Lewis

BigY3: 890293
MDKA Birth: England 1595

Tree Position

A0-T-YP2191 > P305[A1] > A1b > BT/A1b2 > M168/PF1416[CT] > P143[CF] > M89/PF2746[F] > F1329/M3658[GHI > F929[HIJK] > IJK > IJ > M170[I] > Z2647 > L460 > M436 > M223 > CTS10057 > Z76

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
890293
4544359-G-A 4676318-G-A A+
56842948-C-A A*
20045568-T-TTC 17933688-T-TTC P5_Prx 13×TCA*
56831385-A-G A*
56836956-A-C A*
4316799-A-G 4448758-A-G A*
19726236-C-T 17614356-C-T P5_Prx A*
19789450-C-A 17677570-C-A P5_Prx A*
24344938-G-A 22198791-G-A P3_t1 A*
28817534-G-T 26671387-G-T A*
56831221-C-A A*
22468696-G-A 20306810-G-A A787A452 DYZ19 +
17576189-C-T 15464309-C-T Y131517 YY+
28795796-G-A 26649649-G-A FT461999 +
23315795-G-A 21153909-G-A FT182696 YY+
2694299-A-G 2826258-A-G FT333374 YY+
4008198-C-T 4140157-C-T FT341292 +
4980146-T-C 5112105-T-C FT341719 +
5185184-G-A 5317143-G-A FT341803 +
5234075-A-G 5366034-A-G FT341821 +
5430358-C-A 5562317-C-A FT341926 +
5466142-T-C 5598101-T-C FT341951 +
5694193-G-A 5826152-G-A FT342032 +
6887651-C-A 7019610-C-A FT333594 YY+
6943203-G-A 7075162-G-A FT333614 YY+
7303952-C-T 7435911-C-T FT333804 Y+
7538264-A-G 7670223-A-G FT333900 YY+
8237826-G-T 8369785-G-T FT334335 YY+
8355744-G-T 8487703-G-T FT334411 YY+
9080222-A-G 9242613-A-G FT334888 +
9081864-T-C 9244255-T-C FT334890 +
13233196-G-A 11077520-G-A +
13910408-G-A 11789702-G-A FT335102 Y+
13999136-C-G 11878430-C-G FT335192 YY+
14649196-G-T 12537261-G-T FT335693 Y+
14948978-A-T 12837052-A-T FT335866 YY+
16335055-G-A 14223175-G-A FT336709 YY+
16476704-G-A 14364824-G-A FT336829 YY+
16556016-A-C 14444136-A-C FT336891 YY+
16713207-G-A 14601327-G-A FT305139 YY+
16981898-T-C 14870018-T-C FT337143 YY+
17474167-T-C 15362287-T-C FT337459 YY+
19208199-G-T 17096319-G-T FT338560 YY+
19538162-CATT-C 17426282-CATT-C +
21691479-T-C 19529593-T-C FT339325 YY+
24404149-G-A 22258002-G-A FT340586 +
24437611-G-C 22291464-G-C FT340603 Y+
28500581-C-T 26354434-C-T BY150615 Y+
3716572-G-A 3848531-G-A S7747 *
23040748-A-AT 20878862-A-AT 9×T*
56841784-C-A *
20048160-CT-C 17936280-CT-C P5_Prx 10×T**
26514896-ATC-A 24368749-ATC-A P1_Y1 **
19418550-GAGAA-G 17306670-GAGAA-G 4×AGAA**
26514895-A-T 24368748-A-T P1_Y1 **
9623314-G-GA 9785705-G-GA IR3_Prx 9×A**
19686221-CTTTT-C 17574341-CTTTT-C P5_Prx 16×T**
19839617-A-G 17727737-A-G BY196851 P5_Prx **
13612940-G-T 11457264-G-T **
13612925-G-A 11457249-G-A **
18735674-CTTTTTT-C 16623794-CTTTTTT-C 24×T**
22258101-G-C 20096215-G-C DYZ19 **
2699015-A-G 2830974-A-G **
4651680-T-C 4783639-T-C **
8379144-CTTCTTTCTTTCTTTCTTTCTTTCT-C 8511103-CTTCTTTCTTTCTTTCTTTCTTTCT-C 15×TTCT**
13922229-T-C 11801523-T-C **
16635280-A-AAT 14523400-A-AAT **
17449503-T-C 15337623-T-C **
18468354-A-AG 16356474-A-AG P6_Dst **
19031025-C-CT 16919145-C-CT **
19388204-T-C 17276324-T-C **
20377108-C-G 18215222-C-G P5_Dst **
21346975-TTATATATATATATATATATATATATATATATATATA-T 19185089-TTATATATATATATATATATATATATATATATATATA-T 29×TA**
22238791-C-G 20076905-C-G DYZ19 **
22279851-G-A 20117965-G-A DYZ19 **
25240798-T-G 23094651-T-G P2_r1 **
26499920-T-TTGTG 24353773-T-TTGTG P1_Y1 15×TG**
27462488-T-TACAC 25316341-T-TACAC P1_Y2 15×AC**
8100637-CAAAA-C 8232596-CAAAA-C 37×A***
4897963-CAAAA-C 5029922-CAAAA-C 20×A***
5220159-CTTTT-C 5352118-CTTTT-C 21×T***
13545823-TAA-T 11390147-TAA-T 12×A***
22537275-C-CAA 20375389-C-CAA 15×A***
14815623-TTGC-T 12703694-TTGC-T ***
9427835-A-G 9590226-A-G ***
9519886-C-T 9682277-C-T ***
3790878-GTATATATATATATATATATATATATATATATA-G,GTA 3922837-GTATATATATATATATATATATATATATATATA-G,GTA 21×TA***
5905913-AAAA-A,AAAT 6037872-AAAA-A,AAAT ***
7094862-G-A 7226821-G-A ***
8801377-GGAAG-G,GGAA 8933336-GGAAG-G,GGAA ***
13452873-GCATTCCATTCCATTCCATTCCATTC-G,GCATTC 11297197-GCATTCCATTCCATTCCATTCCATTC-G,GCATTC 14×CATTC***
14512349-A-G 12400554-A-G ***
14656415-T-C 12544480-T-C ***
15077904-T-G 12965994-T-G ***
17030992-CAAAA-C,CAAA 14919112-CAAAA-C,CAAA 19×A***
17226760-A-G 15114880-A-G ***
17474945-CTTTTT-C,CTTT 15363065-CTTTTT-C,CTTT 15×T***
18872070-C-T 16760190-C-T ***
19492290-CAAAAAAAAAAAAAAAAAAAAAA-C,CAAA 17380410-CAAAAAAAAAAAAAAAAAAAAAA-C,CAAA 37×A***
22092643-TTATTTATT-T,TTA 19930757-TTATTTATT-T,TTA ***

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.