Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > DF49/S474 > Z2980 > Z2976 > DF23 > Z2961 > M222 > FGC4077 > FGC29480

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
22442273-G-T 20280387-G-T DYZ19 +
14094212-G-A 11973506-G-A FGC29485 YY+
18385043-T-A 16273163-T-A FGC29494 P6_Gap +
17878871-C-G 15766991-C-G FGC29493 YY+
17877064-T-C 15765184-T-C FGC29492 YY+
22469034-C-T 20307148-C-T FGC29499 DYZ19 +
22483798-T-C 20321912-T-C DYZ19 +
17409683-C-T 15297803-C-T FGC29491 YY+
16811788-C-T 14699908-C-T FGC29490 YY+
22540165-C-A 20378279-C-A FGC29500 Y+
23130599-A-G 20968713-A-G FGC29501 YY+
16020293-G-T 13908413-G-T FGC29489 YY+
14977707-T-C 12865782-T-C FGC29487 YY+
2747791-A-G 2879750-A-G YY+
19012050-A-G 16900170-A-G FGC29497 YY+
18748146-G-A 16636266-G-A FGC29495 YY+
8576561-A-G 8708520-A-G FGC29482 YY+
8756371-A-C 8888330-A-C FGC29483 YY+
3161278-C-CA 3293237-C-CA +
6362412-C-T 6494371-C-T FGC29479 +
7421899-C-A 7553858-C-A FGC29481 YY+
9122602-A-T 9284993-A-T FGC29484 Y+
13801267-C-A 11680561-C-A **
23114014-A-T 20952128-A-T PF1242 22×AT**
13203958-C-G 11048282-C-G **
26242506-G-A 24096359-G-A FGC29504 P1_Y1 **
14977328-C-A 12865403-C-A **
13821139-G-C 11700433-G-C ***
13821114-G-A 11700408-G-A ***
13729189-G-T 11573513-G-T ***
13701322-TGGAAG-C 11545646-TGGAAG-C ***
13729188-G-T 11573512-G-T ***
13833441-G-C 11712735-G-C ***
13706086-ATGGCG-A 11550410-ATGGCG-A ***
13448871-C-T 11293195-C-T ***
13674253-GTAAAGGAAA-G 11518577-GTAAAGGAAA-G ***
13457888-G-T 11302212-G-T ***
2971041-G-A 3103000-G-A ***
9292826-T-C 9455217-T-C ***
9745922-G-C 9908313-G-C ***
9983012-A-C 10145403-A-C ***
9983014-G-A 10145405-G-A ***
10016099-CGTC-C,TTCT 10178490-CGTC-C,TTCT ***
10024193-T-C 10186584-T-C ***
13454917-CACTTGTTG-C 11299241-CACTTGTTG-C ***
13459158-T-C 11303482-T-C ***
13480635-CT-C,CC 11324959-CT-C,CC ***
13483112-T-C 11327436-T-C ***
13483143-G-A 11327467-G-A ***
13483157-T-A 11327481-T-A ***
13483158-A-G 11327482-A-G ***
13483181-C-A 11327505-C-A ***
13483184-G-T 11327508-G-T ***
13483185-A-T 11327509-A-T ***
13833862-G-GAATGC 11713156-G-GAATGC ***
14429405-T-TTA,TTATA 12308680-T-TTATA,TTATATA 15×TA***
28802496-G-C 26656349-G-C ***
24982110-C-A 22835963-C-A g1 ***
25094919-G-A 22948772-G-A g1 ***
25381403-C-CT 23235256-C-CT P2_r2 12×T***
25874666-C-G 23728519-C-G P1_Y1 ***
26248367-TTCTC-T 24102220-TTCTC-T P1_Y1 15×TC***
26728677-G-A 24582530-G-A P1_g2 ***
58972846-A-AG,T 56826699-A-AG,T ***
24281887-G-A 22135740-G-A P3_t1 ***
58975919-A-T 56829772-A-T ***
13451105-A-C,T 11295429-A-C,T ***
13686911-ACGAAT-A 11531235-ACGAAT-A ***
13839755-CTAATGGAATG-C 11719049-CTAATGGAATG-C ***
13461120-C-CA 11305444-C-CA ***
59004623-GGAAA-A,G 56858476-GGAAA-A,G 16×GAAA***
13680939-A-C,T 11525263-A-C,T ***
24912188-T-C 22766041-T-C g1 ***
24281369-G-A 22135222-G-A P3_t1 ***
13858562-A-T 11737856-A-T ***
17441175-AAT-A,AA 15329295-AAT-A,AA 20×AT***
13858589-GCAAGT-A,G 11737883-GCAAGT-A,G ***
13858611-A-C 11737905-A-C ***
13865709-G-A 11745003-G-A ***
13878588-GA-G,GAA 11757882-GA-G,GAA 11×A***
13940139-T-A 11819433-T-A ***
13940145-A-C 11819439-A-C ***
22502933-T-A 20341047-T-A DYZ19 ***
22241565-T-C 20079679-T-C DYZ19 ***
22271942-C-A 20110056-C-A DYZ19 ***
22299871-G-T 20137985-G-T KRO2 BY34562 DYZ19 ***
