Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > ZZ45 > Z36/S206 > FGC6417 > FGC6424

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 STRFGC
JO1D9
Manual
Edits
4669709-T-G 4801668-T-G FGC6437 +
16630754-A-C 14518874-A-C FGC6450 YY+
4372136-A-G 4504095-A-G FGC6436 +
8106149-T-A 8238108-T-A FGC6440 YY+
14033292-C-T 11912586-C-T FGC6443 YY+
14049928-T-C 11929222-T-C FGC6444 YY+
14397464-T-G 12276760-T-G FGC6445 YY+
15021057-A-G 12909146-A-G FGC6446 YY+
7568220-T-G 7700179-T-G FGC6439 YY+
15049201-C-T 12937292-C-T FGC6447 YY+
5890358-G-C 6022317-G-C FGC6438 +
16091366-T-C 13979486-T-C FGC6448 Y+
23894559-A-G 21732673-A-G FGC6458 Y+
16493764-T-C 14381884-T-C FGC6449 YY+
23262562-G-T 21100676-G-T FGC8072 YY+
17094925-T-C 14983045-T-C FGC6451 YY+
22474309-G-T 20312423-G-T FGC6432 DYZ19 +
22584898-T-C 20423012-T-C FGC6457 YY+
22547596-T-C 20385710-T-C FGC6456 Y+
21326907-A-T 19165021-A-T FGC6454 YY+
17482699-C-A 15370819-C-A FGC6452 Y+
24886409-CA-C 22740262-CA-C FGC6460 g1 *
22531838-C-A 20369952-C-A FGC6455 Y*
9734247-C-T 9896638-C-T FGC6442 IR3_Prx *
8733235-G-A 8865194-G-A FGC6441 Y*
3217865-C-A 3349824-C-A **
9735605-G-GTTTTTTTTT 9897996-G-GTTTTTTTTT IR3_Prx 30×T**
17214023-GGAAATCATGTGATCTCACCTAGCTATACCT-G 15102143-GGAAATCATGTGATCTCACCTAGCTATACCT-G **
3483826-TAC-T 3615785-TAC-T 13×AC**
4847191-C-A 4979150-C-A **
5338087-ATT-A 5470046-ATT-A 16×T**
8901239-GTA-G 9033198-GTA-G **
19293770-C-CAAAA 17181890-C-CAAAA 29×A**
13223048-G-A 11067372-G-A **
15865946-C-CTTTT 13754066-C-CTTTT 37×T**
23747205-C-CTTTTTT 21585319-C-CTTTTTT 29×T**
17082977-CCTTTCTTTCTTTCTTTCTTT-C 14971097-CCTTTCTTTCTTTCTTTCTTT-C 15×CTTT**
18965976-A-AGCCT 16854096-A-AGCCT **
13662038-AGGAAT-A 11506362-AGGAAT-A 9×GGAAT**
28804452-C-T 26658305-C-T ***
25020996-G-A 22874849-G-A g1 ***
22337283-G-A 20175397-G-A DYZ19 ***
22349039-A-C 20187153-A-C DYZ19 ***
22355249-A-T 20193363-A-T DYZ19 ***
58898570-G-A 56692301-C-T ***
58898526-T-G 56692345-A-C ***
58874500-A-G 56716371-T-C ***
22421081-G-A 20259195-G-A DYZ19 ***
22456686-A-G 20294800-A-G DYZ19 ***
22491406-G-T 20329520-G-T DYZ19 ***
58872993-T-G 56717878-A-C ***
58874434-C-T 56716437-G-A ***
58873016-C-T 56717855-G-A ***
28112918-C-T 25966771-C-T P1_Y2 ***
58863681-C-G 56727190-G-C ***
25626814-G-C 23480667-G-C P1_b3 ***
58846682-T-A 56744189-A-T ***
58843640-C-G 56747231-G-C ***
25626815-T-G 23480668-T-G P1_b3 ***
58843614-C-A 56747257-G-T ***
25626818-T-A 23480671-T-A P1_b3 26×A***
58841057-A-G 56749814-T-C ***
28112917-G-A 25966770-G-A P1_Y2 ***
27637124-A-G 25490977-A-G P1_Y2 ***
8703659-AT-A 8835618-AT-A 18×T***
58904181-C-G 56686690-G-C ***
23350626-C-CTT 21188740-C-CTT 21×T***
17214022-AGGAAATCATGTGATCTCACCTAGCTATACC-A 15102142-AGGAAATCATGTGATCTCACCTAGCTATACC-A ***
18354349-A-AAGAC 16242469-A-AAGAC P6_Prx ***
18965978-C-CCTGG 16854098-C-CCTGG ***
19449428-G-GAAAAAAAAAAAA 17337548-G-GAAAAAAAAAAAA 23×A***
21148589-C-CAAAAAAA 18986703-C-CAAAAAAA 30×A***
21464536-C-CAAAAAAA 19302650-C-CAAAAAAA 19×A***
21556919-C-CTTTTTTTT 19395033-C-CTTTTTTTT 23×T***
