Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > FGC11134 > A353 > Z16250 > A114 > CTS4466/S1136 > S1115 > Z17989 > A2289 > FT33173

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
20000369-A-G 17888489-A-G E462 P5_Prx A+
28801449-A-AGTAG 26655302-A-AGTAG A*
5930901-C-T 6062860-C-T A3241 A*
13719134-T-A 11563458-T-A A*
26328474-C-CT 24182327-C-CT P1_Y1 A*
26145402-G-T 23999255-G-T P1_Y1 A*
19777747-G-A 17665867-G-A P5_Prx A*
10045597-C-T 10207988-C-T FT225539 A*
19741181-A-C 17629301-A-C P5_Prx A*
13687301-C-G 11531625-C-G A*
10045560-G-A 10207951-G-A A*
19109751-T-A 16997871-T-A FT61959 YY+
6748568-A-G 6880527-A-G FT61034 YY+
22053940-C-T 19892054-C-T BY39551BY39551 YY+
14523664-T-C 12411865-T-C FT61443 YY+
15756426-G-T 13644546-G-T FT61572 YY+
14810766-A-G 12698837-A-G FT61466 YY+
21303442-G-A 19141556-G-A FT62055 YY+
14299345-T-G 12178639-T-G FT61415 YY+
2684302-G-C 2816261-G-C FT60481 Y+
4452081-G-A 4584040-G-A FT60721 +
21169214-C-A 19007328-C-A FT62041 YY+
16516987-G-GA 14405107-G-GA 8×A+
6730974-T-C 6862933-T-C FT61032 Y+
23810586-C-T 21648700-C-T FT62268 Y+
22300040-T-G 20138154-T-G DYZ19 *
22319468-T-C 20157582-T-C BY217430 DYZ19 *
13470563-T-C 11314887-T-C *
21562049-T-TCA 19400163-T-TCA 18×CA*
13470535-G-T 11314859-G-T *
18174732-G-A 16062852-G-A F22539 YY*
3100708-C-T 3232667-C-T *
9459384-T-TTG 9621775-T-TTG 18×TG*
18830560-C-T 16718680-C-T YY*
3559293-T-A 3691252-T-A *
5492199-G-T 5624158-G-T *
6519630-T-A 6651589-T-A *
23809092-G-A 21647206-G-A Y*
3384440-T-C 3516399-T-C **
10056634-A-G 10219025-A-G **
3318303-G-T 3450262-G-T **
3459506-C-CTT 3591465-C-CTT 14×T**
5936167-T-G 6068126-T-G **
13467593-G-A 11311917-G-A BY47620 **
24416976-A-G 22270829-A-G **
13474496-G-A 11318820-G-A **
13467525-C-T 11311849-C-T **
13467601-T-A 11311925-T-A **
14131289-T-C 12010583-T-C **
13457747-A-T 11302071-A-T **
18738645-A-G 16626765-A-G **
13457706-C-G 11302030-C-G **
22153858-G-T 19991972-G-T FGC1625 **
21556919-CTTTTT-C 19395033-CTTTTT-C 23×T**
22471694-T-G 20309808-T-G DYZ19 **
22622311-A-G 20460425-A-G **
3240658-A-AT 3372617-A-AT 13×T**
9722500-GAA-G 9884891-GAA-G IR3_Prx 18×A**
16979078-T-C 14867198-T-C **
7758720-CTTT-C,CT 7890679-CTTT-C,CT 17×T***
8501744-TC-T 8633703-TC-T ***
28492954-TGA-T 26346807-TGA-T ***
22101002-CAAAAAAAAA-C 19939116-CAAAAAAAAA-C 27×A***
17136931-CTTT-C,CTT 15025051-CTTT-C,CTT 18×T***
13842818-C-A 11722112-C-A 5×AATGG***
16429726-G-A 14317846-G-A ***
13470540-C-A 11314864-C-A ***
13470587-G-T 11314911-G-T ***
23839026-A-G 21677140-A-G ***
15250858-TAA-T,TA 13138944-TAA-T,TA 15×A***
22981819-TA-T,TAA 20819933-TA-T,TAA 15×A***
16888188-T-C 14776308-T-C ***
21175749-C-CA 19013863-C-CA 27×A***
6686246-T-C 6818205-T-C ***
59004185-G-A 56858038-G-A ***
28545880-CAAAA-C 26399733-CAAAA-C 20×A***
56828827-TGCATTCAATT-A ***
11031569-A-ACCATT ***
21961720-G-GAA 19799834-G-GAA 12×A***
14765676-A-ATT 12653745-A-ATT 21×T***
28787330-A-G 26641183-A-G ***
21548874-A-AT 19386988-A-AT 10×T***
19138349-C-A 17026469-C-A 11×TA***
9942259-G-A 10104650-G-A ***
5471956-G-GA 5603915-G-GA ***
3259004-G-C 3390963-G-C ***
5198935-G-A 5330894-G-A ***
6473334-G-GA 6605293-G-GA 13×A***
9900478-G-GTA 10062869-G-GTA ***
17669700-CATATAT-C 15557820-CATATAT-C 15×AT***
3146672-AGTGT-A 3278631-AGTGT-A 21×GT***
15683628-CAAA-C 13571748-CAAA-C 24×A***
6099384-CAAA-C,CAAAA 6231343-CAAA-C,CAAAA 17×A***
4182879-G-GA 4314838-G-GA 10×A***
3370591-T-C 3502550-T-C ***
2753174-A-G 2885133-A-G ***
21853779-A-T 19691893-A-T BY181 ZS4363 FGC22094 ***
13470594-G-T 11314918-G-T ***
13448797-TCCGTTC-T 11293121-TCCGTTC-T ***
5268741-G-T 5400700-G-T ***
7310571-CTT-C,CT 7442530-CTT-C,CT 21×T***
5882071-A-AT 6014030-A-AT 10×T***
16250624-GTTT-G 14138744-GTTT-G 28×T***
13470584-G-T 11314908-G-T ***
22989652-CTT-C 20827766-CTT-C 14×T***
3344725-AT-A 3476684-AT-A 10×T***
13705548-A-T 11549872-A-T ***
17734039-CA-C 15622159-CA-C 10×A***
6634325-C-A 6766284-C-A ***
21700595-GA-G,GAA 19538709-GA-G,GAA 17×A***
13470565-C-T 11314889-C-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.

Age Analysis Information (work in progress)

Kit: 5861901494267093715668303869
Used in age calculations1494267093715668303869
Counts of SNPs1313
Variant counts last updated 2020-05-04 03:27:57.

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