Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > Z46512 > FGC78762 > ZZ19 > Z31644 > FGC78763 > A2146 > BY1246 > BY19308

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
676741
20707819-T-C 18545933-T-C P4_Prx A*
19677904-A-AC 17566024-A-AC P5_Prx A*
20932034-G-A 18770148-G-A P4_Dst A*
20625582-G-A 18463696-G-A P4_Prx A*
24286870-T-G 22140723-T-G P3_t1 A*
20712144-C-T 18550258-C-T P4_Prx A*
26364045-G-A 24217898-G-A P1_Y1 A*
6857366-T-G 6989325-T-G BY61758 YY+
7916889-C-A 8048848-C-A FT236079 YY+
10823029-C-T FT255336 +
21639592-G-A 19477706-G-A BY134365 YY+
8204627-C-G 8336586-C-G BY70714 YY+
6144999-G-A 6276958-G-A FT152920 IR3_Dst +
22047209-T-C 19885323-T-C BY137326 YY+
5954199-A-G 6086158-A-G FT235745 +
10617024-A-G FT255337 +
8040361-T-C 8172320-T-C BY69551 YY+
13230095-G-A 11074419-G-A BY84720 +
13227976-G-A 11072300-G-A FT165008 +
22262874-C-T 20100988-C-T BY43705 DYZ19 +
13698113-AAATGGAATGG-A 11542437-AAATGGAATGG-A 5×AATGG+
14365127-T-A 12244422-T-A BY95243 YY+
14444522-G-A 12323795-G-A BY95803 Y+
19448648-C-A 17336768-C-A FT154834 YY+
18160219-G-C 16048339-G-C BY120480 YY+
17782498-GA-G 15670618-GA-G +
17761987-G-A 15650107-G-A BY117210 YY+
17617647-C-T 15505767-C-T FT154380 Y+
16972968-G-C 14861088-G-C FT154238 Y+
5759839-G-A 5891798-G-A FT152809 +
5237592-C-G 5369551-C-G FT152644 +
16934964-T-C 14823084-T-C FT237054 YY+
23000865-A-G 20838979-A-G BY44160 YY+
18551143-A-AT 16439263-A-AT 8×T+
14380014-T-C 12259310-T-C FT153748 YY+
3112387-G-A 3244346-G-A FGC47041 +
14568351-C-A 12456551-C-A BY96511 Y+
6667553-G-A 6799512-G-A BY60613 YY+
23801225-G-A 21639339-G-A BY147815 Y+
13815612-G-T 11694906-G-T BY90395 +
10927344-G-A FT255335 +
23163213-C-T 21001327-C-T BY143542 Y+
5169868-A-G 5301827-A-G FT152616 +
23116151-G-A 20954265-G-A BY143043 YY+
22677482-G-C 20515596-G-C BY44135 YY+
2758881-G-A 2890840-G-A BY56290 YY+
5113609-C-T 5245568-C-T FT235524 +
5090683-T-C 5222642-T-C FT152587 +
3942301-G-T 4074260-G-T FT152266 +
16851506-G-A 14739626-G-A BY110572 YY+
3961780-C-T 4093739-C-T FGC63585 +
22317526-A-T 20155640-A-T BY217288 DYZ19 *
9444688-T-TC 9607079-T-TC *
22316973-G-T 20155087-G-T DYZ19 *
56850221-T-C *
28795127-A-C 26648980-A-C *
10787302-C-CTCCAT *
23319154-A-G 21157268-A-G **
21915169-C-T 19753283-C-T **
22476987-T-A 20315101-T-A BY223700 DYZ19 **
22512173-A-G 20350287-A-G BY225820 DYZ19 **
28544948-C-T 26398801-C-T **
26057965-C-T 23911818-C-T P1_Y1 **
56821857-T-G **
7285581-A-G 7417540-A-G **
9529142-CTTTT-C 9691533-CTTTT-C IR3_Prx 15×T**
3640925-C-A 3772884-C-A BY42621 **
9546617-CT-C 9709008-CT-C IR3_Prx 12×T**
6017805-C-A 6149764-C-A **
18970320-CA-C 16858440-CA-C 28×A**
22540525-T-C 20378639-T-C **
16394884-G-A 14283004-G-A **
16422212-T-C 14310332-T-C **
3171902-CAA-C 3303861-CAA-C 13×A***
6642437-C-A 6774396-C-A ***
27525243-CTTTTT-C,CTTT 25379096-CTTTTT-C,CTTT P1_Y2 27×T***
22950193-CT-C,CTT 20788307-CT-C,CTT 21×T***
22881076-CTT-C,CTTT 20719190-CTT-C,CTTT 14×T***
13550384-C-T 11394708-C-T ***
13470569-C-A 11314893-C-A ***
5062473-CAA-C,CA 5194432-CAA-C,CA 21×A***
3076069-CTTTTT-C,CTTT 3208028-CTTTTT-C,CTTT 25×T***
13462610-C-T 11306934-C-T ***
16665471-T-C 14553591-T-C ***
5489121-A-G 5621080-A-G ***
14420787-CTT-C,CT 12300062-CTT-C,CT 18×T***
17170167-CTTTTTT-C,CTTTT 15058287-CTTTTTT-C,CTTTT 21×T***
7076323-C-CA 7208282-C-CA ***
8062363-T-C 8194322-T-C ***
21371289-T-G 19209403-T-G ***
9942037-TTCTG-T 10104428-TTCTG-T ***
13325141-C-T 11169465-C-T ***
13930171-CA-C,CAA 11809465-CA-C,CAA 21×A***
14919572-T-C 12807637-T-C ***
19512088-A-G 17400208-A-G ***
15799160-C-T 13687280-C-T ***
15893596-T-A 13781716-T-A ***
16370648-CA-C,CAA 14258768-CA-C,CAA 17×A***
15084466-CTTTTT-C 12972556-CTTTTT-C 19×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)

AllMcDonaldYFull
Kit: 6767411490660993479758282648
Used in age calculations1490660993479758282648
Counts of SNPs2319
Variant counts last updated 2020-05-13 02:34:03.



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