22236520-TGG-AGA 20074634-TGG-AGA DYZ19 ***
22263737-GTT-TTA 20101851-GTT-TTA DYZ19 ***
22480586-TTGAA-T 20318700-TTGAA-T DYZ19 ***
24283332-T-TAAAAAAAA 22137185-T-TAAAAAAAA P3_t1 27×A***
15340383-CTTTTT-C 13228501-CTTTTTT-C 18×T***
24425337-A-ATGCT 22279190-A-ATGCT ***
24472421-G-GTTTTTTT 22326274-G-GTTTTTTT 25×T***
26210183-AG-GA 24064036-AG-GA P1_Y1 ***
26210219-TG-CA 24064072-TG-CA P1_Y1 ***
26210233-GGGT-TGGG 24064086-GGGT-TGGG P1_Y1 ***
26526566-G-GGT 24380419-G-GGT P1_Y1 16×T***
28112910-TC-T 25966763-TC-T P1_Y2 ***
28620602-G-GT 26474455-G-GT ***
28814590-TC-GA 26668443-TC-GA ***
58874463-ACAGTCC-CCATACT 56716402-GGACTGT-AGTATGG ***
16908451-T-TAAAAAAA 14796571-T-TAAAAAAA 21×A***
14491216-TG-AA ***
58906344-T-G 56684527-A-C ***
5492439-C-CATTTT 5624398-C-CATTTT 18×T***
21558722-C-CA 19396836-C-CA 16×A***
22324940-A-T 20163054-A-T DYZ19 ***
14914672-CT-C 12802739-CT-C 17×T***
3558246-T-TA 3690205-T-TA 16×A***
2651883-C-CTTTTT 2783842-C-CTTTTT 19×T***
3315351-C-CA 3447310-C-CA ***
3315398-AAAT-TCGG 3447357-AAAT-TCGG ***
4346565-A-ATTTTTTTTTTCCTCCTTG 4478524-A-ATTTTTTTTTTCCTCCTTG 22×T***
4897963-CAAAAAAAAA-C 5029922-CAAAAAAAAA-C 20×A***
5191228-C-CTT 5323187-C-CTT 27×T***
6162228-GA-AT 6294187-GA-AT IR3_Dst ***
14324894-C-CTTTT 12204188-C-CTTTT 26×T***
9216146-GGAG-AGAT 9378537-GGAG-AGAT ***
9351179-TA-CC 9513570-TA-CC ***
13129514-TAGGTTC-GTGGTAA 10619000-TAGGTTC-GTGGTAA ***
13450132-TATTCC-T 11294456-TATTCC-T 8×ATTCC***
13453840-CTCCATTCCAT-C 11298164-CTCCATTCCAT-C 10×TCCAT***
13470654-CGGTCT-TGGAGA 11314978-CGGTCT-TGGAGA ***
13488959-GCCCA-TCACT 11333283-GCCCA-TCACT ***
13532875-CAAA-C 11377199-CAAA-C 13×A***
13726487-CAA-AAG 11570811-CAA-AAG ***
13726500-G-GACGCT 11570824-G-GACGCT ***
13923530-CAAAAAAAAAAAAAAAAAAAAAAAAA-C 11802824-CAAAAAAAAAAAAAAAAAAAAAAAAA-C 29×A***
22337224-A-T 20175338-A-T DYZ19 ***
2970336-GGTGT-G 3102295-GGTGT-G 18×GT***
22309548-T-G 20147662-T-G DYZ19 ***
22756974-T-C 20595088-T-C ***
58852107-T-C 56738764-A-G ***
58874455-A-T 56716416-T-A ***
22252927-C-T 20091041-C-T DYZ19 ***
22491012-G-A 20329126-G-A DYZ19 ***
58874479-G-C 56716392-C-G ***
58895472-G-A 56695399-C-T ***
8462064-C-CAAAA 8594023-C-CAAAA 26×A***
58848719-TG-AT 56742151-CA-AT ***
22367518-T-A 20205632-T-A DYZ19 ***
58885486-C-G 56705385-G-C ***
58843643-C-T 56747228-G-A 4×CCATT***
22276447-G-T 20114561-G-T DYZ19 ***
26152085-T-C 24005938-T-C P1_Y1 ***
22971946-C-T 20810060-C-T CTS11137 ***
22971958-T-C 20810072-T-C CTS11138 ***
9961025-AT-GC 10123416-AT-GC ***
22446152-AC-A 20284266-AC-A DYZ19 ***
58873021-T-C 56717850-A-G ***
9428966-T-C 9591357-T-C ***
22481870-T-C 20319984-T-C DYZ19 ***
17835121-G-A 15723241-G-A ***
22282205-C-T 20120319-C-T DYZ19 ***
22236511-C-A 20074625-C-A DYZ19 ***
13469053-G-C 11313377-G-C ***
9962138-C-G 10124529-C-G ***
9202147-C-A 9364538-C-A ***
58898532-G-T 56692339-C-A ***
58912398-C-T 56678473-G-A ***
22421969-G-T 20260083-G-T DYZ19 ***
13203978-CCTC-GTAT 11048302-CCTC-GTAT ***
17402501-CT-C 15290621-CT-C 14×T***
