Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z272 > S450 > Z295/S1217 > ZZ77 > Z216 > S452 > PH1171 > BY189958 > BY191048

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 STRBigY3
517773
BigY2
517773
13449534-C-T 11293858-C-T A*
22281973-G-A 20120087-G-A DYZ19 A*
13463392-G-A 11307716-G-A A*
14852784-C-CT 12740850-C-CT 10×TA*
13449982-C-CTATTG 11294306-C-CTATTG A*
56829223-C-T A*
5569455-C-A 5701414-C-A A*
56831659-T-TTCTTC A*
56834403-C-T A*
13450396-C-T 11294720-C-T A*
56831980-T-C A*
28817905-T-A 26671758-T-A A*
13463314-A-T 11307638-A-T A*
22664418-G-C 20502532-G-C BY191999 YY++
13391-C-G *
56879801-C-T *
13364-T-C *
13371-G-A *
56830540-TGCTGAATTCCATTGCATTCC-T,TATTGAATTCC *
6719441-TAA-T,TA 6851400-TAA-T,TA 14×A*
15049957-C-T 12938048-C-T **
6305913-C-CAA 6437872-C-CAA IR3_Dst 14×A**
15254930-A-G 13143016-A-G **
22207400-C-A 20045514-C-A **
15401850-A-G 13289970-A-G **
13459121-C-G 11303445-C-G **
14134925-CT-C 12014219-CT-C 10×T**
13459072-A-G 11303396-A-G **
56850103-G-A **
56832097-C-A **
16171271-C-A 14059391-C-A **
24406798-A-G 22260651-A-G **
23418834-G-A 21256948-G-A **
21200894-C-CAAA 19039008-C-CAAA 14×A**
16710262-C-A 14598382-C-A **
10682499-T-TGGAAA **
10682544-T-TGGAAA **
18738476-A-G 16626596-A-G **
7231723-C-A 7363682-C-A **
3098846-C-A 3230805-C-A **
19020437-C-A 16908557-C-A **
15422121-C-A 13310241-C-A **
25508997-G-T 23362850-G-T P1_gr1 **
20700781-G-T 18538895-G-T P4_Prx **
24241200-TCA-T 22095053-TCA-T P3_b1 11×CA**
13476330-A-C 11320654-A-C **
21515637-C-T 19353751-C-T **
21745938-A-G 19584052-A-G **
20426054-C-CA 18264168-C-CA P5_Dst 26×A**
17065146-A-G 14953266-A-G **
3306217-GTATA-G 3438176-GTATA-G 10×TA**
14163707-A-G 12043001-A-G **
17407035-GT-G 15295155-GT-G **
19631888-T-A 17520008-T-A P5_Prx **
9734000-A-C 9896391-A-C IR3_Prx **
18329043-CTTTT-C 16217163-CTTTT-C P6_Prx 17×T**
6009481-C-T 6141440-C-T **
5521561-A-G 5653520-A-G **
21352420-G-A 19190534-G-A **
14624323-T-A 12512523-T-A **
11014541-C-G **
10663343-A-T **
19612058-A-AG 17500178-A-AG P5_Prx **
22360160-C-G 20198274-C-G DYZ19 **
18003329-T-TA 15891449-T-TA P7_Gap 10×A**
25961931-C-CTA 23815784-C-CTA P1_Y1 **
11014504-T-C **
10821934-T-C **
3199999-G-A 3331958-G-A **
25961975-A-G 23815828-A-G P1_Y1 **
16077543-CAAAAAAAAAAAAAAAAAAAAA-C,CAAA 13965663-CAAAAAAAAAAAAAAAAAAAAA-C,CAAA 36×A***
14956292-A-T 12844367-A-T ***
19333229-ATTTTTT-A,ATTT 17221349-ATTTTTT-A,ATTT 21×T***
19237951-C-A 17126071-C-A ***
18569850-C-CT 16457970-C-CT ***
28508007-CAAA-C 26361860-CAAA-C 14×A***
23802377-G-A 21640491-G-A ***
18936845-C-A 16824965-C-A ***
18802027-CAA-C,CA 16690147-CAA-C,CA 16×A***
23802384-C-T 21640498-C-T ***
16308339-A-G 14196459-A-G ***
19401642-A-T 17289762-A-T ***
22147190-A-T 19985304-A-T ***
14307918-T-C 12187212-T-C ***
23277560-C-A 21115674-C-A ***
22807900-A-T 20646014-A-T ***
18060393-T-TAG 15948513-T-TAG ***
14452377-C-T 12331650-C-T ***
28624203-C-A 26478056-C-A ***
23435682-CTTTTTT-C,CTTTTT 21273796-CTTTTTT-C,CTTTTT 21×T***
23422818-C-A 21260932-C-A ***
4619254-G-A 4751213-G-A ***
5002046-AT-A 5134005-AT-A 9×T***
23205177-A-G 21043291-A-G ***
21266843-C-A 19104957-C-A ***
