324-G-C FT302280 YY+
22545286-G-A 20383400-G-A Y+
22857437-C-T 20695551-C-T FT302739 Y+
23144056-G-A 20982170-G-A CTS11509 YY+
23545599-G-C 21383713-G-C FT302929 YY+
24389778-C-T 22243631-C-T FT303026 Y+
24408642-G-A 22262495-G-A FTA6305 +
2987545-A-G 3119504-A-G +
3194266-A-T 3326225-A-T +
3403258-ATCC-A 3535217-ATCC-A +
3476406-G-A 3608365-G-A FT317386 +
3755416-C-T 3887375-C-T +
3829517-T-C 3961476-T-C +
4316122-T-C 4448081-T-C K66 +
4468316-C-A 4600275-C-A FT74871 12×A+
4510382-A-T 4642341-A-T +
4525721-C-A 4657680-C-A +
4870173-C-T 5002132-C-T Z5135 +
5227087-C-A 5359046-C-A 21×A+
5350058-T-TTTTA 5482017-T-TTTTA +
5400550-T-C 5532509-T-C +
5486420-G-A 5618379-G-A +
5539324-G-A 5671283-G-A +
5539342-T-A 5671301-T-A +
5716930-C-T 5848889-C-T FT324860 +
5966753-A-C 6098712-A-C +
6006220-G-A 6138179-G-A Z27788 +
6048371-T-TTG 6180330-T-TTG 12×TG+
6684200-G-GAA 6816159-G-GAA +
6698865-G-T 6830824-G-T YY+
7249337-T-C 7381296-T-C M11068 YY+
7249339-T-C 7381298-T-C M11069 YY+
8398857-AG-A 8530816-AG-A +
9740088-C-G 9902479-C-G FT328204 IR3_Prx +
10000888-G-A 10163279-G-A Z17019 Y+
10035107-C-A 10197498-C-A FT303186 +
10069319-T-A 10231710-T-A +
10069332-T-C 10231723-T-C +
10069359-C-A 10231750-C-A +
13127675-A-T 10617161-A-T Z25259 +
13222622-G-A 11066946-G-A +
13260024-C-T 11104348-C-T +
13291272-T-C 11135596-T-C FGC43579 +
13349184-T-C 11193508-T-C +
13379846-T-A 11224170-T-A +
13414538-C-T 11258862-C-T +
13414546-C-A 11258870-C-A +
13422505-A-ATG 11266829-A-ATG +
13422535-A-C 11266859-A-C +
13558845-C-T 11403169-C-T +
13602115-C-T 11446439-C-T +
13611592-G-A 11455916-G-A +
13611754-T-C 11456078-T-C +
13611755-C-T 11456079-C-T +
13621471-C-A 11465795-C-A +
13641461-G-A 11485785-G-A FT219177 +
13641473-C-T 11485797-C-T +
13720247-G-A 11564571-G-A DYZ17 +
13883690-T-G 11762984-T-G Y+
13964485-T-C 11843779-T-C M9684 Y+
14286784-C-CTTTTTT 12166078-C-CTTTTTT 22×T+
14743181-T-A 12631249-T-A Y+
15279232-A-G 13167331-A-G YY+
15279261-T-G 13167360-T-G YY+
16344768-A-C 14232888-A-C YY+
17385413-T-A 15273533-T-A YY+
18230822-G-T 16118942-G-T +
19407597-G-T 17295717-G-T YY+
19407604-GTC-G 17295724-GTC-G +
20516480-G-A 18354594-G-A BY212189 P5_Dst +
21464232-G-GAAAC 19302346-G-GAAAC +
21464556-G-A 19302670-G-A YY+
21477809-GAAAA-G 19315923-GAAAA-G +
22133841-A-G 19971955-A-G FT302590 YY+
22145225-C-G 19983339-C-G FT302597 YY+
22156239-T-G 19994353-T-G YY+
22628170-C-T 20466284-C-T FT302665 Y+
22902106-T-A 20740220-T-A YY+
22902108-C-A 20740222-C-A YY17×A+
22961993-G-T 20800107-G-T YY+
23218630-G-GGAAA 21056744-G-GGAAA +
23544844-TTC-T 21382958-TTC-T +
24126674-T-C 21980527-T-C FGC473 P3_b1 +
24127064-A-G 21980917-A-G P3_b1 +
24466748-C-A 22320601-C-A ZP8Z8191 ZP8 Y+
28523360-A-C 26377213-A-C +
28580387-T-G 26434240-T-G ZS7733 +
59001389-AAAG-A 56855242-AAAG-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:

Kit POSITION-REF-ALT (hg19) POSITION-REF-ALT (hg38) Note
Manual16113387-C-A14001507-C-A2C 2A
Manual23054925-T-C20893039-T-C3C
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.