Simmont

BigY3: 31455
MDKA Birth: United States > Maryland 1869

Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z272 > S450 > ZZ40 > S21184 > S19290 > 20069574-T-C > S16785 > ZZ74 > ZZ75 > BY33254

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
31455
10626825-C-T A*
9967985-G-T 10130376-G-T YA*
16097130-C-A 13985250-C-A A*
16097136-C-T 13985256-C-T A*
25985125-T-A 23838978-T-A P1_Y1 A*
8902035-C-T 9033994-C-T FT20216 Y+
10934307-A-G FT437166 +
3300978-C-A 3432937-C-A FT15133 +
3730108-A-G 3862067-A-G FT15623 +
3811482-A-G 3943441-A-G FT15730 +
4202369-A-G 4334328-A-G FT16195 +
5456188-C-T 5588147-C-T FT17591 +
6877064-G-A 7009023-G-A FT18815 YY+
7220372-C-T 7352331-C-T FT19054 YY+
7604798-C-T 7736757-C-T FT19290 YY+
8162126-A-C 8294085-A-C FT19680 YY+
8570875-A-G 8702834-A-G FT19986 YY+
9160419-A-T 9322810-A-T FT20354 +
9735254-G-C 9897645-G-C FT20495 IR3_Prx +
10780212-A-T FT430893 +
14485223-T-G 12364492-T-G FT21401 YY+
15719330-G-A 13607450-G-A FT22219 YY+
17237657-T-C 15125777-T-C YY+
17765247-G-C 15653367-G-C FT23764 YY+
17782526-G-A 15670646-G-A FT23778 YY+
21507127-C-G 19345241-C-G FT25419 YY+
21869671-C-T 19707785-C-T FT25734 YY+
28643949-A-C 26497802-A-C FT27212 +
28777658-G-A 26631511-G-A FT461570 +
8589565-A-AAC 8721524-A-AAC 11×AC*
17109091-A-AACAC 14997211-A-AACAC 25×AC*
9906513-A-ACCACCT 10068904-A-ACCACCT 5×CCACCT*
10678303-C-T *
22235319-C-G 20073433-C-G DYZ19 *
20842517-GGAAAGAAA-G 18680631-GGAAAGAAA-G P4_Dst 14×GAAA**
21940037-CATAT-C 19778151-CATAT-C 22×AT**
22480098-G-C 20318212-G-C DYZ19 **
13480291-C-G 11324615-C-G **
3798116-C-A 3930075-C-A **
7107220-A-G 7239179-A-G **
14712078-A-G 12600145-A-G **
15863007-A-G 13751127-A-G **
17125159-A-T 15013279-A-T **
18344529-T-TTA 16232649-T-TTA P6_Prx 13×TG**
21337924-A-G 19176038-A-G **
22987702-C-A 20825816-C-A **
26376432-G-T 24230285-G-T P1_Y1 **
27039053-A-G 24892906-A-G P1_r4 **
28680570-A-G 26534423-A-G **
13466016-T-A,G 11310340-T-A,G ***
17713850-CTTTTT-C 15601970-CTTTTT-C 23×T***
15131865-TCCTC-T 13019952-TCCTC-T 5×CCTC***
9438099-CTT-C 9600490-CTT-C 30×T***
16598984-CAAAAAA-C 14487104-CAAAAAA-C 25×A***
5081843-GA-G 5213802-GA-G 10×A***
6430439-TTATA-T 6562398-TTATA-T 19×TA***
13466006-C-A 11310330-C-A ***
16374686-GA-G,GAA 14262806-GA-G,GAA 19×A***
13467154-TC-T 11311478-TC-T ***
21639069-T-G 19477183-T-G ***
14795080-CTTTTT-C 12683151-CTTTTT-C 24×T***
2994629-AT-A 3126588-AT-A ***
18612759-GTATA-G,GTA 16500879-GTATA-G,GTA 15×TA***
13489960-C-G 11334284-C-G ***
13489915-C-T 11334239-C-T ***
5960696-AT-A,ATT 6092655-AT-A,ATT 30×T***
17351381-C-CT 15239501-C-CT 10×T***
56867491-ATTTTTTT-A,ATTTTTT 11×T***
9915997-A-G 10078388-A-G ***
4305519-C-T 4437478-C-T ***
5260380-C-T 5392339-C-T ***
6100552-TA-T,TAAA 6232511-TA-T,TAAA 15×A***
13279976-C-A 11124300-C-A ***
13318810-G-A 11163134-G-A ***
13461718-G-A 11306042-G-A ***
13616240-G-A 11460564-G-A ***
13745738-G-A 11590062-G-A ***
18795604-C-T 16683724-C-T ***
18972150-T-C 16860270-T-C ***
22263528-G-A 20101642-G-A DYZ19 ***
23290612-A-G 21128726-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.