22339905-A-T 20178019-A-T DYZ19 ***
22358475-G-A 20196589-G-A DYZ19 ***
22502916-G-A 20341030-G-A DYZ19 ***
2971040-T-G 3102999-T-G ***
58908894-CCATTCCATTG-C 56681957-GAATGGAATGC-G ***
13652181-TGGAAC-T 11496505-TGGAAC-T ***
58972889-C-G 56826742-C-G ***
58975938-C-T 56829791-C-T ***
28786771-A-G 26640624-A-G ***
9745916-T-C 9908307-T-C ***
10032108-G-A 10194499-G-A ***
13818648-T-G 11697942-T-G ***
13818655-G-A 11697949-G-A ***
13858431-C-A 11737725-C-A ***
28786611-A-G 26640464-A-G ***
13869227-A-T 11748521-A-T ***
58975920-T-C 56829773-T-C ***
24118042-A-AT 21971895-A-AT P3_b1 15×T***
13674248-A-T 11518572-A-T ***
13680926-G-A 11525250-G-A ***
13801558-C-A 11680852-C-A ***
13817996-A-T 11697290-A-T ***
13862203-A-C 11741497-A-C ***
13452670-T-C 11296994-T-C ***
13651473-G-C 11495797-G-C ***
13702819-G-A 11547143-G-A ***
58975930-C-G 56829783-C-G ***
13847345-G-A 11726639-G-A ***
13447736-T-A 11292060-T-A ***
9745913-G-C 9908304-G-C ***
13801226-A-G 11680520-A-G ***
22504295-C-G 20342409-C-G DYZ19 ***
3279734-T-TAAAC 3411693-T-TAAAC ***
13452975-A-T 11297299-A-T ***
13664816-A-G 11509140-A-G ***
13804755-T-A 11684049-T-A ***
13821105-G-A 11700399-G-A ***
13821236-A-T 11700530-A-T ***
13457505-G-T 11301829-G-T ***
13858597-C-A 11737891-C-A ***
13686953-G-A 11531277-G-A ***
13869108-T-C 11748402-T-C A8862 ***
24990474-C-CT 22844327-C-CT g1 15×T***
13813519-T-A 11692813-T-A ***
18378988-G-T 16267108-G-T P6_Prx ***
18378989-C-T 16267109-C-T P6_Prx ***
13480683-G-A 11325007-G-A ***
13817886-G-T 11697180-G-T ***
13858467-A-G 11737761-A-G ***
13447742-T-C 11292066-T-C ***
13861633-T-C 11740927-T-C ***
13452823-C-T 11297147-C-T ***
13461124-G-C 11305448-G-C ***
13674228-G-A 11518552-G-A ***
13674236-A-T 11518560-A-T ***
13842241-A-T 11721535-A-T ***
13452776-A-C 11297100-A-C ***
13452777-T-A 11297101-T-A ***
10017739-C-T 10180130-C-T ***
13821119-G-T 11700413-G-T ***
13447306-A-G 11291630-A-G ***
5471888-A-G 5603847-A-G ***
13674243-A-G 11518567-A-G ***
22502437-A-G 20340551-A-G DYZ19 ***
58977773-T-C 56831626-T-C ***
58980266-A-T 56834119-A-T ***
13461120-C-T 11305444-C-T ***
22275103-G-A 20113217-G-A BY1922 DYZ19 ***
13680840-G-C 11525164-G-C ***
13810111-A-T 11689405-A-T ***
13845590-G-C 11724884-G-C ***
13845591-G-A 11724885-G-A ***
13674225-A-G 11518549-A-G ***
21023249-GT-G 18861363-GT-G P4_Dst 14×T***
13866042-A-G 11745336-A-G ***
13143779-C-T 10633265-C-T ***
13447312-C-T 11291636-C-T ***
13680800-A-G,T 11525124-A-G,T ***
13801557-T-A 11680851-T-A ***
13817520-A-G 11696814-A-G ***
13818023-G-A 11697317-G-A ***
13456165-A-T 11300489-A-T ***
19809599-CA-C 17697719-CA-C P5_Prx 10×A***
13483228-C-G,T 11327552-C-G,T ***
13454233-A-T 11298557-A-T ***
13801221-A-T 11680515-A-T ***
13805306-A-C,T 11684600-A-C,T ***
58819408-C-G 56771463-G-C ***
27810333-G-A 25664186-G-A P1_Y2 ***
19966688-A-AAAGAAG 17854808-A-AAAGAAG P5_Prx 26×AAG***
13452815-A-C,T 11297139-A-C,T ***
13141382-CCCCAA-T 10630868-CCCCAA-T ***
13447710-A-G 11292034-A-G ***
19645682-C-CT 17533802-C-CT P5_Prx 14×T***
13680945-C-G 11525269-C-G ***
58981759-T-C,TGATTC 56835612-T-C,TGATTC ***

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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