Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > DF21/S192 > S5488 > BY518 > S7200 > S6003 > Z16543 > S6000 > FGC43483 > FGC43477 > FGC43478 > FGC53206 > BY11119

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
739015
3694957-G-C 3826916-G-C A+
20978956-T-A 18817070-T-A P4_Dst A*
13478921-C-A 11323245-C-A A*
20431207-G-GA 18269321-G-GA P5_Dst 12×AA*
56837158-G-T A*
23180554-G-A 21018668-G-A YA*
7165589-T-C 7297548-T-C YYA*
28816789-T-C 26670642-T-C A*
20665222-A-T 18503336-A-T P4_Prx A*
18372348-C-T 16260468-C-T P6_Prx A*
10631416-C-CAATTT A*
3094544-T-C 3226503-T-C A*
13449572-C-T 11293896-C-T A*
5491261-C-CA 5623220-C-CA 18×AA*
19743718-C-CA 17631838-C-CA P5_Prx 13×AA*
22812402-G-A 20650516-G-A CTS10872 YY+
16516292-G-T 14404412-G-T YY+
16529004-G-C 14417124-G-C YY+
4023373-T-C 4155332-T-C *
7165775-C-T 7297734-C-T Y*
13470029-A-T 11314353-A-T *
15636155-A-G 13524275-A-G **
15574755-T-C 13462875-T-C **
22989652-CTT-C 20827766-CTT-C 14×T**
14850463-T-C 12738529-T-C **
14691823-T-C 12579889-T-C **
9188620-A-C 9351011-A-C **
5744781-A-G 5876740-A-G **
4524441-C-G 4656400-C-G **
4287943-G-A 4419902-G-A **
3327827-T-C 3459786-T-C **
21438785-TAAAAAAAA-T 19276899-TAAAAAAAA-T 31×A**
3350514-CAAA-C 3482473-CAAA-C 15×A**
21669476-C-T 19507590-C-T **
17491437-G-A 15379557-G-A **
4287922-G-GA 4419881-G-GA 9×A**
5781208-GTAAA-G 5913167-GTAAA-G 6×TAAA**
18131499-G-A 16019619-G-A FGC23677 **
20802688-T-C 18640802-T-C P4_Gap **
26435391-C-T 24289244-C-T P1_Y1 **
26090563-T-C 23944416-T-C P1_Y1 **
4878246-CAA-C 5010205-CAA-C 18×A**
17090839-ATTTTT-A,ATTTTTT 14978959-ATTTTT-A,ATTTTTT 29×T***
6526325-G-A 6658284-G-A ***
6522995-C-T 6654954-C-T ***
22423600-G-T 20261714-G-T DYZ19 ***
22538511-TA-T 20376625-TA-T ***
4134484-CA-C,CAAA 4266443-CA-C,CAAA 18×A***
23049129-A-G 20887243-A-G ***
6892847-A-T 7024806-A-T ***
4123309-T-C 4255268-T-C ***
28498440-A-C 26352293-A-C ***
3972229-T-C 4104188-T-C ***
21992963-TAAA-T,TA 19831077-TAAA-T,TA 23×A***
21797224-C-CTT 19635338-C-CTT 11×T***
21964091-A-G 19802205-A-G ***
9028893-TAAA-T,TAAAA 9191284-TAAA-T,TAAAA 18×A***
16627758-G-A 14515878-G-A ***
13239650-A-G 11083974-A-G ***
13969865-C-T 11849159-C-T ***
21700636-G-T 19538750-G-T ***
12374666-G-A ***
14825125-CTTT-C,CTTTTT 12713192-CTTT-C,CTTTTT 20×T***
21196768-C-A 19034882-C-A ***
15061014-C-A 12949106-C-A ***
15912055-CT-C,CTT 13800175-CT-C,CTT 21×T***
15971225-CTT-C,CTTT 13859345-CTT-C,CTTT 18×T***
17617528-C-T 15505648-C-T ***
17608404-A-G 15496524-A-G ***
16625560-A-G 14513680-A-G ***
13478109-G-T 11322433-G-T ***
3970967-T-C 4102926-T-C ***
6473334-GA-G 6605293-GA-G 13×A***
8907707-G-A 9039666-G-A ***
14794351-CTTT-C 12682422-CTTT-C 14×T***
3736474-AT-A 3868433-AT-A 10×T***
6878073-CAA-C,CA 7010032-CAA-C,CA 17×A***
16909178-CTT-C,CTTT 14797298-CTT-C,CTTT 16×T***
16863543-ATTT-A 14751663-ATTT-A 14×T***
16308486-C-CTT 14196606-C-CTT 25×T***
18636612-CTTT-C,CT 16524732-CTTT-C,CT 17×T***
4567312-CAA-C 4699271-CAA-C 13×A***
16588668-TA-T 14476788-TA-T A7983 10×A***
24072062-C-T 21925915-C-T P3_b1 ***
15402152-CA-C 13290272-CA-C 9×A***
22238375-G-C 20076489-G-C BY40870 DYZ19 ***
4880701-A-T 5012660-A-T ***
13546989-ATT-A 11391313-ATT-A 16×T***
28529232-C-CA 26383085-C-CA 23×A***
28539174-CAA-C 26393027-CAA-C 20×A***
13565166-T-C 11409490-T-C ***
3999627-A-G 4131586-A-G ***
2960682-G-A 3092641-G-A ***
7758720-CTTT-C 7890679-CTTT-C 17×T***
18863609-A-AT 16751729-A-AT 11×T***
3857282-C-CT 3989241-C-CT 10×T***
3256271-G-A 3388230-G-A ***
22190660-G-GA 20028774-G-GA 8×A***
10045598-G-A 10207989-G-A BY209689 ***
10045603-T-G 10207994-T-G ***
2840099-CAAAA-C,CA 2972058-CAAAA-C,CA 20×A***
25201099-G-A 23054952-G-A BY22638 g1 ***
6521551-GTT-G 6653510-GTT-G 17×T***
5766563-CA-C 5898522-CA-C 8×A***
23041258-T-C 20879372-T-C ***
21446217-CTTT-C,CTT 19284331-CTTT-C,CTT 23×T***
10776137-CTCAAT-C,CTCCAT ***
4941409-GA-G 5073368-GA-G 11×A***
3298985-GA-G 3430944-GA-G 11×A***
22555369-G-GT 20393483-G-GT 9×T***
5205635-ATT-A 5337594-ATT-A 14×T***
17141709-CAAAAA-C 15029829-CAAAAA-C 21×A***
13199164-C-CA,CAA 11043488-C-CA,CAA 18×A***
4483292-A-AT,ATT 4615251-A-AT,ATT 14×T***
11008990-A-C ***
56834251-TC-T ***
4765550-A-AT 4897509-A-AT 10×T***
4537586-C-CT 4669545-C-CT 21×T***
5792505-G-GT 5924464-G-GT 11×T***
13532875-C-CA 11377199-C-CA 13×A***
28581686-T-G 26435539-T-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.

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: 7390151467608792058818201369
Used in age calculations1467608792058818201369
Counts of SNPs64
Variant counts last updated 2019-06-18 01:11:57.



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