Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z272 > S450 > Z295/S1217 > S25783 > CTS4065 > 15548847GACAC-G > FGC15710 > CTS10029 > FGC29721 > FGC29724

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
271076
FGC
RMFBM
2824644-G-A 2956603-G-A FGC34771 YY++
19300826-T-C 17188946-T-C FGC34777 Y+
9016286-A-G 9178677-A-G FGC34773 Y++
15636163-A-G 13524283-A-G FGC34775 Y+
14097684-C-T 11976978-C-T FGC34774 YY++
16060129-G-A 13948249-G-A FGC34776 Y+
17634317-T-C 15522437-T-C YY+**
5107850-G-A 5239809-G-A FGC34772 +
5594809-A-AT 5726768-A-AT *
13529749-T-G 11374073-T-G FGC24549 *
19501553-A-T 17389673-A-T FGC34778 YY*
4953820-T-TTG 5085779-T-TTG 16×TG**
22467199-C-A 20305313-C-A DYZ19 *****
5462508-CCA-C 5594467-CCA-C **
5786608-C-CAAAAAAAAAAAAA 5918567-C-CAAAAAAAAAAAAA 20×A**
24193896-C-T 22047749-C-T P3_b1 ***
26444447-C-T 24298300-C-T P1_Y1 ***
27462520-A-C 25316373-A-C P1_Y2 ***
27462497-A-C 25316350-A-C P1_Y2 ***
27371247-G-A 25225100-G-A P1_g3 ***
22337546-C-T 20175660-C-T DYZ19 ***
22337698-T-A 20175812-T-A DYZ19 ***
27145622-A-T 24999475-A-T P1_g3 ***
26533692-C-A 24387545-C-A P1_g2 ***
22342907-G-C 20181021-G-C DYZ19 ***
22344224-T-A 20182338-T-A DYZ19 ***
22852291-G-A 20690405-G-A ***
22344781-A-T 20182895-A-T DYZ19 ***
25305561-C-T 23159414-C-T P2_r1 ***
22354994-T-A 20193108-T-A DYZ19 ***
22358362-A-T 20196476-A-T DYZ19 ***
22365469-G-C 20203583-G-C DYZ19 ***
22456595-T-A 20294709-T-A DYZ19 ***
22337015-G-T 20175129-G-T DYZ19 ***
24905084-G-T 22758937-G-T g1 ***
24513426-G-A 22367279-G-A ***
22499144-C-G 20337258-C-G DYZ19 ***
22499105-T-C 20337219-T-C DYZ19 ***
22268353-T-C 20106467-T-C DYZ19 ***
22332985-G-A 20171099-G-A DYZ19 ***
19977331-C-T 17865451-C-T P5_Prx ***
14565670-G-A 12453870-G-A ***
15248010-C-A 13136096-C-A ***
17090839-A-T 14978959-A-T 29×T***
18434419-T-A 16322539-T-A P6_Dst ***
18437825-G-A 16325945-G-A P6_Dst ***
18437831-C-T 16325951-C-T P6_Dst ***
18437860-G-A 16325980-G-A P6_Dst ***
18618993-T-G 16507113-T-G ***
18906391-G-A 16794511-G-A 6×TAA***
18906392-T-A 16794512-T-A ***
18906393-A-T 16794513-A-T ***
19029057-A-C 16917177-A-C ***
19646039-G-A 17534159-G-A P5_Prx ***
20243909-C-T 18082023-C-T P5_Dst ***
22316282-T-A 20154396-T-A DYZ19 ***
20376048-T-C 18214162-T-C P5_Dst ***
20411626-C-T 18249740-C-T P5_Dst ***
20736301-C-A 18574415-C-A P4_Prx ***
20948660-A-T 18786774-A-T P4_Dst ***
