Tree Position

R-P312/S116 > DF19/S232 > Z302/S233 > Z8193 > BY3448

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
IN55541
5315325-G-A 5447284-G-A A+
27947300-A-G 25801153-A-G P1_Y2 A+
56836661-C-T A*
26010014-G-C 23863867-G-C P1_Y1 A*
19607363-A-T 17495483-A-T P5_Prx YA*
13449951-C-CCTCCA 11294275-C-CCTCCA A*
16117270-T-C 14005390-T-C P8_Prx A*
25899452-C-A 23753305-C-A P1_Y1 A*
20888363-G-A 18726477-G-A P4_Dst A*
13451152-C-A 11295476-C-A A*
13450965-C-G 11295289-C-G A*
22286083-C-T 20124197-C-T DYZ19 A*
13489656-C-T 11333980-C-T A*
26015102-T-C 23868955-T-C P1_Y1 A*
26052380-C-T 23906233-C-T P1_Y1 A*
26076447-T-G 23930300-T-G P1_Y1 A*
26397434-G-A 24251287-G-A P1_Y1 A*
28816722-G-T 26670575-G-T A*
20572409-T-A 18410523-T-A P5_Dst A*
15532037-G-A 13420157-G-A FT130984 YY+
17017158-A-T 14905278-A-T FT131234 YY+
17658688-GC-G 15546808-GC-G +
17758943-CAT-C 15647063-CAT-C +
17806178-G-A 15694298-G-A FT131388 YY+
18099534-C-T 15987654-C-T FT131439 YY+
14158300-G-C 12037594-G-C FT130756 YY+
19040853-G-A 16928973-G-A FT131582 Y+
22928049-G-C 20766163-G-C FT131988 YY+
21365615-C-G 19203729-C-G FT131746 YY+
21428436-T-G 19266550-T-G FT131761 YY+
22008084-C-A 19846198-C-A FT131875 YY+
22112683-A-G 19950797-A-G FT131894 YY+
22480599-T-C 20318713-T-C DYZ19 +
22833224-T-G 20671338-T-G FT131974 YY+
22967613-C-A 20805727-C-A YY+
23140311-G-A 20978425-G-A FT132032 YY+
23301275-C-T 21139389-C-T FT132062 YY+
24405418-G-C 22259271-G-C FT132178 +
24432560-G-A 22286413-G-A FT132184 Y+
24501942-T-C 22355795-T-C FT132193 +
28633199-T-C 26487052-T-C Y+
13995372-C-T 11874666-C-T FT130717 Y+
11652132-A-T +
6149770-C-G 6281729-C-G FT130157 IR3_Dst +
8467282-C-A 8599241-C-A YY+
3335250-A-T 3467209-A-T FT129610 +
5252507-C-G 5384466-C-G FT129983 +
5311907-CAAACTTCACATGT-C 5443866-CAAACTTCACATGT-C +
5399946-C-A 5531905-C-A FT130012 +
6691583-G-T 6823542-G-T FT130232 Y+
7065290-G-C 7197249-G-C FT130299 YY+
7192374-A-T 7324333-A-T FT130315 YY+
7374498-C-T 7506457-C-T FT130339 Y+
7540722-T-C 7672681-T-C FT130352 YY+
7629759-G-T 7761718-G-T YY+
3177393-T-C 3309352-T-C FT129585 +
8114269-C-A 8246228-C-A FT130413 YY+
8525688-G-A 8657647-G-A FT130479 YY+
10057528-T-C 10219919-T-C +
8600015-T-C 8731974-T-C FT130493 YY+
18549264-C-T 16437384-C-T FT131492 Y+
21983504-G-T 19821618-G-T BY35149BY35149 YY+
21403477-C-A 19241591-C-A FT131755 YY+
10773695-C-T +
2736204-A-G 2868163-A-G FT129499 YY+
9846686-A-G 10009077-A-G FT130635 YY+
20931853-A-ATGTGTG 18769967-A-ATGTGTG P4_Dst 18×TG*
3015896-G-A 3147855-G-A *
13194286-T-TTTCCATTCCA 11038610-T-TTTCCATTCCA 9×TTCCA*
13821177-AGGAATGGAATGGAATGGAAT-A 11700471-AGGAATGGAATGGAATGGAAT-A 10×GGAAT*
13468645-T-A 11312969-T-A **
10622328-CAAAA-C 20×A**
24247414-CACA-C 22101267-CACA-C P3_b1 **
27546837-G-A 25400690-G-A P1_Y2 **
13468740-C-T 11313064-C-T **
13468654-C-CT 11312978-C-CT **
25553216-T-C 23407069-T-C P1_gr1 **
13369553-T-C 11213877-T-C **
22984080-T-G 20822194-T-G **
10061985-G-T 10224376-G-T **
13468692-G-C 11313016-G-C **
13468730-G-T 11313054-G-T **
13554117-A-G 11398441-A-G **
13468651-C-G 11312975-C-G **
7502352-TTC-T 7634311-TTC-T IR1_L 8×TC**
18352183-G-T 16240303-G-T P6_Prx **
19325810-A-G 17213930-A-G **
13464675-A-C 11308999-A-C **
6402049-A-C 6534008-A-C ***
9493317-C-T 9655708-C-T ***
22303832-G-C 20141946-G-C DYZ19 ***
9852944-A-T 10015335-A-T ***
18740841-T-A 16628961-T-A ***
26415601-C-T 24269454-C-T P1_Y1 ***
22288951-G-C 20127065-G-C DYZ19 ***
17669725-A-G 15557845-A-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: IN555411515825194777728365428
Used in age calculations1515825194777728365428
Counts of SNPs3228
Variant counts last updated 2019-12-01 02:33:49.



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