Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > BY2823 > BY2827

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
HG01941
Manual
Edits
14680311-CAG-C 12568377-CAG-C +
15057756-TG-T 12945848-TG-T +
14159518-G-GTA 12038812-G-GTA +
14200746-A-AT 12080040-A-AT +
14200747-TAGA-T 12080041-TAGA-T +
14245290-T-G 12124584-T-G YY+
14329734-C-CT 12209028-C-CT +
14422146-C-A 12301421-C-A Y+
15092766-AT-A 12980854-AT-A +
14035344-T-G 11914638-T-G YY+
15541026-G-T 13429146-G-T YY+
15604374-AG-A 13492494-AG-A +
15787902-A-C 13676022-A-C YY+
16050949-TC-T 13939069-TC-T +
16201436-G-A 14089556-G-A YY+
16300685-G-A 14188805-G-A FT336685 YY+
17013777-G-T 14901897-G-T YY+
14115575-T-G 11994869-T-G FT335281 YY+
13963669-T-G 11842963-T-G Y+
17246106-G-T 15134226-G-T Y+
9957449-T-A 10119840-T-A FTA9304 Y+
7613833-G-GAA 7745792-G-GAA 31×A+
8389561-C-T 8521520-C-T YY+
8468018-T-C 8599977-T-C YY+
8600008-TC-T 8731967-TC-T +
8606877-GCA-G 8738836-GCA-G +
8880853-T-G 9012812-T-G FT334791 Y+
9013093-A-T 9175484-A-T Y+
13291567-T-C 11135891-T-C +
13638645-G-T 11482969-G-T +
13319162-T-C 11163486-T-C +
13389651-GTATATA-G 11233975-GTATATA-G 8×TA+
13431640-A-G 11275964-A-G +
13431666-G-T 11275990-G-T +
13448358-CCT-C 11292682-CCT-C +
13503314-G-GA 11347638-G-GA +
13621065-C-G 11465389-C-G +
17107991-C-A 14996111-C-A YY+
17332794-C-T 15220914-C-T YY+
7567753-C-CTTT 7699712-C-CTTT 25×T+
22297528-C-A 20135642-C-A DYZ19 +
22136874-T-G 19974988-T-G YY+
22167258-C-G 20005372-C-G YY+
22189233-AC-A 20027347-AC-A +
22236221-A-T 20074335-A-T DYZ19 +
22245357-A-AG 20083471-A-AG DYZ19 +
22260743-TCAAG-T 20098857-TCAAG-T DYZ19 +
22468216-A-G 20306330-A-G DYZ19 +
21141195-TTA-T 18979309-TTA-T +
22733807-C-A 20571921-C-A YY+
23827539-AT-A 21665653-AT-A +
26508182-C-T 24362035-C-T FGC8528 P1_Y1 +
28496033-AG-A 26349886-AG-A +
28810132-T-C 26663985-T-C +
58973113-A-T 56826966-A-T +
59004615-AGAAG-A 56858468-AGAAG-A +
22025233-T-G 19863347-T-G YY+
19328891-C-G 17217011-C-G FTA6156 Y+
17387952-G-T 15276072-G-T YY+
18354229-A-G 16242349-A-G P6_Prx +
17641982-TGGC-T 15530102-TGGC-T +
17641985-C-T 15530105-C-T Y+
17709091-A-G 15597211-A-G YY+
17952049-C-A 15840169-C-A YY+
18025402-C-T 15913522-C-T Y+
18252258-C-A 16140378-C-A Y+
18354228-G-A 16242348-G-A P6_Prx +
18354233-A-G 16242353-A-G P6_Prx +
19108591-T-A 16996711-T-A YY+
18392973-CTCCT-C 16281093-CTCCT-C P6_Gap +
18412165-C-T 16300285-C-T P6_Gap +
18454761-CTTT-C 16342881-CTTT-C P6_Dst +
18607293-GTA-G 16495413-GTA-G +
18872258-CTTTCT-C 16760378-CTTTCT-C +
18896530-G-C 16784650-G-C YY+
19019894-T-G 16908014-T-G Y+
7591558-C-A 7723517-C-A YY+
7409900-AT-A 7541859-AT-A +
58917658-N-G 56673213-N-C +
17273037-T-C 15161157-T-C FT337318 YY+
15498828-A-G 13386948-A-G FT336193 YY+
15585410-G-T 13473530-G-T YY+
15742695-T-C 13630815-T-C FT336348 Y+
15923676-T-G 13811796-T-G FT336471 Y+
16041384-C-T 13929504-C-T FT336563 YY+
16847360-C-A 14735480-C-A FT337069 YY+