22227923-C-A 20066037-C-A DYZ19 ***
22232098-T-C 20070212-T-C DYZ19 ***
22234968-G-T 20073082-G-T DYZ19 ***
22234981-T-C 20073095-T-C DYZ19 ***
22234982-T-G 20073096-T-G DYZ19 ***
22241315-T-C 20079429-T-C DYZ19 ***
22265766-C-A 20103880-C-A DYZ19 ***
22273663-A-G 20111777-A-G DYZ19 ***
22276055-T-A 20114169-T-A DYZ19 ***
22268282-C-A 20106396-C-A DYZ19 ***
28819338-T-A 26673191-T-A ***
27482660-A-G 25336513-A-G P1_Y2 ***
13468738-AACTAA-GGCAAT 11313062-AACTAA-GGCAAT ***
4697475-T-TA 4829434-T-TA 14×A***
6434921-T-TAAAAA 6566880-T-TAAAAA 20×A***
9147317-C-CCACACA 9309708-C-CCACACA ***
9301404-G-GAT 9463795-G-GAT ***
9398653-G-GA 9561044-G-GA ***
9951785-AG-TC 10114176-AG-TC ***
9954526-TTTA-GTTAC 10116917-TTTA-GTTAC ***
10034819-TGGACTCCT-GGGATGCCG 10197210-TGGACTCCT-GGGATGCCG ***
13110943-TTTTT-GTTTC 10600429-TTTTT-GTTTC ***
13140089-CATTAAATCAGAATTCCTTTCCAATCCATTAA-C 10629575-CATTAAATCAGAATTCCTTTCCAATCCATTAA-C ***
13464459-GCACT-ACACC 11308783-GCACT-ACACC ***
13466743-CCG-ACT 11311067-CCG-ACT ***
13482882-CT-AA 11327206-CT-AA ***
3838601-CT-C 3970560-CT-C 31×T***
13611827-AACCTTTTTTTTT-A 11456151-AACCTTTTTTTTT-A ***
17046715-GTTTTTTTTTTTTT-G 14934835-GTTTTTTTTTTTTT-G 25×T***
21062762-ATGTGTGTGTGTG-A 18900876-ATGTGTGTGTGTG-A 17×TG***
22251446-GTGGA-CAGGT 20089560-GTGGA-CAGGT DYZ19 ***
22251516-TCAATCTGG-ACCTTCTCT 20089630-TCAATCTGG-ACCTTCTCT DYZ19 ***
22252645-TCTTCCTTTTGGC-CTTTAATTCTGGG 20090759-TCTTCCTTTTGGC-CTTTAATTCTGGG DYZ19 ***
22273573-G-GT 20111687-G-GT DYZ19 ***
22344755-CC-AT 20182869-CC-AT DYZ19 ***
22421838-GGTT-ATTG 20259952-GGTT-ATTG DYZ19 ***
24836739-GGAAG-AGAAA 22690592-GGAAG-AGAAA P3_b2 ***
25288465-TCAAAAA-T 23142318-TCAAAAA-T P2_r1 ***
25651212-GTTA-ATT 23505065-GTTA-ATT P1_b3 ***
28802794-GACATGAA-AACTGGAG 26656647-GACATGAA-AACTGGAG ***
4275437-CAA-C 4407396-CAA-C 19×A***
9424598-GAA-G 9586989-GAA-G 16×A***
27743630-C-T 25597483-C-T P1_Y2 ***
58913310-C-T 56677561-G-A ***
28802821-T-C 26656674-T-C ***
13923535-A-T 11802829-A-T ***
58832655-T-A 56758216-A-T ***
58833038-G-A 56757833-C-T ***
58838205-C-T 56752666-G-A ***
58839309-A-G 56751562-T-C ***
58865729-C-A 56725142-G-T ***
58867665-T-C 56723206-A-G ***
58880098-C-T 56710773-G-A ***
58903521-C-G 56687350-G-C ***
58908634-C-T 56682237-G-A ***
58913043-G-C 56677828-C-G ***
58913307-T-C 56677564-A-G ***
58913333-A-G 56677538-T-C ***
4654832-CA-C 4786791-CA-C 15×A***
