Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > FGC11134 > A353 > Z16250 > A114 > CTS4466/S1136 > S1115 > A212 > A7699 > BY3535 > BY43588

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 STRBigY3
804057
28019583-C-T 25873436-C-T P1_Y2 A+
6403148-G-A 6535107-G-A A*
19817537-C-CA 17705657-C-CA P5_Prx 22×AA*
13842757-G-A 11722051-G-A A*
56830917-G-T A*
6402110-G-T 6534069-G-T A*
13478419-G-T 11322743-G-T A*
20950550-C-CA 18788664-C-CA P4_Dst 13×AA*
16099087-C-CTG 13987207-C-CTG P8_Prx 23×TGA*
20333835-C-CA 18171949-C-CA P5_Dst 24×AA*
5833035-A-G 5964994-A-G A*
10826919-C-T +
21657247-G-A 19495361-G-A FT25579 YY+
21397115-T-G 19235229-T-G FT25331 YY+
23001360-C-T 20839474-C-T FT26323 YY+
19533133-G-T 17421253-G-T FT25046 YY+
19010632-G-A 16898752-G-A FT24606 YY+
6441604-G-A 6573563-G-A FT18490 +
17195012-C-T 15083132-C-T FT23287 YY+
3021409-G-C 3153368-G-C FT14814 +
14950029-G-A 12838103-G-A FT21727 YY+
3899643-G-T 4031602-G-T FT15836 +
5456554-G-T 5588513-G-T FT17592 +
8706283-T-C 8838242-T-C FT20087 YY+
5684268-C-T 5816227-C-T FT17889 +
22320081-G-T 20158195-G-T DYZ19 *
7097450-G-A 7229409-G-A YY*
14784974-A-G 12673044-A-G **
18055488-G-T 15943608-G-T **
14784973-C-A 12673043-C-A **
22445976-C-T 20284090-C-T BY27406 DYZ19 **
20802798-A-G 18640912-A-G P4_Gap **
13455521-T-G 11299845-T-G **
21698309-TAA-T 19536423-TAA-T 24×A**
18878462-A-G 16766582-A-G **
19609664-A-T 17497784-A-T P5_Prx **
2698122-A-G 2830081-A-G **
7632529-C-T 7764488-C-T **
2888615-A-T 3020574-A-T **
2994178-T-C 3126137-T-C **
16905655-G-A 14793775-G-A **
3669850-T-C 3801809-T-C **
14784954-G-C 12673024-G-C **
14784914-C-G 12672984-C-G **
8095700-T-C 8227659-T-C **
14784966-A-G 12673036-A-G **
3662166-T-TTA 3794125-T-TTA 9×TA**
19121920-C-CTT 17010040-C-CTT 17×T**
27861907-ACT-A 25715760-ACT-A P1_Y2 **
3963833-CAAAAA-C 4095792-CAAAAA-C 22×A**
14784976-C-A 12673046-C-A **
21575637-C-T 19413751-C-T **
14456346-C-CA 12335619-C-CA 9×A**
6527627-G-A 6659586-G-A **
16027323-A-G 13915443-A-G ***
16712406-A-G 14600526-A-G ***
18391212-C-T 16279332-C-T P6_Gap ***
10803095-ACAATC-A ***
17419439-ATTT-A,ATT 15307559-ATTT-A,ATT 25×T***
17505779-G-A 15393899-G-A ***
15102498-T-C 12990586-T-C ***
56851243-C-A ***
23590764-C-CAA 21428878-C-CAA 15×A***
13223497-A-AG 11067821-A-AG ***
4896649-CAA-C 5028608-CAA-C 16×A***
4571254-CAA-C 4703213-CAA-C 29×A***
13823204-AATGGAATGGAATGGA-A,AATGGAATGGAATGGG 11702498-AATGGAATGGAATGGA-A,AATGGAATGGAATGGG ***
19431601-A-G 17319721-A-G ***
8498338-CAAA-C 8630297-CAAA-C 16×A***
20804079-T-C 18642193-T-C P4_Gap ***
59019425-T-A 56873278-T-A ***
21556696-T-C 19394810-T-C ***
59012740-G-C 56866593-G-C ***
21853422-T-C 19691536-T-C ***
17106925-TAC-T 14995045-TAC-T ***
22469155-CT-C 20307269-CT-C DYZ19 ***
23556204-TAAA-T,TAA 21394318-TAAA-T,TAA 12×A***
24508205-CTTTTTTT-C,CTTT 22362058-CTTTTTTT-C,CTTT 22×T***
8160178-CAAAAA-C 8292137-CAAAAA-C 20×A***
13617868-A-G 11462192-A-G ***
13641007-A-G 11485331-A-G ***
5349961-G-A 5481920-G-A ***
14488773-CAAAA-C,CAAA 12368042-CAAAA-C,CAAA 16×A***
3475308-G-C 3607267-G-C ***
28613771-CTTT-C 26467624-CTTT-C 16×T***
28534940-C-CTT 26388793-C-CTT 18×T***
13931739-CTT-C,CT 11811033-CTT-C,CT 22×T***
5035398-G-GA 5167357-G-GA 10×A***
4174030-TA-T 4305989-TA-T 9×A***
13463183-TAC-CAC,T 11307507-TAC-CAC,T ***
4793991-A-AT 4925950-A-AT 13×T***
6600473-C-CT 6732432-C-CT 9×T***
13470435-G-A 11314759-G-A ***
13463734-T-C 11308058-T-C ***
5493864-G-GTT 5625823-G-GTT 22×T***
3851279-AGT-A 3983238-AGT-A 9×GT***
28492932-ATTTT-A 26346785-ATTTT-A 22×T***
3635747-A-C 3767706-A-C ***
3758621-A-G 3890580-A-G ***
4377969-CTTTT-C,CTTTTT 4509928-CTTTT-C,CTTTTT 19×T***
7100954-CTTTT-C 7232913-CTTTT-C 32×T***
13267597-CA-C 11111921-CA-C 11×A***
16739069-GAA-G 14627189-GAA-G 17×A***
4179020-TAAA-T 4310979-TAAA-T 17×A***
13462334-CA-C 11306658-CA-C ***
3695724-CAA-C 3827683-CAA-C 14×A***
3736474-A-AT 3868433-A-AT 10×T***
10618351-C-A ***
3559501-C-A 3691460-C-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.

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: 8040571464862892088288204343
Used in age calculations1464862892088288204343
Counts of SNPs99
Variant counts last updated 2019-10-11 02:48:41.



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