17626866-C-A 15514986-C-A FT337562 Y+
14291320-T-C 12170614-T-C BY3488 Y+
18046334-G-A 15934454-G-A FT337852 YY+
18573379-C-T 16461499-C-T BY158153 YY+
19073106-T-A 16961226-T-A FT338448 Y+
21105514-A-T 18943628-A-T YY13×T+
21931407-C-T 19769521-C-T PR3657 YY+
22116421-C-A 19954535-C-A FT339615 YY+
22594593-G-C 20432707-G-C M1049 Z793 YY+
14370596-A-G 12249892-A-G FT335515 YY+
14236446-A-G 12115740-A-G FT335383 YY+
23154479-T-G 20992593-T-G FT340162 YY+
23633377-T-C 21471491-T-C YY+
22438869-A-C 20276983-A-C DYZ19 +
2685639-C-T 2817598-C-T YY+
24706184-T-G 22560037-T-G P3_b2 +
28672226-C-T 26526079-C-T CTS12691 +
16215735-A-G 14103855-A-G Y+
15363811-A-C 13251931-A-C YY+
18633073-G-A 16521193-G-A A6458Y17099 YY+
7197232-C-T 7329191-C-T FT333750 YY+
9073124-C-T 9235515-C-T FT401413 Y+
7289473-C-A 7421432-C-A A20684 YY+
7305982-C-T 7437941-C-T FT333806 YY+
7709751-T-C 7841710-T-C FT334002 Y+
8405012-C-T 8536971-C-T Y3939 F4765 YY+
8692827-G-A 8824786-G-A Z25985 F14333 Y+
8770589-A-G 8902548-A-G FT334724 YY+
8798168-G-A 8930127-G-A FTA5876 YY+
22848638-A-C 20686752-A-C FT339928 YY+
23300266-GA-G 21138380-GA-G 10×A+
6350909-G-GA 6482868-G-GA 9×A+
5248789-G-A 5380748-G-A +
5177552-G-A 5309511-G-A +
5177566-T-A 5309525-T-A FT47317 +
5177576-C-G 5309535-C-G +
5204354-C-T 5336313-C-T +
5246328-ATACAC-A 5378287-ATACAC-A +
5248783-G-A 5380742-G-A +
5252555-C-G 5384514-C-G +
4615078-A-G 4747037-A-G FTA9300 +
5381063-T-G 5513022-T-G +
5418139-T-A 5550098-T-A +
5420959-A-G 5552918-A-G +
5554945-C-A 5686904-C-A +
5644847-T-C 5776806-T-C +
5962148-ATG-A 6094107-ATG-A +
6004255-C-A 6136214-C-A FTA9302 +
4783994-C-T 4915953-C-T FT123424 +
4602837-G-T 4734796-G-T +
23594185-C-A 21432299-C-A FTA6292 YY+
2685623-C-T 2817582-C-T M5575 YY+
23631233-G-T 21469347-G-T FT340456 YY+
23850284-C-T 21688398-C-T BY155709 Y+
28707511-C-A 26561364-C-A FT340789 Y+
22245367-A-C 20083481-A-C DYZ19 +
2685634-C-T 2817593-C-T YY+
2685629-C-T 2817588-C-T M4581 YY+
22245388-A-G 20083502-A-G DYZ19 +
2719553-C-T 2851512-C-T YY+
4474668-A-G 4606627-A-G +
2909255-G-A 3041214-G-A M12324 YY+
3097676-C-G 3229635-C-G FTA9299 +
3117336-G-A 3249295-G-A +
3403380-G-T 3535339-G-T +
3720269-G-A 3852228-G-A FTA9297 +
3720270-C-A 3852229-C-A FTA9298 +
4460350-A-G 4592309-A-G 8×T+
59030482-C-CAAAA 56884335-C-CAAAA +

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
Manual21527519-T-TA19365633-T-TA5 reads, all match the hg19 reference sequence.
Manual7188081-GAT-G7320040-GAT-GJust one read, but it has the deletion.
Manual19836539-C-A17724659-C-A2A 2C
Manual20632649-G-T18470763-G-T4G 5T
Manual21916166-A-G19754280-A-G3G
Manual22264989-T-A20103103-T-A1A 4T
Manual22464995-TG-T20303109-TG-T7 reads, all show the deletion.
Manual5211584-A-G5343543-A-G1G
Manual6711888-G-A6843847-G-A2A
Manual14367556-C-A12246852-C-A2A
Manual26408151-G-C24262004-G-C3C 1G



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