59013631-T-A 56867484-T-A ***
13199183-C-AAA 11043507-C-AAA ***
10015084-TGGT-CGGG 10177475-TGGT-CGGG ***
7013599-A-AT 7145558-A-AT 13×T***
21490373-AT-A 19328487-AT-A 15×T***
22178488-C-CT 20016602-C-CT 15×T***
17828086-G-GT 15716206-G-GT 12×T***
2992436-A-AT 3124395-A-AT 15×T***
19121920-C-CT 17010040-C-CT 17×T***
28545694-T-TAAA 26399547-T-TAAA ***
3128625-CA-C 3260584-CA-C 20×A***
17564912-GAA-G 15453032-GAA-G 16×A***
15865572-C-TT 13753692-C-TT ***
14341494-G-T 12220789-G-T ***
13606877-C-A 11451201-C-A 25×A***
13730247-A-G 11574571-A-G ***
24899930-C-A 22753783-C-A g1 ***
10015025-A-G 10177416-A-G ***
22617232-G-GT 20455346-G-GT 15×T***
13110038-C-A 10599524-C-A ***
22456650-T-A 20294764-T-A DYZ19 ***
58821155-C-T 56769716-G-A ***
22481757-G-T 20319871-G-T DYZ19 ***
58831492-C-A 56759379-G-T ***
20769005-G-A 18607119-G-A P4_Prx ***
22313156-C-G 20151270-C-G DYZ19 ***
22455439-G-C 20293553-G-C DYZ19 ***
22475471-C-T 20313585-C-T DYZ19 ***
24273231-A-C 22127084-A-C P3_b1 ***
17312504-GA-G 15200624-GA-G 10×A***
4998922-C-CA 5130881-C-CA 12×A***
22332659-A-G 20170773-A-G DYZ19 ***
22234984-T-A 20073098-T-A DYZ19 ***
58875224-C-A 56715647-G-T ***
16057666-CT-C 13945786-CT-C 15×T***
58914500-C-T 56676371-G-A ***
21148589-C-CAAAAA 18986703-C-CAAAAA 30×A***
22319286-T-TGA 20157400-T-TGA DYZ19 ***
58828784-C-A 56762087-G-T ***
24636349-C-CT 22490202-C-CT P3_t2 17×T***
13444976-GACTAC-AAATAT 11289300-GACTAC-AAATAT ***
16818883-G-GTA 14707003-G-GTA ***
22495764-CTTGC-GTTG 20333878-CTTGC-GTTG DYZ19 ***
22481210-G-C 20319324-G-C DYZ19 ***
10019063-GGGTA-TGGTG 10181454-GGGTA-TGGTG ***
5535149-CTA-C 5667108-CTA-C 10×TA***
13472071-A-C 11316395-A-C ***
25963857-C-A 23817710-C-A P1_Y1 ***
22365691-C-A 20203805-C-A DYZ19 ***
22499499-C-T 20337613-C-T DYZ19 ***
58875220-T-G 56715651-A-C ***
26228689-C-CTTTT 24082542-C-CTTTT P1_Y1 27×T***
17242978-TAC-T 15131098-TAC-T 18×AC***
58843750-A-T 56747121-T-A ***
22287028-C-T 20125142-C-T DYZ19 ***
22502032-T-C 20340146-T-C DYZ19 ***
58870396-A-T 56720475-T-A ***
22241322-G-A 20079436-G-A DYZ19 ***
19656650-C-T 17544770-C-T P5_Prx ***
22360249-G-A 20198363-G-A DYZ19 ***
27462490-C-A 25316343-C-A P1_Y2 ***
58909239-T-C 56681632-A-G ***
58845143-TTCCATTGATTTGAC-T 56745707-GAATGGAGTCAAATC-G ***
58869729-C-T 56721142-G-A ***
13110931-C-T 10600417-C-T ***
22251462-C-A 20089576-C-A DYZ19 ***
22456727-C-T 20294841-C-T DYZ19 ***
