Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z41150 > DF90 > FGC14641 > S18462 > A11708 > BY4244

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
66616
BigY2
66616
26519229-G-A 24373082-G-A P1_Y1 A*
18315279-C-T 16203399-C-T P6_Prx A*
22272363-T-C 20110477-T-C BY215365 DYZ19 A*
24297789-C-T 22151642-C-T P3_t1 A*A*
19831240-A-T 17719360-A-T P5_Prx A*A*
20703924-C-T 18542038-C-T P4_Prx A*
22313458-T-A 20151572-T-A DYZ19 A*
18293926-G-A 16182046-G-A P6_Prx A*
22305461-G-T 20143575-G-T DYZ19 A*A*
19592514-T-C 17480634-T-C P5_Prx YA*
19772861-A-G 17660981-A-G P5_Prx A*
26209856-G-A 24063709-G-A P1_Y1 A*
25907396-G-C 23761249-G-C P1_Y1 A*
20640793-C-T 18478907-C-T P4_Prx A*
13711999-G-C 11556323-G-C BY192404 **+
17508704-C-T 15396824-C-T BY192683 YY++
17599597-T-C 15487717-T-C BY192685 YY++
8436968-T-C 8568927-T-C BY192509 YY++
18899373-T-C 16787493-T-C BY192720 YY++
19563588-C-A 17451708-C-A BY192745 Y++
19443555-C-G 17331675-C-G BY192739 YY++
17153214-C-G 15041334-C-G BY192667 YY++
8207747-C-A 8339706-C-A YY++
21175274-C-CA 19013388-C-CA 8×T++
21331347-C-T 19169461-C-T BY192761 YY++
21865334-C-T 19703448-C-T BY192777 YY++
17280678-G-A 15168798-G-A BY192671 YY++
7987219-A-T 8119178-A-T BY192486 YY++
16368518-T-A 14256638-T-A BY192644 YY++
4235942-A-G 4367901-A-G BY192431 ++
7682862-G-A 7814821-G-A BY192470 YY++
7525072-C-T 7657031-C-T BY192460 YY++
9092476-C-T 9254867-C-T BY192530 Y++
9142177-A-T 9304568-A-T BY192532 Y++
6646079-C-T 6778038-C-T FT137070 Y+**
6037778-G-A 6169737-G-A BY192433 ++
3160917-C-T 3292876-C-T BY192428 ++
7916386-A-G 8048345-A-G BY192483 YY++
2859642-A-C 2991601-A-C BY192427 YY++
13652242-G-C 11496566-G-C +**
13938966-C-T 11818260-C-T BY192553 Y++
14911752-G-A 12799819-G-A BY192592 YY++
15988804-T-C 13876924-T-C BY192631 YY++
16198587-C-T 14086707-C-T BY192635 YY++
11667961-A-G +**
8243161-A-C 8375120-A-C BY192499 YY++
22507408-G-T 20345522-G-T BY225346 DYZ19 +
8078233-G-A 8210192-G-A FT137550 Y+
4166891-C-T 4298850-C-T FT135916 +
3142022-C-T 3273981-C-T FT135405 +
3265100-C-T 3397059-C-T FT135457 +
6618690-A-G 6750649-A-G FT137060 Y+
28660076-A-G 26513929-A-G BY192845 ++
17259-T-G **+
6054345-A-T 6186304-A-T FT136920 +
3404915-C-T 3536874-C-T FT135515 +
3744321-T-C 3876280-T-C FT135683 +
4816521-C-G 4948480-C-G FT136261 +
4493948-T-C 4625907-T-C FT136073 +
22929194-A-G 20767308-A-G BY192808 YY++
3978449-T-A 4110408-T-A FT135808 +
28792091-A-T 26645944-A-T **
18277975-G-T 16166095-G-T P6_Prx 20×T**
10921788-C-A *
10951748-T-C **
13460413-C-A 11304737-C-A **
13372016-C-A 11216340-C-A **
10978705-C-T **
11010212-A-T **
11038149-CCACT-C **
11022777-T-C **
11033861-CA-C **
11033869-T-C **
10895714-A-C **
10877935-G-A FT73608 **
10887460-T-C **
7127962-A-AAAAT 7259921-A-AAAAT 4×AAAT**
8679357-A-C 8811316-A-C **
21771250-T-C 19609364-T-C **
19709752-G-T 17597872-G-T P5_Prx **
8739078-C-A 8871037-C-A **
13465846-T-C 11310170-T-C **
8901023-TTA-T 9032982-TTA-T **
8901018-T-A 9032977-T-A **
10625639-C-A **
10670990-C-G **
10887445-T-C **
10692521-CCAT-C **
10692536-C-G **
10793461-C-T **
10813925-T-C **
10825802-C-A **
10852726-C-A **
10877293-C-A **
10887390-C-T **
13571102-G-T 11415426-G-T **
14212300-A-G 12091594-A-G **
