Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > DF49/S474 > Z2980 > Z2976 > DF23 > Z2961 > FGC6540 > FGC6562 > ZP92

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 STRFTDNA
338578
15055407-TC-T 12943499-TC-T +
22969732-G-A 20807846-G-A FGC40112 YY+
23303613-G-A 21141727-G-A FGC40113 YY+
23375612-A-G 21213726-A-G FGC40114 YY+
22263380-A-G 20101494-A-G FGC40111 DYZ19 +
21757422-A-AT 19595536-A-AT +
21431241-G-T 19269355-G-T FGC40110 YY+
19087609-C-A 16975729-C-A Y20778 FGC40109 YY+
18944940-G-C 16833060-G-C FGC40108 YY+
17413055-A-T 15301175-A-T FGC40106 YY+
17383062-C-A 15271182-C-A FGC40105 YY+
17143376-G-A 15031496-G-A FGC40104 YY+
16902300-G-A 14790420-G-A FGC40103 YY+
16477782-C-T 14365902-C-T FGC40102 YY+
16287994-A-G 14176114-A-G FGC40101 YY+
14126574-G-A 12005868-G-A FGC40100 YY+
8691510-A-G 8823469-A-G FGC40098 YY+
9996595-TA-T 10158986-TA-T +
8144636-G-C 8276595-G-C FGC40097 YY+
7811508-A-G 7943467-A-G DC96Z1370 YY+
7046411-G-A 7178370-G-A FGC40096 YY+
8546324-A-AC 8678283-A-AC +
18115059-GTCTA-G 16003179-GTCTA-G 7×TCTA+
2662409-C-G 2794368-C-G FGC40095 YY+
28780919-C-T 26634772-C-T FGC40115 **
24550179-G-A 22404032-G-A P3_t2 **
13456500-T-G 11300824-T-G FGC40099 **
24328532-C-T 22182385-C-T P3_t1 ***
24807653-T-G 22661506-T-G BY24929 P3_b2 ***
28811371-T-A 26665224-T-A ***
26483914-C-T 24337767-C-T P1_Y1 ***
24807657-C-G 22661510-C-G BY24930 P3_b2 ***
25204336-C-T 23058189-C-T g1 ***
26015293-A-T 23869146-A-T P1_Y1 ***
25349183-T-C 23203036-T-C P2_r1 ***
25342557-G-A 23196410-G-A P2_r1 ***
25250612-G-T 23104465-G-T P2_r1 21×GT***
25239856-G-A 23093709-G-A P2_r1 ***
23152127-T-G 20990241-T-G ***
24807641-A-G 22661494-A-G BY2292 P3_b2 ***
22441303-C-A 20279417-C-A DYZ19 ***
6228390-G-A 6360349-G-A IR3_Dst ***
22359735-T-A 20197849-T-A DYZ19 ***
13458012-A-G 11302336-A-G ***
22508779-G-C 20346893-G-C DYZ19 ***
25192574-G-T 23046427-G-T g1 ***
20728992-G-T 18567106-G-T BY1684 P4_Prx ***
13722417-T-A 11566741-T-A ***
24807644-C-T 22661497-C-T BY24928 P3_b2 ***
6334934-C-G 6466893-C-G IR3_Dst ***
22438576-G-A 20276690-G-A DYZ19 ***
13730992-C-G 11575316-C-G ***
19853025-A-G 17741145-A-G P5_Prx ***
22285880-G-A 20123994-G-A DYZ19 ***
22218332-C-A 20056446-C-A DYZ19 ***
22220404-C-T 20058518-C-T DYZ19 ***
22224648-C-G 20062762-C-G DYZ19 ***
22315517-C-G 20153631-C-G DYZ19 ***
20786441-C-T 18624555-C-T P4_Prx ***

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.

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