9932701-GT-AC 10095092-GT-AC ***
22273911-TTCT-CTCA 20112025-TTCT-CTCA DYZ19 ***
9954500-G-C 10116891-G-C ***
6765638-C-T 6897597-C-T ***
13641031-C-G 11485355-C-G ***
58868288-A-C 56722583-T-G ***
22367457-T-C 20205571-T-C FGC35522 DYZ19 ***
58820472-C-T 56770399-G-A ***
58879555-A-G 56711316-T-C ***
22241295-C-A 20079409-C-A DYZ19 ***
13700711-A-T 11545035-A-T ***
13206784-C-A 11051108-C-A 14×A***
3548689-A-G 3680648-A-G ***
6127385-T-A 6259344-T-A ***
9779792-C-A 9942183-C-A ***
9930713-C-G 10093104-C-G ***
10034792-T-C 10197183-T-C ***
10040023-A-G 10202414-A-G ***
13109769-G-A 10599255-G-A ***
13109791-C-A 10599277-C-A ***
13109805-C-T 10599291-C-T ***
13109814-G-A 10599300-G-A ***
13110149-C-A 10599635-C-A ***
13112778-A-G 10602264-A-G ***
13263785-A-G 11108109-A-G ***
3459459-G-A 3591418-G-A ***
13288088-G-A 11132412-G-A ***
13353190-C-T 11197514-C-T ***
13372033-C-T 11216357-C-T ***
13411304-G-C 11255628-G-C ***
13464450-G-A 11308774-G-A ***
13475919-A-C 11320243-A-C ***
13484397-T-G 11328721-T-G ***
13485201-A-G 11329525-A-G ***
13497540-A-C 11341864-A-C ***
22252638-C-T 20090752-C-T DYZ19 ***
13700699-G-A 11545023-G-A ***
13700704-G-A 11545028-G-A ***
13700707-A-T 11545031-A-T ***
3548688-G-T 3680647-G-T ***
3394337-C-T 3526296-C-T 21×T***
9952729-ATAGCCAGTT-TTTGTCAGGC 10115120-ATAGCCAGTT-TTTGTCAGGC ***
22252612-TCC-CAA 20090726-TCC-CAA DYZ19 ***
13465562-A-T 11309886-A-T ***
13529004-T-G 11373328-T-G ***
13537569-A-T 11381893-A-T ***
13537581-C-T 11381905-C-T ***
23059593-A-AT 20897707-A-AT 12×T***
24836734-G-A 22690587-G-A P3_b2 15×GGAA***
58867683-T-A 56723188-A-T ***
22252626-A-T 20090740-A-T DYZ19 ***
22251476-A-G 20089590-A-G DYZ19 ***
14491320-GT-CA ***
22252577-GGTC-AGTG 20090691-GGTC-AGTG DYZ19 ***
22252598-TAC-AAA 20090712-TAC-AAA DYZ19 ***
22236527-AT-A 20074641-AT-A DYZ19 ***
3315341-G-A 3447300-G-A ***
58831537-CTTTCC-GATTCA 56759329-GGAAAG-TGAATC ***
10039508-A-T 10201899-A-T ***
13472064-T-C 11316388-T-C ***
13603629-A-T 11447953-A-T 15×T***
13603644-T-G 11447968-T-G ***
24836743-G-A 22690596-G-A P3_b2 ***
24836750-A-G 22690603-A-G P3_b2 ***
14471469-CTTT-C 12350738-CTTT-C 19×T***
18926872-CAA-C 16814992-CAA-C 17×A***
13110090-C-T 10599576-C-T ***
22344706-A-T 20182820-A-T DYZ19 ***
22274113-A-C 20112227-A-C DYZ19 ***
13470393-G-A 11314717-G-A ***
13453738-TATGAA-T,TATTTC 11298062-TATGAA-T,TATTTC ***

