Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > ZZ19 > Z31644 > FGC13109 > FGC13113 > FGC31444 > ~9316674-T-C > FGC13120 > FGC13122

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
7010384-C-A 7142343-C-A FGC31440 YY+
17134499-G-C 15022619-G-C FGC31443 YY+
18651355-A-G 16539475-A-G FGC31445 Y+
28336668-C-CAAAAAA 26190521-C-CAAAAAA P1_b4 31×A**
20326007-C-CTTTTTTTTT 18164121-C-CTTTTTTTTT P5_Dst 29×T**
16533538-CAT-C 14421658-CAT-C **
13287553-T-C 11131877-T-C **
27352357-G-A 25206210-G-A P1_g3 ***
27432945-C-A 25286798-C-A P1_g3 ***
27367976-A-T 25221829-A-T P1_g3 ***
27155065-T-A 25008918-T-A P1_g3 ***
27352354-G-T 25206207-G-T P1_g3 ***
27155064-G-A 25008917-G-A P1_g3 ***
27155063-T-A 25008916-T-A P1_g3 ***
27155056-G-T 25008909-G-T P1_g3 ***
27155012-G-A 25008865-G-A P1_g3 ***
27586050-A-T 25439903-A-T P1_Y2 ***
27586116-G-T 25439969-G-T P1_Y2 ***
27586059-C-A 25439912-C-A P1_Y2 ***
26924333-C-T 24778186-C-T P1_r3 ***
27692643-A-T 25546496-A-T P1_Y2 ***
28008591-C-A 25862444-C-A P1_Y2 11×A***
28418264-G-T 26272117-G-T P1_gr2 ***
28418284-A-C 26272137-A-C P1_gr2 ***
58820128-G-A 56770743-C-T ***
58820175-G-T 56770696-C-A ***
58830648-C-T 56760223-G-A ***
58830725-C-A 56760146-G-T ***
58833005-G-A 56757866-C-T ***
58843135-C-A 56747736-G-T ***
58843141-T-C 56747730-A-G ***
58843143-T-A 56747728-A-T ***
27155006-G-A 25008859-G-A P1_g3 ***
13486129-G-A 11330453-G-A ***
26902147-C-A 24756000-C-A P1_r3 ***
23223298-C-A 21061412-C-A ***
22360334-C-T 20198448-C-T DYZ19 ***
22361044-G-A 20199158-G-A DYZ19 ***
22365607-A-C 20203721-A-C DYZ19 ***
22421343-T-C 20259457-T-C DYZ19 ***
22503457-C-G 20341571-C-G DYZ19 ***
22503611-T-G 20341725-T-G DYZ19 ***
22535473-G-A 20373587-G-A ***
22535474-C-G 20373588-C-G ***
22535508-G-A 20373622-G-A ***
22535510-T-C 20373624-T-C ***
22535514-C-G 20373628-C-G ***
22636832-C-T 20474946-C-T ***
24538507-T-A 22392360-T-A P3_t2 ***
26391289-G-A 24245142-G-A P1_Y1 ***
24538545-T-A 22392398-T-A P3_t2 ***
24614372-A-G 22468225-A-G P3_t2 ***
25173384-A-T 23027237-A-T g1 ***
25581436-T-C 23435289-T-C P1_gr1 ***
25815218-C-T 23669071-C-T P1_b3 ***
26139495-T-A 23993348-T-A P1_Y1 ***
26139496-T-A 23993349-T-A P1_Y1 ***
26139501-T-A 23993354-T-A P1_Y1 ***
26139506-A-T 23993359-A-T P1_Y1 ***
26207913-A-T 24061766-A-T P1_Y1 ***
26346307-C-A 24200160-C-A P1_Y1 ***
58843144-T-A 56747727-A-T ***
26346308-C-A 24200161-C-A P1_Y1 ***
58864169-A-G 56726702-T-C ***
58854195-C-T 56736676-G-A ***
20025478-TCTCT-CCCCC 17913598-TCTCT-CCCCC P5_Prx ***
13463771-CG-TCA 11308095-CG-TCA ***
13463836-CGTTT-GGGTC 11308160-CGTTT-GGGTC ***
13463860-CA-GT 11308184-CA-GT ***
13478480-AGGT-GGGC 11322804-AGGT-GGGC ***
13478505-TGCATT-CGTGGG 11322829-TGCATT-CGTGGG ***
13480771-GCCAA-ACCAG 11325095-GCCAA-ACCAG ***
15161292-G-GAAAAA 13049378-G-GAAAAA 22×A***
