Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > ZZ45 > Z36/S206

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
166207
2846806-A-G 2978765-A-G BY56814 YY+
6698193-A-C 6830152-A-C BY53578 YY+
7361676-G-A 7493635-G-A BY64783 YY+
7543791-A-G 7675750-A-G BY65778 YY+
8532913-G-T 8664872-G-T BY73750 YY+
8576320-G-T 8708279-G-T BY74182 YY+
8668204-T-C 8800163-T-C BY75072 YY+
9376380-C-G 9538771-C-G BY78889 Y+
9378180-A-G 9540571-A-G Y+
13848531-T-A 11727825-T-A BY91342 +
14183819-C-T 12063113-C-T BY93609 YY+
15230312-G-A 13118398-G-A BY100328 Y+
15364356-C-T 13252476-C-T BY101145 YY+
15982727-G-A 13870847-G-A BY105303 YY+
16257455-G-A 14145575-G-A BY106441 YY+
17054934-T-A 14943054-T-A Z29053 YY+
17320953-A-C 15209073-A-C BY113782 YY+
17525873-T-C 15413993-T-C BY115447 YY+
17577371-A-G 15465491-A-G BY115861 YY+
17770004-G-C 15658124-G-C BY117301 YY+
18570747-G-T 16458867-G-T BY122275 YY+
18895821-GTGA-G 16783941-GTGA-G +
21050783-ATCTG-A 18888897-ATCTG-A +
21399274-A-G 19237388-A-G BY132613 YY+
21645180-C-G 19483294-C-G BY134423 YY+
21645876-G-T 19483990-G-T BY134427 YY+
21645877-G-T 19483991-G-T BY134428 YY+
21652705-T-C 19490819-T-C BY134484 YY+
21801235-T-C 19639349-T-C BY135535 YY+
22190394-T-C 20028508-T-C BY138348 YY+
22271349-T-C 20109463-T-C BY215176 DYZ19 +
22272853-T-A 20110967-T-A BY215474 DYZ19 +
22293749-G-C 20131863-G-C BY216409 DYZ19 +
22460854-C-A 20298968-C-A BY220627 DYZ19 +
22552998-G-C 20391112-G-C BY138922 YY+
23160087-T-C 20998201-T-C BY143497 Y+
23345372-G-T 21183486-G-T BY144719 YY+
23466552-T-C 21304666-T-C BY145479 YY+
23851212-G-A 21689326-G-A BY148366 Y+
25088402-A-T 22942255-A-T g1 +
28760658-G-A 26614511-G-A BY151049 Y+
2869110-G-T 3001069-G-T YY*
5458820-C-G 5590779-C-G BY58708 **
10008101-G-A 10170492-G-A BY82806 **
22507682-T-A 20345796-T-A BY225386 DYZ19 **
28779468-C-G 26633321-C-G BY151169 **
7460924-G-C 7592883-G-C IR1_L ***
13458085-C-G 11302409-C-G BY85509 ***
10016582-C-T 10178973-C-T BY82940 ***
19815798-C-CA 17703918-C-CA P5_Prx ***
19877769-G-A 17765889-G-A P5_Prx ***
20644416-A-G 18482530-A-G P4_Prx ***
22230649-C-A 20068763-C-A DYZ19 ***
22231734-G-C 20069848-G-C DYZ19 ***
22253823-C-G 20091937-C-G DYZ19 ***
22261967-T-G 20100081-T-G DYZ19 ***
22261969-C-T 20100083-C-T DYZ19 ***
22265327-G-C 20103441-G-C DYZ19 ***
22276806-G-A 20114920-G-A DYZ19 ***
22286625-A-T 20124739-A-T DYZ19 ***
22289852-G-T 20127966-G-T DYZ19 ***
22290977-T-C 20129091-T-C DYZ19 ***
22326109-T-C 20164223-T-C DYZ19 ***
22328691-T-A 20166805-T-A DYZ19 ***
22357825-T-C 20195939-T-C DYZ19 ***
22359680-G-T 20197794-G-T DYZ19 ***
22429575-T-C 20267689-T-C DYZ19 ***
22453604-C-A 20291718-C-A DYZ19 ***
24122658-C-A 21976511-C-A P3_b1 ***
24343143-T-C 22196996-T-C P3_t1 ***
24989798-A-G 22843651-A-G g1 ***
25049985-T-C 22903838-T-C g1 ***
25310594-C-G 23164447-C-G P2_r1 ***
25731946-C-A 23585799-C-A P1_b3 ***
26047275-T-C 23901128-T-C P1_Y1 ***
26225716-G-T 24079569-G-T P1_Y1 ***
26273911-C-A 24127764-C-A P1_Y1 ***

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.