Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > ZZ10 > Z253 > BY4086 > A1001

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
257069
21189162-A-G 19027276-A-G A1030 YY+
17748823-G-A 15636943-G-A A1026 YY+
15590931-A-AT 13479051-A-AT 10×T+
16840179-A-G 14728299-A-G A1024 YY+
16990810-T-C 14878930-T-C A1025 YY+
26722335-A-G 24576188-A-G P1_g2 +
24436066-A-G 22289919-A-G Y+
24365563-A-G 22219416-A-G +
23207649-G-A 21045763-G-A Y+
17939925-C-T 15828045-C-T A1027 YY+
15343113-A-T 13231232-A-T A1022 YY+
18234021-G-A 16122141-G-A A1028 Y+
23126877-G-A 20964991-G-A YY+
19256428-T-C 17144548-T-C A1029 YY+
22475007-G-T 20313121-G-T DYZ19 +
22447814-T-C 20285928-T-C DYZ19 +
22293943-A-C 20132057-A-C A1033 DYZ19 +
22159826-G-A 19997940-G-A A1032 YY+
15495498-T-C 13383618-T-C A1023 YY+
14461699-G-A 12340972-G-A A1021 YY+
22147095-C-G 19985209-C-G A1031 YY+
8623329-C-T 8755288-C-T A1011 YY+
7340780-C-T 7472739-C-T A1004 YY+
7445411-A-G 7577370-A-G A1005 Y+
7543449-G-A 7675408-G-A A1006 YY+
7671330-A-G 7803289-A-G A1007 YY+
7921609-T-A 8053568-T-A A1008 YY+
7922218-T-G 8054177-T-G A1009 YY+
8578141-T-A 8710100-T-A A1010 YY+
8633221-C-T 8765180-C-T A1012 YY+
14277455-T-C 12156749-T-C A1020 YY+
8821828-C-A 8953787-C-A A1013 YY+
8841117-G-T 8973076-G-T A1014 YY+
9007226-A-T 9169617-A-T A1015 Y+
9111931-T-A 9274322-T-A A1016 Y+
9398551-T-C 9560942-T-C A1017 YY+
9855608-T-C 10017999-T-C A1018 YY+
16051415-C-CA 13939535-C-CA 8×A+
14209428-G-A 12088722-G-A A1019 YY+
23048048-CA-C 20886162-CA-C **
3990781-C-T 4122740-C-T **
17358832-G-GT 15246952-G-GT 9×T**
18541298-A-C 16429418-A-C CTS8908 **
16029356-A-C 13917476-A-C PF7521 S4567 Z2908 AM01872 **
5358726-T-C 5490685-T-C **
21761907-A-G 19600021-A-G ***
22512023-C-T 20350137-C-T DYZ19 ***
13453771-TC-T 11298095-TC-T ***
17196744-A-G 15084864-A-G M4595 ***
26154488-G-A 24008341-G-A P1_Y1 ***
26071791-C-A 23925644-C-A P1_Y1 ***
25417612-T-G 23271465-T-G P2_r2 ***
25064160-A-G 22918013-A-G g1 ***
17196745-A-T 15084865-A-T ***
17196752-A-G 15084872-A-G ***
24213400-C-T 22067253-C-T P3_b1 ***
17196753-A-T 15084873-A-T ***
18287169-G-A 16175289-G-A P6_Prx ***
22466905-G-A 20305019-G-A DYZ19 ***
19683350-G-A 17571470-G-A P5_Prx ***
21761903-T-TG 19600017-T-TG ***
22435570-T-C 20273684-T-C DYZ19 ***
22421261-C-T 20259375-C-T DYZ19 ***
22335077-A-G 20173191-A-G DYZ19 ***
22315061-T-A 20153175-T-A DYZ19 ***
22310374-A-C 20148488-A-C DYZ19 ***
20674434-G-A 18512548-G-A P4_Prx ***
22290707-G-T 20128821-G-T DYZ19 ***
22285326-A-C 20123440-A-C DYZ19 ***
22249316-G-T 20087430-G-T DYZ19 ***
22245229-T-A 20083343-T-A DYZ19 ***
22232136-G-A 20070250-G-A DYZ19 ***
22224974-A-T 20063088-A-T DYZ19 ***
20791038-G-A 18629152-G-A P4_Prx ***
19783105-C-T 17671225-C-T 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. 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
L21/S1451324141111-14121212131329179-1011112515192915-15-17-17111119-231615181736-38121211915-1681010810101223-231610121215812222013121113111112123515916122526191211131211912121011113012132413101020151913241712152412231810141791211
Robertson1324141011-11121212131329179-1011112515192915-15-17-18121219-231516181835-38121211915-1681012810101223-231610121216812232014121113111112123615916122526191211131211913121011113012132413101021151814241712152412232010141791211

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: 2570691068987577338727814843
Used in age calculations1068987577338727814843
Counts of SNPs2830
Variant counts last updated 2017-11-13 20:44:27.



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