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.

Uncertain Mutations

NGS tests don't always cover all of the Y chromosome and, even when they do, the results can be inconclusive. The following mutations don't have clear results and have been assumed to be positive or negative. For those mutations that are assumed to be positive, the assumed SNP/INDEL will likely be found on the tree in some upstream block. It is unclear if it should be placed upstream of your results or parallel to them. The situation is reversed for mutations assumed negative. Those SNPs/INDELs will likely be found on a parallel branch on the tree, and it is unclear if they should be positioned upstream. As more results come in, the ambiguity may resolve itself, or it may be necessary to consult the BAM file for your test (available from FamilyTreeDNA or FullGenomes Corp) or by direct SNP testing (Sanger Sequencing - YSEQ or FamilyTreeDNA).

SNPs/INDELs:

BlockRegionPOS-REF-ALT (hg19)POS-REF-ALT (hg38)NamesNotes
637 3295252-A-C 3427211-A-C FGC29722 Y14477 Uncertain, but assumed negative.
637 3448827-G-A 3580786-G-A FGC29723 Y14478 Uncertain, but assumed negative.
637 4055303-T-G 4187262-T-G FGC29720 Uncertain, but assumed negative.
637 5536606-T-C 5668565-T-C FGC29725 Uncertain, but assumed negative.
637 5986783-T-A 6118742-T-A FGC29726 Uncertain, but assumed negative.
637 6712764-G-A 6844723-G-A FGC29727 Y14480 Uncertain, but assumed negative.
637 7021197-T-C 7153156-T-C FGC29728 Uncertain, but assumed negative.
637 9890433-G-T 10052824-G-T FGC29733 Uncertain, but assumed negative.
637 13581743-T-G 11426067-T-G FGC29734 Uncertain, but assumed negative.
637 13603265-T-C 11447589-T-C FGC29735 Uncertain, but assumed negative.
637 13917711-A-G 11797005-A-G FGC29736 Uncertain, but assumed negative.
637 14114551-C-T 11993845-C-T FGC29737 Y14482 Uncertain, but assumed negative.
637 16466259-C-T 14354379-C-T FGC29741 Y14483 Uncertain, but assumed negative.
637 16501801-T-A 14389921-T-A FGC29742 Uncertain, but assumed negative.
637 16724939-C-T 14613059-C-T FGC29743 Y14484 Uncertain, but assumed negative.
637 17125843-A-T 15013963-A-T FGC29744 Uncertain, but assumed negative.
637 18054002-G-T 15942122-G-T FGC29746 Uncertain, but assumed negative.
637 18189555-T-C 16077675-T-C FGC29747 Y14485 Uncertain, but assumed negative.
637 19017501-A-T 16905621-A-T FGC29748 Uncertain, but assumed negative.
637 21794564-A-G 19632678-A-G FGC29753 Y14487 Uncertain, but assumed negative.
637 21955317-A-G 19793431-A-G FGC29754 Y14488 Uncertain, but assumed negative.
637DYZ19 22430873-C-G 20268987-C-G FGC33361 Uncertain, but assumed negative.
637 23111775-G-A 20949889-G-A FGC29757 Y14490 Uncertain, but assumed negative.

*Mutations whose exact position can not be determined precisely from NGS tests, such as those in palindromes, are shown with a pink background.

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
Meister1325151111-141212121313291710-1011112514182915-15-17-17111019-231615171837-37121211915-1681011810101223-2316101212148122220131211131111121236159151226271912111212109121210111130121223131011211519132417121524122318101416101211

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: 2710761031757874198667480468
Kit: RMFBM*16000000100000008300000
Used in age calculations16000000100000008300000
Counts of SNPs75
Variant counts last updated 2017-11-05 23:03:26.

* BED data not available. Using default values.


Big Tree Main Page