Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > A9507 > S7323

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
13143284-G-C 10632770-G-C +
13143306-T-A 10632792-T-A +
28804779-A-T 26658632-A-T BY24944 +
4408904-G-GAAAA 4540863-G-GAAAA 13×A+
13430833-T-C 11275157-T-C +
16978999-G-A 14867119-G-A Y14×A+
14610920-G-C 12499126-G-C Y16148S16207 YY+
15612157-T-C 13500277-T-C PF7273PF7273 YY+
16583392-G-A 14471512-G-A YY10×A+
18687904-C-T 16576024-C-T YY+
6656021-G-A 6787980-G-A Z13995 YY+
6948601-C-A 7080560-C-A PH334 YY+
15868568-T-A 13756688-T-A S3690 CTS4855 YY+
21351148-G-T 19189262-G-T FT291901 Y+
22782101-G-C 20620215-G-C FT292334 Y+
23037882-A-C 20875996-A-C F25718 YY+
24464461-T-C 22318314-T-C FT292690 Y+
17998979-G-A 15887099-G-A P7_Gap Y+
17998972-A-C 15887092-A-C P7_Gap Y+
13441588-A-T 11285912-A-T +
9231660-G-A 9394051-G-A Y+
28799002-G-A 26652855-G-A +
13641902-G-C 11486226-G-C +
28759466-T-G 26613319-T-G Y+
18390102-AG-A 16278222-AG-A P6_Gap +
3019392-T-A 3151351-T-A +
3176482-T-G 3308441-T-G FT14983 +
3582771-C-G 3714730-C-G +
3759084-G-T 3891043-G-T +
3786823-G-A 3918782-G-A FT318490 +
3866274-A-G 3998233-A-G +
4015437-A-G 4147396-A-G +
4041969-A-T 4173928-A-T +
4188915-T-C 4320874-T-C +
4416630-T-G 4548589-T-G +
4511696-T-A 4643655-T-A +
4804806-G-T 4936765-G-T FT14404 +
5188168-G-A 5320127-G-A FGC24490 +
5240909-T-C 5372868-T-C +
5249482-T-C 5381441-T-C +
5263800-G-A 5395759-G-A +
5400500-C-T 5532459-C-T +
5540423-G-A 5672382-G-A FT28453 +
5574098-G-C 5706057-G-C +
6006482-A-T 6138441-A-T +
6758310-A-C 6890269-A-C YY+
6946523-G-T 7078482-G-T YY+
6948123-TGGTG-T 7080082-TGGTG-T +
7017578-C-T 7149537-C-T Y+
7075264-T-G 7207223-T-G YY+
7138343-C-T 7270302-C-T MF2055 YY+
7297514-G-A 7429473-G-A Y+
7353793-G-T 7485752-G-T YY+
7573263-T-G 7705222-T-G Y+
8454883-T-A 8586842-T-A YY+
8740673-TTG-T 8872632-TTG-T +
8857267-A-C 8989226-A-C S12021 YY+
9125891-A-C 9288282-A-C Y+
9377326-T-G 9539717-T-G FGC7103 Y4005 Y+
9429495-AAAAG-A 9591886-AAAAG-A +
9451278-T-C 9613669-T-C YY+
9921843-T-C 10084234-T-C Y+
10020656-C-T 10183047-C-T Y+
13143276-C-A 10632762-C-A +
13256651-T-TC 11100975-T-TC +
13257307-TC-T 11101631-TC-T +
13398996-T-C 11243320-T-C +
13431758-G-A 11276082-G-A +
13435795-C-T 11280119-C-T +
13440520-G-C 11284844-G-C +
13451540-A-ACTCCC 11295864-A-ACTCCC +
13470538-G-A 11314862-G-A +
13494607-A-G 11338931-A-G +
13636312-A-G 11480636-A-G +
13636346-A-G 11480670-A-G +
13743966-C-T 11588290-C-T +
13857267-G-A 11736561-G-A FT308908 +
13886781-A-G 11766075-A-G Y+
13952630-C-G 11831924-C-G Y+
13971572-GGA-G 11850866-GGA-G 8×GA+
14067329-A-C 11946623-A-C M3799 YY+
14214240-C-T 12093534-C-T YY+
14234336-T-G 12113630-T-G YY+
14408534-G-T 12287832-G-T YY+
14420786-AC-A 12300061-AC-A +
14574621-C-T 12462821-C-T Z16118 Y+
14600814-T-C 12489014-T-C S16197 YY+
14954417-T-TTA 12842492-T-TTA +
14986751-CACA-C 12874817-CACA-C +
15044347-C-A 12932437-C-A YY+
15305459-A-G 13193558-A-G YY+
15646848-T-G 13534968-T-G Y+
15655326-C-A 13543446-C-A M3986 Y+
15799221-T-C 13687341-T-C YY+
15865571-TCAA-T 13753691-TCAA-T +
16453782-G-A 14341902-G-A YY+
16486836-A-G 14374956-A-G CTS5800 YY+
16715983-G-A 14604103-G-A YY+
17443812-A-G 15331932-A-G YY+
18855776-T-G 16743896-T-G YY+
19205430-C-A 17093550-C-A M9281 YY+
19350197-T-C 17238317-T-C FT291679 YY+
19354307-A-T 17242427-A-T PF5818 Y+
19359482-C-T 17247602-C-T FT331278 YY+
19394050-TC-T 17282170-TC-T +
19500158-A-G 17388278-A-G YY+
21461822-C-G 19299936-C-G YY+
21523471-A-C 19361585-A-C Y+
21596709-C-A 19434823-C-A YY+
22603402-G-T 20441516-G-T YY+
22628431-T-A 20466545-T-A Y+
22658142-T-G 20496256-T-G YY+
22661997-C-T 20500111-C-T FT177516 YY+
22737249-AG-A 20575363-AG-A +
22838373-A-C 20676487-A-C M12092 Y+
22849795-A-G 20687909-A-G YY+
22871984-A-C 20710098-A-C Y+
23021359-C-T 20859473-C-T YY+
24465695-G-T 22319548-G-T Y+
24503788-A-G 22357641-A-G Z24248 +
24895365-G-C 22749218-G-C g1 +
26325585-G-A 24179438-G-A P1_Y1 +
26325611-A-C 24179464-A-C P1_Y1 +
28207187-C-T 26061040-C-T P1_b4 +
28573166-A-G 26427019-A-G +
59030836-AT-A 56884689-AT-A +

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:

Manual16109952-C-T13998072-C-T1C 3T
Manual22273174-G-A20111288-G-A2G 3A
Manual22294687-T-C20132801-T-C1T 2C
Manual22475708-TC-T20313822-TC-T2 reads, both show the deletion. Really, the mutation combines with a near by related one, and show be written 22475708-TCC-TG.
Manual22479665-A-T20317779-A-T1A 2T
Manual25012093-G-A22865946-G-A2G 3A
Manual25240670-A-G23094523-A-G3A 2G
Manual26135355-T-G23989208-T-GJust one read, a G.