Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z198 > L165/S68 > BY129

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
678272
16921799-A-G 14809919-A-G FGC69610 YY+
9821017-TAAG-T 9983408-TAAG-T +
21282074-C-T 19120188-C-T FGC35600 YY+
22471593-C-T 20309707-C-T DYZ19 +
17847981-A-G 15736101-A-G FGC69611 YY+
17844885-T-A 15733005-T-A BY117755 YY+
17409342-G-A 15297462-G-A BY114540 YY+
23191210-T-A 21029324-T-A FGC69612 Y+
16775519-G-A 14663639-G-A FGC69609 YY+
23297178-C-A 21135292-C-A BY144410 YY+
15783921-CCTT-C 13672041-CCTT-C +
14368066-C-T 12247362-C-T FGC69606 YY+
23847934-GA-G 21686048-GA-G +
13845003-C-T 11724297-C-T +
23978536-T-A 21832389-T-A FGC69613 Y+
22238779-C-T 20076893-C-T DYZ19 +
10005115-C-A 10167506-C-A FGC69603 Y+
9515721-C-A 9678112-C-A BY80074 +
8263149-G-A 8395108-G-A FGC69601 YY+
2686365-C-T 2818324-C-T FGC69591 YY+
25102128-G-A 22955981-G-A FGC69614 g1 +
6735167-G-A 6867126-G-A Z30728 Y13113 YY+
7602361-G-T 7734320-G-T FGC69599 YY+
7825818-TG-T 7957777-TG-T +
9480657-C-T 9643048-C-T FGC69602 +
7941345-C-T 8073304-C-T FGC69600 YY+
8619434-C-G 8751393-C-G br1 YY+
8881641-C-A 9013600-C-A BY76599 Y+
9048756-A-G 9211147-A-G BY77680 Y+
14266547-T-C 12145841-T-C **
6827030-G-C 6958989-G-C **
22512692-A-C 20350806-A-C BY53423 DYZ19 **
25010018-G-A 22863871-G-A g1 ***
24813288-G-A 22667141-G-A P3_b2 ***
22503134-A-C 20341248-A-C DYZ19 ***
24279317-T-C 22133170-T-C P3_t1 ***
22428054-C-G 20266168-C-G DYZ19 ***
24133668-A-C 21987521-A-C P3_b1 ***
22310372-G-T 20148486-G-T DYZ19 ***
22278779-C-T 20116893-C-T DYZ19 ***
9993020-C-T 10155411-C-T ***
22241573-C-T 20079687-C-T DYZ19 ***
13853123-G-C 11732417-G-C FGC69605 ***
6283780-A-C 6415739-A-C IR3_Dst ***
8097691-T-TTG 8229650-T-TTG ***
9320478-A-C 9482869-A-C ***
9366489-G-C 9528880-G-C ***
9960287-T-C 10122678-T-C ***
13488718-G-GA 11333042-G-GA ***
16257973-G-T 14146093-G-T ***
22230823-C-T 20068937-C-T DYZ19 ***
13488713-GC-G 11333037-GC-G ***
18320073-G-T 16208193-G-T P6_Prx ***
19934188-C-T 17822308-C-T P5_Prx ***
19962616-T-C 17850736-T-C P5_Prx ***
20749152-C-T 18587266-C-T P4_Prx ***
22224541-T-A 20062655-T-A DYZ19 ***
26121044-G-A 23974897-G-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.

Haplotype Progression

The data below reveals the progression of changes in the haplotype. The bottom row is the haplotype for this man and above him are the inferred ancestral haplotypes for various upstream blocks. These inferred haplotypes are very much a work in progress, and any suggested modifications are appreciated. I think we can use our vast collection of haplotype data to refine these haplotypes. Mutations made from each upstream block are shown in sequence. The cell color is determined by the block in which the mutation took place.

DYS393
DYS390
DYS19
DYS391
DYS385
DYS426
DYS388
DYS439
DYS389i
DYS392
DYS389ii
DYS458
DYS459
DYS455
DYS454
DYS447
DYS437
DYS448
DYS449
DYS464
DYS460
Y-GATA-H4
YCAII
DYS456
DYS607
DYS576
DYS570
CDY
DYS442
DYS438
DYS531
DYS578
DYF395S1
DYS590
DYS537
DYS641
DYS472
DYF406S1
DYS511
DYS425
DYS413
DYS557
DYS594
DYS436
DYS490
DYS534
DYS450
DYS444
DYS481
DYS520
DYS446
DYS617
DYS568
DYS487
DYS572
DYS640
DYS492
DYS565
DYS710
DYS485
DYS632
DYS495
DYS540
DYS714
DYS716
DYS717
DYS505
DYS556
DYS549
DYS589
DYS522
DYS494
DYS533
DYS636
DYS575
DYS638
DYS462
DYS452
DYS445
Y-GATA-A10
DYS463
DYS441
Y-GGAAT-1B07
DYS525
DYS712
DYS593
DYS650
DYS532
DYS715
DYS504
DYS513
DYS561
DYS552
DYS726
DYS635
DYS587
DYS643
DYS497
DYS510
DYS434
DYS461
DYS435
P312/S1161324141111-14121212131329179-1011112515192915-15-17-17111119-231615181736-38121211915-1681010810101223-231610121215812222013121113111112123315916122626191211131210912121011113012132413101020151913241712152412231810141791211
Stephens1225141011-13121212131330189-1011112516203014-15-15-16111119-231715191736-38121211915-1681010810101223-231610121214812222013121113111112123615916122626191211131210912121011113012132413101022151813241612152412231810141791211

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: 6782721068500077810047869370
Used in age calculations1068500077810047869370
Counts of SNPs1617
Variant counts last updated 2018-05-28 20:28:58.



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