Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > ZZ10 > Z253 > Z2534 > ZZ5 > Z2185 > Z2186 > L1066 > PR4692

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
237481
22476231-G-C 20314345-G-C DYZ19 +
15524227-CT-C 13412347-CT-C +
22261173-G-T 20099287-G-T DYZ19 +
14410499-C-T 12289796-C-T BY95568 YY+
8501689-CTCTTCT-C 8633648-CTCTTCT-C 18×TCT+
22848291-C-T 20686405-C-T BY141227 YY+
14744722-A-G 12632791-A-G BY97350 YY+
15138732-A-G 13026819-A-G BY99894 YY+
22261196-C-T 20099310-C-T BY24397 DYZ19 +
22261170-G-A 20099284-G-A DYZ19 +
9904732-C-T 10067123-C-T BY42858 Y+
18613135-A-C 16501255-A-C BY122600 YY+
8218013-TTTTCTTTC-T 8349972-TTTTCTTTC-T 15×TTTC+
22261167-A-G 20099281-A-G DYZ19 +
19139901-T-C 17028021-T-C S21846 L1443 YY+
21731580-A-G 19569694-A-G BY135072 YY+
13855635-C-G 11734929-C-G **
15619125-C-A 13507245-C-A **
16450159-C-A 14338279-C-A F339 M2324 **
13452837-ACTC-A 11297161-ACTC-A **
28802841-T-G 26656694-T-G **
13858120-C-T 11737414-C-T **
9444545-C-T 9606936-C-T PF5535 M2443 **
20602077-G-A 18440191-G-A P5_Dst **
20045274-A-AAAAGAAAAG 17933394-A-AAAAGAAAAG P5_Prx 14×AAAG**
13459206-CATTCCAACTG-C 11303530-CATTCCAACTG-C ***
13837385-T-C 11716679-T-C ***
13476794-C-A 11321118-C-A ***
58972721-A-C 56826574-A-C ***
13479393-T-G 11323717-T-G ***
13479404-G-T 11323728-G-T ***
13866034-A-G 11745328-A-G ***
13480383-C-G 11324707-C-G ***
22147729-T-A 19985843-T-A ***
59004683-AG-A 56858536-AG-A ***
13657089-A-T 11501413-A-T ***
23196176-G-GTT 21034290-G-GTT 20×T***
23899401-CGT-C,CTT 21737515-CGT-C,CTT 17×GT***
13810088-G-A 11689382-G-A ***
13810099-G-T 11689393-G-T ***
13810111-A-T 11689405-A-T ***
13458056-CTTTCA-C,CATTCC 11302380-CTTTCA-C,CATTCC ***
14116679-GATAC-G 11995973-GATAC-G 10×ATAC***
13858000-C-T 11737294-C-T ***
13657094-C-A 11501418-C-A ***
13862170-T-C,G 11741464-T-C,G ***
13813555-T-G 11692849-T-G ***
10024193-T-C 10186584-T-C ***
13833165-A-T 11712459-A-T ***
13479383-G-T 11323707-G-T ***
13657068-G-A 11501392-G-A ***
13657084-A-T 11501408-A-T ***
26564051-A-G 24417904-A-G P1_g2 ***
13657102-C-A 11501426-C-A ***
13864517-ACTCGC-A 11743811-ACTCGC-A ***
59004680-GAA-G 56858533-GAA-G ***
13455671-T-C 11299995-T-C ***
26538436-GTT-G 24392289-GTT-G P1_g2 17×T***
13479408-T-G 11323732-T-G ***
13857886-G-A 11737180-G-A ***
13808724-G-GGAATGATACGGAATA 11688018-G-GGAATGATACGGAATA ***
13664621-A-ATGGAG 11508945-A-ATGGAG ***
13657095-A-G 11501419-A-G ***
13657081-C-T 11501405-C-T ***
13489338-C-A 11333662-C-A BY26223 ***
13455648-A-C,T 11299972-A-C,T ***
13865906-C-A 11745200-C-A ***
13451885-T-C 11296209-T-C ***
10019241-G-A 10181632-G-A BY83000 ***
8886122-TCA-T 9018081-TCA-T 9×CA***
13141094-GT-G 10630580-GT-G ***
13664424-A-C,G 11508748-A-C,G ***
22147730-CTTTCT-A,C 19985844-CTTTCT-A,C 19×TTTCT***
13858560-G-GAAACT 11737854-G-GAAACT ***
16157779-GA-G 14045899-GA-G P8_Dst ***
26152181-T-TTC 24006034-T-TTC P1_Y1 ***
22230192-C-T 20068306-C-T DYZ19 ***
26113917-T-G 23967770-T-G P1_Y1 ***
25319235-C-T 23173088-C-T P2_r1 ***
24971082-CTT-C 22824935-CTT-C g1 14×T***
24956282-A-G 22810135-A-G g1 ***
24819804-T-TA 22673657-T-TA P3_b2 9×A***
24365177-A-AAGAGAT,T 22219030-A-AAGAGAT,T 8×AGAGAT***
22422248-G-C 20260362-G-C DYZ19 ***
18672379-T-TTTTA 16560499-T-TTTTA 8×TTTA***
22265491-G-A 20103605-G-A DYZ19 ***
22225916-G-C 20064030-G-C FGC20008 DYZ19 ***
20696739-TA-T 18534853-TA-T P4_Prx ***
20680521-C-T 18518635-C-T P4_Prx ***
19698347-G-A 17586467-G-A P5_Prx ***
19669154-A-G 17557274-A-G P5_Prx ***
13862244-T-A 11741538-T-A ***
13479349-C-A 11323673-C-A ***
13862166-G-A 11741460-G-A ***
