Tree Position

R-P312/S116 > Z40481 > FGC84729 > DF99/S11987 > Z29643 > FGC16982 > S23540 > FGC16979 > ZZ73 > Y31433

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
23801787-C-A 21639901-C-A Y+
6741203-G-C 6873162-G-C CTS418 YY+
7733742-C-G 7865701-C-G FT289462 YY+
7869092-G-A 8001051-G-A Y12198 YY+
7964243-A-G 8096202-A-G FT289539 YY+
8019401-A-G 8151360-A-G FT289547 YY+
8292050-G-A 8424009-G-A K129 YY+
8491641-T-C 8623600-T-C FT289712 YY+
14030964-C-T 11910258-C-T CTS1714 YY+
14327566-C-T 12206860-C-T S4251 CTS2492 YY+
17250024-C-A 15138144-C-A Y+
17297681-C-G 15185801-C-G PH2941 YY+
18108520-T-A 15996640-T-A FT291318 YY+
19300668-G-T 17188788-G-T FT291661 Y+
19325093-T-A 17213213-T-A CTS10202 S4253 Y+
21321509-C-A 19159623-C-A FT291887 Y+
22926083-T-C 20764197-T-C S24888 YY+
28696283-G-T 26550136-G-T FT292768 +
17090827-T-C 14978947-T-C YY+
2806181-A-C 2938140-A-C YY+
2940708-T-G 3072667-T-G FT315493 +
3107597-C-G 3239556-C-G +
3174372-TTC-T 3306331-TTC-T +
3174373-TC-T 3306332-TC-T +
3603491-A-T 3735450-A-T 24×T+
3888675-A-C 4020634-A-C +
4072018-ACG-A 4203977-ACG-A +
4275856-T-A 4407815-T-A FT320109 +
4365041-C-G 4497000-C-G +
4827776-C-T 4959735-C-T +
4959161-A-C 5091120-A-C FT322255 +
4983776-TC-T 5115735-TC-T +
4986389-A-C 5118348-A-C +
5012892-G-A 5144851-G-A FGC77 Z8133 +
5031310-G-A 5163269-G-A +
5542571-A-G 5674530-A-G FT324262 +
5980372-G-A 6112331-G-A FT325697 +
8531058-AT-A 8663017-AT-A +
8818289-G-A 8950248-G-A YY+
8874969-TC-T 9006928-TC-T +
9310573-TAC-T 9472964-TAC-T +
9781279-G-C 9943670-G-C A4927 K695 Y+
9823441-GTT-G 9985832-GTT-G +
9914280-G-A 10076671-G-A Y+
13319231-C-T 11163555-C-T +
13345655-G-A 11189979-G-A +
13347882-G-A 11192206-G-A +
13363857-A-T 11208181-A-T +
13375330-G-T 11219654-G-T +
13382712-T-C 11227036-T-C +
13404615-C-A 11248939-C-A +
13419895-A-C 11264219-A-C +
13441121-A-G 11285445-A-G +
13443381-T-G 11287705-T-G +
13451026-C-CACTCT 11295350-C-CACTCT +
13462276-T-C 11306600-T-C +
13682420-T-A 11526744-T-A +
13847199-G-A 11726493-G-A +
14195817-C-A 12075111-C-A Y14×A+
14329735-T-TG 12209029-T-TG +
14425195-C-A 12304470-C-A Y15×A+
14570752-G-A 12458952-G-A FT157077 YY+
14785550-TG-T 12673620-TG-T +
15078101-A-T 12966191-A-T YY+
15209610-A-T 13097696-A-T YY+
15363979-G-A 13252099-G-A Y38253 YY+
15388454-T-G 13276574-T-G YY+
15514675-G-A 13402795-G-A Z17444 V3003 YY+
16027144-T-G 13915264-T-G Y+
16063227-C-T 13951347-C-T Y+
16063228-T-C 13951348-T-C Y+
16300328-A-T 14188448-A-T YY+
16772376-A-C 14660496-A-C BY109997 YY+
16945898-AG-A 14834018-AG-A +
17270493-T-G 15158613-T-G YY+
18423886-AC-A 16312006-AC-A P6_Gap +
18615959-T-TTTTG 16504079-T-TTTTG +
19064624-G-A 16952744-G-A Y+
19550973-C-T 17439093-C-T YY+
21149569-GT-G 18987683-GT-G +
21152527-C-T 18990641-C-T Y+
21824316-G-A 19662430-G-A Y+
21953550-TA-T 19791664-TA-T +
22486916-G-T 20325030-G-T DYZ19 +
23155833-C-A 20993947-C-A FT340165 YY+
23802106-AG-A 21640220-AG-A +
23802120-T-G 21640234-T-G Y+
23888157-C-T 21726271-C-T Y+
23969667-G-A 21823520-G-A Y+
25250655-C-G 23104508-C-G P2_r1 +
27330479-TC-T 25184332-TC-T P1_g3 +
28462074-G-T 26315927-G-T +
28692903-G-A 26546756-G-A +
58844027-T-A 56746844-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:

Manual4404325-G-A4536284-G-A3 reads, 2 are A, but one is G. None of the reads have mates which allow an unambiguous determination of whether these reads belong to the Y or nearly identical X chromosomes.
Manual4686466-G-C4818425-G-C4 reads, all show the change. This is actually part of 4686465-CG-TC.
Manual14539162-G-A12427363-G-A3 reads, all A.
Manual4585565-A-G4717524-A-GNeeded to check paired-end reads, but at least two reads are unique to the Y, rather than the very similar X region.
Manual5811497-C-T5943456-C-TJust one read, a T.
Manual24141718-G-A21995571-G-A2 reads, both A.
Manual4686465-CG-TC4818424-CG-TC4 reads, all show the MNP.
Manual25232573-G-A23086426-G-A2G 1A
Manual26576637-T-C24430490-T-C3T 3C