Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > DF21/S192 > S5488

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
9850346-A-G 10012737-A-G L1444 BY16472Z17640 Y9130 YY+
6670374-T-G 6802333-T-G Y60787 YY+
6872068-G-A 7004027-G-A BY53590 YY+
7634974-G-A 7766933-G-A Y62277 YY+
8433859-T-C 8565818-T-C Y63744 YY+
13220886-CA-C 11065210-CA-C +
13845005-G-A 11724299-G-A Y65638 +
13895618-G-T 11774912-G-T BY91872 YY+
14661682-A-G 12549747-A-G Y67060 YY+
14746239-C-T 12634308-C-T Y67160 YY+
15754890-C-T 13643010-C-T Y68830 YY+
16450664-A-G 14338784-A-G BY107893 YY+
16463897-G-A 14352017-G-A YY+
16805320-T-C 14693440-T-C Y70524 YY+
16864101-G-T 14752221-G-T Y70633 YY+
17091936-C-A 14980056-C-A Y71054 YY+
17985394-C-A 15873514-C-A Y72802 Y+
18416967-G-A 16305087-G-A Y73528 P6_Gap +
18778518-G-T 16666638-G-T Y74026 YY+
18893667-T-C 16781787-T-C Y74224 YY+
19242815-C-G 17130935-C-G Y74952 YY+
19390714-A-G 17278834-A-G Y75237 Y+
21182114-G-A 19020228-G-A Y75937 YY+
21255592-G-T 19093706-G-T Y76074 YY+
21512754-G-A 19350868-G-A Y76650 YY+
21647967-T-C 19486081-T-C Y76899 YY+
22263329-A-T 20101443-A-T BY214718 DYZ19 +
22442371-G-C 20280485-G-C BY219107 DYZ19 +
22459313-G-C 20297427-G-C FT457492 DYZ19 +
22460006-T-G 20298120-T-G BY52792 DYZ19 +
22460014-T-A 20298128-T-A DYZ19 +
22460015-T-G 20298129-T-G DYZ19 +
22460018-T-G 20298132-T-G DYZ19 +
22460027-C-G 20298141-C-G ZS2743 DYZ19 +
22579741-A-G 20417855-A-G Y78271 YY+
23056885-A-T 20894999-A-T Y79143 YY+
24332466-G-T 22186319-G-T P3_t1 +
16985031-CT-C 14873151-CT-C +
13720447-C-A 11564771-C-A **
13720448-A-G 11564772-A-G F11033 BY12857 **
28597407-C-A 26451260-C-A **
13880605-C-T 11759899-C-T FGC32392 Y12295 **
16186441-G-A 14074561-G-A Y69411 **
3279698-A-AAAAT 3411657-A-AAAAT 9×AAAT***
21052567-T-TG 18890681-T-TG 8×G***
22469327-C-CAT 20307441-C-CAT DYZ19 ***
6283163-A-C 6415122-A-C IR3_Dst ***
13466607-T-G 11310931-T-G BY85739 ***
18379971-T-C 16268091-T-C P6_Prx ***
22240422-T-A 20078536-T-A DYZ19 ***
22257527-A-G 20095641-A-G DYZ19 ***
22258572-G-C 20096686-G-C DYZ19 ***
22259221-G-A 20097335-G-A DYZ19 ***
22276322-GT-G 20114436-GT-G DYZ19 ***
22284872-G-C 20122986-G-C DYZ19 ***
22296527-G-C 20134641-G-C DYZ19 ***
22299552-C-T 20137666-C-T DYZ19 ***
22313367-G-A 20151481-G-A DYZ19 ***
22316630-T-C 20154744-T-C DYZ19 ***
22451582-C-A 20289696-C-A DYZ19 ***
22453746-A-T 20291860-A-T DYZ19 ***
22473992-C-T 20312106-C-T BY53080 DYZ19 ***
22510791-A-C 20348905-A-C BY225688 DYZ19 ***
24161905-C-G 22015758-C-G P3_b1 ***
24973662-G-T 22827515-G-T g1 ***
25031584-G-A 22885437-G-A g1 ***
25034191-C-G 22888044-C-G g1 ***
25933176-C-T 23787029-C-T P1_Y1 ***
26142883-T-A 23996736-T-A P1_Y1 ***
26268514-G-T 24122367-G-T P1_Y1 ***
14990011-T-TCCCTCC 12878096-T-TCCCTCC ***
17819937-A-ATG 15708057-A-ATG 9×TG***
20698614-C-CAT 18536728-C-CAT 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.