13812237-A-C 11691531-A-C ***
6224717-CA-C 6356676-CA-C IR3_Dst 12×A***
20771714-G-A 18609828-G-A P4_Prx 25×A***
28800259-A-G 26654112-A-G ***
13476793-C-G 11321117-C-G ***
13837370-T-G 11716664-T-G ***
58979654-A-C,T 56833507-A-C,T ***
13801547-T-A 11680841-T-A ***
58972694-C-T 56826547-C-T ***
13837358-A-T 11716652-A-T ***
13455112-T-G 11299436-T-G ***
13837364-T-A 11716658-T-A ***
13865715-C-G 11745009-C-G ***
13480608-A-G,T 11324932-A-G,T ***
13664634-G-C 11508958-G-C ***
13867983-A-C 11747277-A-C ***
13486018-T-G 11330342-T-G ***
13830256-A-C 11709550-A-C ***
13830257-A-T 11709551-A-T ***
18365613-A-AT 16253733-A-AT P6_Prx 11×T***
26152241-T-C 24006094-T-C P1_Y1 ***
22147866-T-C 19985980-T-C ***
58975652-G-C 56829505-G-C ***
13865720-A-G 11745014-A-G ***
13846548-T-C 11725842-T-C ***
6126105-GA-G 6258064-GA-G 11×A***
13862157-AATCAG-A 11741451-AATCAG-A ***
22284866-G-C 20122980-G-C DYZ19 ***
13143648-T-A 10633134-T-A ***
13829428-A-T 11708722-A-T ***
15260684-C-CT 13148768-C-CT 25×T***
58975654-G-T 56829507-G-T 4×TCCAT***
13852245-A-T 11731539-A-T ***
13657030-T-A 11501354-T-A ***
13805306-A-C 11684600-A-C ***
13813493-A-AC 11692787-A-AC ***
58865990-G-T 56724881-C-A ***
13652195-ATGGAG-A 11496519-ATGGAG-A ***
13459218-C-T 11303542-C-T ***
13829429-A-G 11708723-A-G ***
13476665-C-T 11320989-C-T ***
22147861-T-C 19985975-T-C ***
9968247-T-A 10130638-T-A ***
13862165-G-C 11741459-G-C ***
58979483-CACTCT-C,CACTCC 56833336-CACTCT-C,CACTCC ***
13808789-G-C 11688083-G-C ***
13452978-C-A 11297302-C-A ***
13869565-G-C 11748859-G-C ***
13869209-G-C 11748503-G-C ***
27080520-G-GT 24934373-G-GT P1_r4 16×T***
13838532-G-A 11717826-G-A ***
22228064-A-G 20066178-A-G DYZ19 ***
13455536-C-CTCCAG 11299860-C-CTCCAG ***
13843402-T-G 11722696-T-G ***
25441211-ATT-A,AT 23295064-ATT-A,AT P2_r2 22×T***
13836415-C-A 11715709-C-A ***
13837341-G-T 11716635-G-T ***
13837350-C-T 11716644-C-T BY91021 ***
16157785-A-G 14045905-A-G P8_Dst ***
19436764-G-GAGAGAA 17324884-G-GAGAGAA 12×AGAA***
13479339-G-C 11323663-G-C ***
13455728-C-T 11300052-C-T ***
13479365-GATTTAC-G 11323689-GATTTAC-G ***
13454321-C-G 11298645-C-G BY30620 ***
13833909-T-G 11713203-T-G ***
13804721-G-T 11684015-G-T ***
13852238-A-G 11731532-A-G ***
13804726-A-G 11684020-A-G ***
13818692-C-T 11697986-C-T ***
13862607-A-C 11741901-A-C ***
27016158-CTT-C 24870011-CTT-C P1_r4 19×T***
13812226-T-A 11691520-T-A ***
13812234-A-C 11691528-A-C ***
13657035-C-T 11501359-C-T ***
13657036-A-AAATGG 11501360-A-AAATGG ***
13852239-A-G 11731533-A-G ***
13810208-G-A 11689502-G-A ***
58978466-C-G 56832319-C-G ***
13865939-C-G 11745233-C-G ***
58978451-C-T 56832304-C-T ***
13830239-G-A 11709533-G-A ***
13830241-T-C 11709535-T-C BY90856 ***
13658887-A-G 11503211-A-G ***
58975882-T-TCATTCCATTC 56829735-T-TCATTCCATTC ***
13852255-T-C 11731549-T-C ***
16157783-AG-A,AA 14045903-AG-A,AA P8_Dst ***

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
L21/S1451324141111-14121212131329179-1011112515192915-15-17-17111119-231615181736-38121211915-1681010810101223-231610121215812222013121113111112123515916122526191211131211912121011113012132413101020151913241712152412231810141791211
O'Shea1325141012-13121212151431179-1011112515202715-15-16-17111119-231514181737-40121211915-1681010810101223-2316101281481222201312111311111212

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: 2374811024743673436797404292
Used in age calculations1024743673436797404292
Counts of SNPs87
Variant counts last updated 2018-06-18 21:15:27.



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