58841100-T-C 56749771-A-G ***
14258596-G-A 12137890-G-A ***
58906363-C-G 56684508-G-C ***
13740850-C-T 11585174-C-T ***
58841085-A-C 56749786-T-G ***
19098471-AC-A 16986591-AC-A ***
58823284-TCTCAT-A 56767582-ATGAGA-T ***
15557124-AATATATAT-A 13445244-AATATATAT-A 19×AT***
58836372-T-A 56754499-A-T ***
58898478-C-G 56692393-G-C ***
22723386-C-CAAAAAAA 20561500-C-CAAAAAAA 17×A***
13708405-C-G 11552729-C-G ***
58882015-C-G 56708856-G-C ***
22282092-G-C 20120206-G-C DYZ19 ***
16381043-T-G 14269163-T-G ***
13311599-A-G 11155923-A-G ***
13368545-G-T 11212869-G-T ***
13377446-G-C 11221770-G-C ***
13460747-T-A 11305071-T-A ***
13483974-G-A 11328298-G-A ***
13726514-A-G 11570838-A-G ***
15350271-G-T 13238390-G-T ***
16379335-C-A 14267455-C-A ***
17898635-A-T 15786755-A-T ***
13110315-T-C 10599801-T-C ***
18464136-C-G 16352256-C-G P6_Dst ***
19035961-C-A 16924081-C-A ***
19926981-A-T 17815101-A-T P5_Prx ***
22226442-T-A 20064556-T-A DYZ19 ***
22248092-C-T 20086206-C-T DYZ19 ***
22248383-A-C 20086497-A-C DYZ19 ***
22252515-G-A 20090629-G-A DYZ19 ***
22265740-T-A 20103854-T-A DYZ19 ***
22268377-T-G 20106491-T-G DYZ19 ***
13311593-C-A 11155917-C-A ***
9345065-A-G 9507456-A-G ***
20459042-C-CA 18297156-C-CA P5_Dst 21×A***
26210214-A-G 24064067-A-G P1_Y1 ***
26210152-G-A 24064005-G-A P1_Y1 ***
26210158-C-A 24064011-C-A P1_Y1 ***
26210238-C-T 24064091-C-T P1_Y1 ***
5433985-A-G 5565944-A-G ***
9428985-T-C 9591376-T-C ***
9428998-A-C 9591389-A-C ***
25719570-A-T 23573423-A-T P1_b3 ***
14845268-CT-C 12733334-CT-C 15×T***
13480171-T-C 11324495-T-C ***
3316353-T-A 3448312-T-A ***
9345054-G-C 9507445-G-C ***
3316951-T-C 3448910-T-C ***
4844572-A-G 4976531-A-G ***
4844580-A-G 4976539-A-G ***
4844607-C-T 4976566-C-T ***
5926872-A-G 6058831-A-G ***
6162207-C-G 6294166-C-G IR3_Dst ***
6483318-G-A 6615277-G-A ***
7996720-G-T 8128679-G-T ***
9216152-C-G 9378543-C-G ***
17835127-G-C 15723247-G-C ***

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.

Mutation Notes:

Kit POSITION-REF-ALT (hg19) POSITION-REF-ALT (hg38) Note
Manual22299247-G-C13A 387C 496G 33T. The A reads and T reads look mostly misaligned.
Manual26394771-T-C64T 53C and 3A which are clearly misaligned.

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
ZZ451324141111-14121212141330179-1011112515192915-15-17-17111019-231615191736-381212111015-1681010811101223-23161012121681222201412111311111212331591612252619121112128912121011113012132413101020151713231712152412231810141791211
Mosimann1324151111-15121212131329179-1011112514202915-15-17-17111119-231615181836-36121211915-168101081091222-231710121216812222013121113111112123214916132526191211131210912121011113012132413101021151912241812152412231810141891211

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: JO1D9*16000000100000008300000
Used in age calculations16000000100000008300000
Counts of SNPs1814
Variant counts last updated 2017-11-05 23:06:55.

* BED data not available. Using default values.


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