16533418-CA-GT 14421538-CA-GT ***
18297876-C-CTTTTTTTT 16185996-C-CTTTTTTTT P6_Prx 31×T***
19694852-T-TGTG 17582972-T-TGTG P5_Prx ***
20025482-T-TCCCCC 17913602-T-TCCCCC P5_Prx 14×C***
13430391-AAC-A 11274715-AAC-A ***
22341822-CTA-TTT 20179936-CTA-TTT DYZ19 ***
22421683-TCC-ACA 20259797-TCC-ACA DYZ19 ***
22535473-GC-AG 20373587-GC-AG ***
24425340-C-CGTGT 22279193-C-CGTGT ***
27952081-GTC-G 25805934-GTC-G P1_Y2 ***
28491339-A-ACACCCCCAC 26345192-A-ACACCCCCAC ***
13445010-CAATAT-AAATGA 11289334-CAATAT-AAATGA ***
9700802-A-AAAAGGAAC 9863193-A-AAAAGGAAC IR3_Prx ***
22354658-G-A 20192772-G-A DYZ19 ***
16447158-AACACACAC-A 14335278-AACACACAC-A 22×AC***
58866382-C-T 56724489-G-A ***
58877041-A-T 56713830-T-A ***
58877102-T-C 56713769-A-G ***
58883993-C-A 56706878-G-T ***
58888780-A-C 56702091-T-G ***
58889871-C-T 56701000-G-A ***
58903766-C-T 56687105-G-A ***
58904842-A-T 56686029-T-A ***
58909134-C-A 56681737-G-T ***
58909151-A-T 56681720-T-A ***
58916688-A-T 56674183-T-A ***
59013629-T-A 56867482-T-A ***
4834269-C-AAAA 4966228-C-AAAA ***
8901076-C-CACATAT 9033035-C-CACATAT 15×AT***
13467653-AGAAT-GCAAG 11311977-AGAAT-GCAAG ***
22230648-A-AC 20068762-A-AC DYZ19 ***
3695724-CA-C 3827683-CA-C 14×A***
14062045-T-AAA 11941339-T-AAA ***
5426382-C-TT 5558341-C-TT ***
13444193-A-AAG 11288517-A-AAG ***
2729648-C-CTTTTTT 2861607-C-CTTTTTT 25×T***
2810366-A-ATTTTTT 2942325-A-ATTTTTT 23×T***
3606672-G-GTTT 3738631-G-GTTT 19×T***
5241241-TT-C 5373200-TT-C ***
6684237-C-AA 6816196-C-AA ***
22359820-C-A 20197934-C-A DYZ19 ***
22337363-C-G 20175477-C-G DYZ19 ***
22341778-C-T 20179892-C-T DYZ19 ***
58894510-C-T 56696361-G-A ***
13467654-G-C 11311978-G-C ***
58868431-C-CACT 56722439-G-GAGT ***
22421550-A-T 20259664-A-T DYZ19 ***
22421727-A-G 20259841-A-G DYZ19 ***
58854376-C-A 56736495-G-T 4×CCATT***
22361232-A-G 20199346-A-G DYZ19 ***
10084067-T-A 10246458-T-A ***
10084129-A-C 10246520-A-C ***
13411356-AT-GG 11255680-AT-GG ***
13468677-A-T 11313001-A-T ***
22367929-C-G 20206043-C-G DYZ19 ***
10090726-C-T 10253117-C-T ***
58843770-C-A 56747101-G-T ***
15171226-C-CTTTTTTT 13059312-C-CTTTTTTT 19×T***
5009331-G-A 5141290-G-A ***
5009335-C-T 5141294-C-T ***
24127680-C-T 21981533-C-T P3_b1 ***
13468688-C-T 11313012-C-T ***
13480124-T-A 11324448-T-A ***
10084379-T-A 10246770-T-A ***
58890562-A-T 56700309-T-A ***
28814693-G-C 26668546-G-C ***
22289463-A-G 20127577-A-G DYZ19 ***
22354326-G-A 20192440-G-A DYZ19 ***
13254160-CTTT-TTTC 11098484-CTTT-TTTC ***
3312721-T-G 3444680-T-G ***
27060079-CTATTTC-TTTTTTT 24913932-CTATTTC-TTTTTTT P1_r4 ***
58893237-T-G 56697634-A-C ***
10022156-T-C 10184547-T-C FGC19274 ***
19646223-A-T 17534343-A-T P5_Prx ***
22248516-A-C 20086630-A-C DYZ19 ***
22252918-T-A 20091032-T-A DYZ19 ***
58843145-G-C 56747726-C-G ***
