Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > DF21/S192 > S5488 > Z16294 > BY11121 > ZZ21 > BY3827

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
16552010-A-G 14440130-A-G Z36488 YY+
2910390-T-C 3042349-T-C Y60490 YY+
7104559-CTT-C 7236518-CTT-C +
7249193-G-A 7381152-G-A Y61767 YY+
7273336-G-A 7405295-G-A Y16717 YY+
8228780-A-G 8360739-A-G Y63332 YY+
8355090-A-G 8487049-A-G Y63568 YY+
8455908-C-A 8587867-C-A Y63795 YY+
8899254-A-G 9031213-A-G BY76767 Y+
13846046-G-C 11725340-G-C BY91292 +
14171160-C-A 12050454-C-A Y66087 YY+
14186062-C-T 12065356-C-T Y66122 YY+
14334549-G-T 12213844-G-T Y66502 YY+
14873649-A-G 12761719-A-G Y67370 YY+
15032958-C-CA 12921046-C-CA +
15499084-G-A 13387204-G-A Y68351 YY+
16808964-CTCTT-C 14697084-CTCTT-C +
16985717-C-T 14873837-C-T Y70855 YY+
17099213-A-G 14987333-A-G Y71062 YY+
17150618-G-T 15038738-G-T Y71145 YY+
17275825-AG-A 15163945-AG-A +
17319599-C-T 15207719-C-T Y71436 YY+
17742610-C-A 15630730-C-A Y72254 YY+
17971650-A-AAAC 15859770-A-AAAC 8×AAC+
18641934-C-T 16530054-C-T BY55091 YY+
19052669-T-A 16940789-T-A BY125839 YY+
19205452-A-T 17093572-A-T Y74874 YY+
19515915-G-A 17404035-G-A Y75504 YY+
19515985-G-T 17404105-G-T Y75505 YY+
21406581-G-A 19244695-G-A Y76426 YY+
21431128-C-T 19269242-C-T Y76456 YY+
22036772-T-G 19874886-T-G Y77643 YY+
22272260-A-T 20110374-A-T BY43730 DYZ19 +
22889695-C-T 20727809-C-T Y78836 YY+
23196928-TTTA-T 21035042-TTTA-T +
23311560-G-A 21149674-G-A Z40496 YY+
23617345-T-C 21455459-T-C Y80188 YY+
24430448-T-G 22284301-T-G BY149844 Y+
27842234-AGAAGGAAG-A 25696087-AGAAGGAAG-A P1_Y2 8×GAAG+
4700701-G-T 4832660-G-T BY58276 **
15171082-G-GT 13059168-G-GT **
22507554-G-C 20345668-G-C DYZ19 **
22507562-C-A 20345676-C-A BY225375 DYZ19 **
22507567-T-C 20345681-T-C DYZ19 **
13724861-C-G 11569185-C-G ***
13711423-A-AG 11555747-A-AG ***
13723808-G-A 11568132-G-A ***
13826803-C-A 11706097-C-A ***
13826815-G-A 11706109-G-A BY90743 ***
13704114-C-CAATGG 11548438-C-CAATGG ***
13724244-C-T 11568568-C-T ***
13726530-A-C 11570854-A-C ***
13726589-C-CAATGG 11570913-C-CAATGG ***
13827026-G-T 11706320-G-T ***
13724179-T-A 11568503-T-A ***
13724180-G-C 11568504-G-C ***
6113225-C-T 6245184-C-T FT388043 ***
13724243-C-G 11568567-C-G ***
58975097-A-G 56828950-A-G ***
13728014-T-A 11572338-T-A ***
13745129-C-T 11589453-C-T ***
13722940-ATGTC-A,ATGGC 11567264-ATGTC-A,ATGGC ***
22428559-A-T 20266673-A-T DYZ19 ***
6270137-A-G 6402096-A-G IR3_Dst ***
8901434-ATG-A 9033393-ATG-A ***
13481189-G-C 11325513-G-C ***
13715179-C-G,T 11559503-C-G,T ***
13722621-T-A 11566945-T-A ***
13728223-T-A 11572547-T-A ***
18273595-A-G 16161715-A-G P6_Prx ***
19587376-G-C 17475496-G-C P5_Prx ***
19788658-G-A 17676778-G-A P5_Prx ***
21043167-C-A 18881281-C-A PR3139 ***
22249724-T-G 20087838-T-G DYZ19 ***
22253465-G-T 20091579-G-T DYZ19 ***
22265582-T-A 20103696-T-A DYZ19 ***
22266910-C-T 20105024-C-T DYZ19 ***
22282575-A-C 20120689-A-C DYZ19 ***
22292835-G-A 20130949-G-A DYZ19 ***
22303360-T-G 20141474-T-G DYZ19 ***
22304242-T-C 20142356-T-C DYZ19 ***
22308119-A-G 20146233-A-G DYZ19 ***
22308151-A-C 20146265-A-C DYZ19 ***
22309896-C-T 20148010-C-T DYZ19 ***
22312404-C-T 20150518-C-T DYZ19 ***
22314106-T-C 20152220-T-C DYZ19 ***
22428562-T-A 20266676-T-A DYZ19 ***
22428568-A-G 20266682-A-G DYZ19 ***
22444231-C-A 20282345-C-A DYZ19 ***
22459710-G-A 20297824-G-A BY220367 DYZ19 ***
23177788-G-A 21015902-G-A ***
23728246-G-A 21566360-G-A ***
24196961-C-T 22050814-C-T P3_b1 ***
24273212-C-T 22127065-C-T P3_b1 ***
24287851-A-G 22141704-A-G P3_t1 ***
25101560-C-T 22955413-C-T g1 ***
25289440-A-C 23143293-A-C P2_r1 ***
26009495-G-A 23863348-G-A P1_Y1 ***
26175748-G-T 24029601-G-T P1_Y1 ***
28789034-G-C 26642887-G-C ***
28789039-G-GAGCA 26642892-G-GAGCA ***
28789042-G-GT 26642895-G-GT ***
28789043-A-T 26642896-A-T ***
28789049-G-A 26642902-G-A ***
28789059-G-A 26642912-G-A ***
28789072-A-G 26642925-A-G ***

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.