23063670-C-A 20901784-C-A ***
22800591-C-A 20638705-C-A ***
7258755-CAAAA-C 7390714-CAAAA-C 25×A***
22164865-A-G 20002979-A-G ***
13607598-CAAAA-C 11451922-CAAAA-C 18×A***
13476550-C-G 11320874-C-G ***
22142971-C-A 19981085-C-A ***
21564060-GA-G 19402174-GA-G ***
14809156-C-A 12697227-C-A ***
13470629-C-T 11314953-C-T ***
14393639-C-A 12272935-C-A ***
18607365-CATAT-C 16495485-CATAT-C 10×AT***
21502782-C-CT 19340896-C-CT 16×T***
28792470-G-A 26646323-G-A ***
17386774-TAAA-T 15274894-TAAA-T 15×A***
22040881-C-A 19878995-C-A 19×A***
10672228-C-A ***
5191228-CTTTTT-C 5323187-CTTTTT-C 27×T***
14510449-GAA-G 12398654-GAA-G 21×A***
13489734-C-G,T 11334058-C-G,T ***
10965571-T-A ***
10965577-T-TGTATTCCATCCTATC ***
8666723-GTTTTTT-G 8798682-GTTTTTT-G 25×T***
8648172-GATAT-G 8780131-GATAT-G 14×AT***
28531858-C-A 26385711-C-A ***
7195227-CAAA-C,CAA 7327186-CAAA-C,CAA 17×A***
13480351-T-G 11324675-T-G ***
9935473-C-A 10097864-C-A ***
15518278-CT-C 13406398-CT-C 10×T***
13470542-G-A 11314866-G-A ***
7996584-A-G 8128543-A-G ***
16336896-TG-T 14225016-TG-T ***
19504905-GTC-G 17393025-GTC-G ***
59008520-A-T 56862373-A-T ***
59032844-C-A 56886697-C-A ***
18883955-CATCT-C 16772075-CATCT-C 6×ATCT***
14096618-TAA-T,TA 11975912-TAA-T,TA 17×A***
18837739-A-AT 16725859-A-AT 10×T***
13468448-C-A 11312772-C-A ***
13924970-C-A 11804264-C-A 20×A***
5986595-G-GT 6118554-G-GT 28×T***
5007689-CAAA-C 5139648-CAAA-C 22×A***
20804885-GTATATA-G 18642999-GTATATA-G P4_Gap 15×TA***
17086015-C-A 14974135-C-A ***
28686423-CAAA-C 26540276-CAAA-C 21×A***
14145364-C-A 12024658-C-A ***
8286992-C-A 8418951-C-A ***
6024536-TTGTG-T,TTG 6156495-TTGTG-T,TTG 15×TG***
13833639-G-A 11712933-G-A ***
2860458-GTTTTT-G,GTTTTTT 2992417-GTTTTT-G,GTTTTTT 18×T***
4901922-C-A 5033881-C-A ***
5644943-C-A 5776902-C-A ***
7775249-A-G 7907208-A-G ***
9832678-C-A 9995069-C-A ***
9361301-G-A 9523692-G-A ***
11014469-T-G ***
13451188-CTTTC-C,CTTTCCATTCT 11295512-CTTTC-C,CTTTCCATTCT ***
13469968-G-A 11314292-G-A ***
13469989-C-G 11314313-C-G ***
13617355-C-A 11461679-C-A ***
14101717-CAAAA-C,CAAA 11981011-CAAAA-C,CAAA 15×A***
14224563-C-A 12103857-C-A ***
11014477-C-A ***
21414510-A-AT 19252624-A-AT 10×T***
17787106-CAAAAAA-C 15675226-CAAAAAA-C 19×A***
3279762-C-A 3411721-C-A ***
22962414-GT-G,GTT 20800528-GT-G,GTT 20×T***
5080362-C-CT 5212321-C-CT 15×T***
13468671-G-T 11312995-G-T ***
7139608-AT-A,ATT 7271567-AT-A,ATT 17×T***
13470021-G-C 11314345-G-C ***
3499681-TA-T 3631640-TA-T 10×A***
2763773-CAAAAAA-C 2895732-CAAAAAA-C 20×A***
13489617-CCA-C,CCCGTCCTCA 11333941-CCA-C,CCCGTCCTCA ***
3542368-C-CT 3674327-C-CT 13×T***
14102318-TA-T,TATCTA 11981612-TA-T,TATCTA ***
4669265-ATT-A 4801224-ATT-A 15×T***
14771649-CTTT-C,CTTTT 12659718-CTTT-C,CTTTT 17×T***
22163726-C-A 20001840-C-A ***
23109-G-A ***

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.

Age Analysis Information (work in progress)

AllMcDonaldYFull
Kit: 517773898805474325057412622
Kit: 5177731492557193420698302197
Used in age calculations1492557193420698302197
Counts of SNPs11
Variant counts last updated 2019-08-26 23:04:11.



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