22337597-A-T 20175711-A-T DYZ19 ***
22268224-G-T 20106338-G-T DYZ19 ***
22421952-G-T 20260066-G-T DYZ19 ***
22488377-T-A 20326491-T-A DYZ19 ***
22341680-C-CT 20179794-C-CT DYZ19 ***
13467676-T-A 11312000-T-A ***
58913068-C-A 56677803-G-T ***
22359836-C-A 20197950-C-A DYZ19 ***
19753954-AT-A 17642074-AT-A P5_Prx 15×T***
22337584-T-A 20175698-T-A DYZ19 ***
13263676-TGCG-AGCT 11108000-TGCG-AGCT ***
13411367-G-A 11255691-G-A ***
13411377-G-A 11255701-G-A ***
23832825-TTT-C 21670939-TTT-C ***
22289674-C-A 20127788-C-A DYZ19 ***
13467703-A-C 11312027-A-C ***
58864160-C-G 56726711-G-C ***
22503555-G-A 20341669-G-A DYZ19 ***
58843776-G-T 56747095-C-A ***
58840436-T-C 56750435-A-G ***
2803245-G-A 2935204-G-A ***
3603568-G-T 3735527-G-T ***
22337373-G-A 20175487-G-A DYZ19 ***
20426961-A-T 18265075-A-T P5_Dst ***
13728354-C-A 11572678-C-A ***
15012545-G-A 12900633-G-A ***
16152183-T-A 14040303-T-A P8_Dst ***
17187458-C-A 15075578-C-A ***
19694857-C-G 17582977-C-G P5_Prx ***
19775300-G-A 17663420-G-A P5_Prx ***
19775302-C-T 17663422-C-T P5_Prx 32×T***
19903096-G-A 17791216-G-A P5_Prx ***
20402255-A-T 18240369-A-T P5_Dst ***
20402259-A-T 18240373-A-T P5_Dst ***
20425341-A-G 18263455-A-G P5_Dst ***
20425346-T-G 18263460-T-G P5_Dst ***
20426967-A-T 18265081-A-T P5_Dst ***
13728339-A-G 11572663-A-G ***
20677562-G-T 18515676-G-T P4_Prx ***
22099834-G-A 19937948-G-A ***
22232041-A-G 20070155-A-G DYZ19 ***
22267312-C-A 20105426-C-A DYZ19 ***
22267318-G-A 20105432-G-A DYZ19 ***
22273662-C-A 20111776-C-A DYZ19 ***
22292254-C-T 20130368-C-T DYZ19 ***
22292259-G-T 20130373-G-T DYZ19 ***
22292738-G-T 20130852-G-T DYZ19 ***
22332481-G-A 20170595-G-A DYZ19 ***
22337361-T-A 20175475-T-A DYZ19 ***
22337365-T-A 20175479-T-A DYZ19 ***
13728350-T-G 11572674-T-G ***
13716403-G-A 11560727-G-A ***
3902081-G-T 4034040-G-T ***
13106031-G-A 10595517-G-A ***
6478321-G-T 6610280-G-T ***
6577430-T-C 6709389-T-C ***
9301402-T-A 9463793-T-A ***
9301403-A-G 9463794-A-G ***
9302419-G-T 9464810-G-T ***
9342871-G-A 9505262-G-A ***
9665088-G-A 9827479-G-A IR3_Prx ***
10084327-G-A 10246718-G-A ***
10084364-C-T 10246755-C-T ***
10090669-T-C 10253060-T-C ***
10090685-T-A 10253076-T-A ***
13106020-C-G 10595506-C-G ***
13106034-A-G 10595520-A-G ***
13716391-T-A 11560715-T-A ***
13222693-G-A 11067017-G-A ***
13249822-A-G 11094146-A-G ***
13311819-C-A 11156143-C-A ***
13335581-G-A 11179905-G-A ***
13335587-C-A 11179911-C-A ***
13346379-G-C 11190703-G-C ***
13348352-A-G 11192676-A-G ***
13373806-A-T 11218130-A-T ***
13484502-G-C 11328826-G-C ***
13485341-A-T 11329665-A-T ***
13487498-C-T 11331822-C-T ***
13489659-C-T 11333983-C-T ***
13699762-T-A 11544086-T-A ***
59007435-T-TATTTTTA 56861288-T-TATTTTTA ***

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.

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