Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > Z39589 > Y14240 > FGC35999

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
2708979-A-G 2840938-A-G FGC35997 YY+
2841556-T-C 2973515-T-C FGC35998 YY+
7050919-G-A 7182878-G-A FGC36001 YY+
7067395-A-C 7199354-A-C FGC36002 YY+
7069457-C-T 7201416-C-T Z30246 FGC36003 YY+
7172924-A-G 7304883-A-G FGC36004 YY+
7657271-C-A 7789230-C-A FGC36006 YY+
8466284-C-T 8598243-C-T FGC36007 FGC72700 YY+
9153330-C-T 9315721-C-T FGC36008 Y+
14577328-G-A 12465528-G-A PR1498 FT74190 YY+
15089634-A-G 12977723-A-G FGC36011 YY+
15096349-T-C 12984437-T-C FGC36012 YY+
15471784-C-T 13359904-C-T FGC36013 YY+
15538979-T-G 13427099-T-G FGC36014 YY+
15615594-A-T 13503714-A-T FGC36015 YY+
15653673-C-T 13541793-C-T FGC36016 YY+
15792326-A-T 13680446-A-T FGC36017 YY+
16361621-G-T 14249741-G-T FGC36018 YY+
16481351-C-T 14369471-C-T FGC36019 YY+
16656110-G-A 14544230-G-A FGC36020 YY+
16987877-C-T 14875997-C-T FGC36021 YY+
17128834-G-A 15016954-G-A FGC36022 YY+
18175237-AG-A 16063357-AG-A +
18680602-G-A 16568722-G-A FGC36023 YY+
19154847-G-A 17042967-G-A FGC36024 YY+
19364732-G-T 17252852-G-T FGC36025 YY+
21045510-T-C 18883624-T-C FGC36026 Y+
21319738-G-A 19157852-G-A FGC36027 YY+
21478902-C-CA 19317016-C-CA +
21548328-G-A 19386442-G-A Y56872 YY+
21548329-A-T 19386443-A-T Y56873 YY+
22466888-T-C 20305002-T-C FGC36028 DYZ19 +
22478848-G-C 20316962-G-C FGC36029 DYZ19 +
22553420-T-G 20391534-T-G FGC36030 YY+
23332074-T-G 21170188-T-G FGC36032 YY+
23392163-C-A 21230277-C-A FGC36033 YY+
23733394-C-A 21571508-C-A FGC36034 +
24361875-C-G 22215728-C-G FGC36035 +
24497036-T-G 22350889-T-G FGC36036 +
2751958-T-TA 2883917-T-TA 8×A+
7225815-TACAC-T 7357774-TACAC-T BY18067 10×AC+
16234721-TA-T 14122841-TA-T +
19178527-G-A 17066647-G-A CTS9965 **
18925318-G-T 16813438-G-T FGC18451BY40511 **
27920437-C-T 25774290-C-T FGC80702 P1_Y2 **
28501073-T-C 26354926-T-C **
22310068-G-A 20148182-G-A DYZ19 ***
9131437-T-G 9293828-T-G Z8908Z8908 Z4436 ***
13452081-T-A 11296405-T-A ***
22431175-G-A 20269289-G-A DYZ19 ***
9372305-A-T 9534696-A-T ***
15927255-C-T 13815375-C-T ***
19719978-C-T 17608098-C-T P5_Prx ***
19775851-G-A 17663971-G-A P5_Prx ***
19976367-A-G 17864487-A-G P5_Prx ***
22220493-T-C 20058607-T-C BY52081 DYZ19 ***
22246871-T-C 20084985-T-C FGC80700 DYZ19 ***
22261852-G-T 20099966-G-T DYZ19 ***
22288814-C-T 20126928-C-T FT272340 DYZ19 ***
22292904-A-G 20131018-A-G DYZ19 ***
22364539-T-A 20202653-T-A DYZ19 ***
22423255-C-G 20261369-C-G DYZ19 ***
22424176-C-T 20262290-C-T DYZ19 ***
22437588-A-C 20275702-A-C BY218395 DYZ19 ***
22443769-G-A 20281883-G-A FT456714 DYZ19 ***
24107679-A-G 21961532-A-G P3_b1 ***
24120934-TTGAATATTAAG-T 21974787-TTGAATATTAAG-T P3_b1 ***
24298801-C-A 22152654-C-A P3_t1 ***
24893572-G-T 22747425-G-T g1 ***
25195491-C-T 23049344-C-T g1 ***
25278076-A-G 23131929-A-G P2_r1 ***
25284748-C-CAG 23138601-C-CAG P2_r1 ***
25955184-G-C 23809037-G-C P1_Y1 ***
26011763-C-G 23865616-C-G P1_Y1 ***
26121895-A-G 23975748-A-G P1_Y1 ***
26167301-A-G 24021154-A-G BY23061 P1_Y1 ***
26576851-G-T 24430704-G-T P1_g2 ***
26728915-T-C 24582768-T-C P1_g2 ***
19576574-GA-G 17464694-GA-G P5_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.