11652852-A-C **
20767601-A-T 18605715-A-T P4_Prx **
28773563-CT-C 26627416-CT-C **
19211615-C-A 17099735-C-A **
28565773-G-T 26419626-G-T **
19517852-C-A 17405972-C-A **
28505274-T-A 26359127-T-A **
28484787-A-C 26338640-A-C **
19872493-A-AG 17760613-A-AG P5_Prx **
20775129-ATG-A 18613243-ATG-A P4_Prx **
18165983-G-T 16054103-G-T **
26626579-CT-C 24480432-CT-C P1_g2 **
25606355-C-A 23460208-C-A P1_gr1 **
21575199-C-T 19413313-C-T **
21575251-TTGAG-T 19413365-TTGAG-T **
23276643-G-C 21114757-G-C **
23007737-G-T 20845851-G-T **
23007094-A-C 20845208-A-C **
18403214-C-A 16291334-C-A P6_Gap **
28798828-T-A 26652681-T-A **
11660197-A-G **
15406793-A-T 13294913-A-T **
13855002-G-T 11734296-G-T **
14432137-C-T 12311410-C-T **
12374820-G-T **
14649391-C-A 12537456-C-A **
14686078-TC-T 12574144-TC-T **
14715120-C-A 12603187-C-A **
14725177-G-A 12613245-G-A **
15631968-T-G 13520088-T-G **
56841604-G-T **
15732175-T-G 13620295-T-G **
15732285-C-T 13620405-C-T **
16319736-C-G 14207856-C-G **
20775193-G-T 18613307-G-T P4_Prx **
17006327-C-T 14894447-C-T **
17276163-A-C 15164283-A-C **
56883135-A-C **
17500820-G-A 15388940-G-A **
18080432-T-G 15968552-T-G **
58974193-T-G 56828046-T-G **
8673014-C-A 8804973-C-A **
13457694-TCCACTC-T 11302018-TCCACTC-T **
21042981-C-A 18881095-C-A **
19000142-C-A 16888262-C-A **
14531260-C-A 12419461-C-A **
7670837-C-A 7802796-C-A **
10887385-A-T **
22132915-C-A 19971029-C-A **
18733558-C-A 16621678-C-A **
10887400-C-T **
14422693-T-G 12301968-T-G **
28734890-C-A 26588743-C-A **
13457693-T-TG 11302017-T-TG **
19678423-G-T 17566543-G-T P5_Prx **
14077069-C-A 11956363-C-A **
15429752-C-A 13317872-C-A **
11014576-C-A **
14735166-C-A 12623234-C-A **
8080585-A-C 8212544-A-C **
4568460-G-T 4700419-G-T **
15696856-C-A 13584976-C-A **
21033581-C-A 18871695-C-A **
15222030-C-A 13110116-C-A **
11008759-A-T **
11008769-A-T **
3875874-C-A 4007833-C-A **
13485641-G-A 11329965-G-A **
4235658-C-A 4367617-C-A **
11028134-C-A **
15748800-C-A 13636920-C-A **
10849468-C-A **
28732942-G-T 26586795-G-T **
10935488-A-C **
11033868-T-C **
10852736-C-T **
11028115-T-C **
14036228-C-A 11915522-C-A **
2970085-C-A 3102044-C-A **
8160178-CAAAAAAAA-C 8292137-CAAAAAAAA-C 20×A**
19938632-A-C 17826752-A-C P5_Prx **
28764187-C-A 26618040-C-A **
13485614-A-T 11329938-A-T **
3439159-C-A 3571118-C-A **
6523747-C-A 6655706-C-A **
11020810-C-T **
28462252-G-T 26316105-G-T **
26328620-C-A 24182473-C-A P1_Y1 **
28101345-TTG-T 25955198-TTG-T P1_Y2 **
16090418-C-A 13978538-C-A **
13888605-G-T 11767899-G-T **
26273278-G-T 24127131-G-T P1_Y1 **
15323680-G-T 13211798-G-T **
3991780-C-A 4123739-C-A **
16429633-G-T 14317753-G-T **
17500585-G-T 15388705-G-T **
10977966-C-A **
22092790-C-A 19930904-C-A **
10013937-C-A 10176328-C-A **
13522965-T-G 11367289-T-G **
15542146-C-A 13430266-C-A **
5252833-ATTT-A 5384792-ATTT-A 16×T**
3328912-A-C 3460871-A-C **
3439186-T-A 3571145-T-A **
3633435-C-T 3765394-C-T **
4531389-C-A 4663348-C-A **
4538509-T-C 4670468-T-C **
4540733-C-A 4672692-C-A **
4628998-G-T 4760957-G-T **
4902975-G-T 5034934-G-T **
22303523-T-G 20141637-T-G DYZ19 **
5062792-A-T 5194751-A-T **
5249120-G-T 5381079-G-T **
5454714-T-A 5586673-T-A **
2785264-T-G 2917223-T-G **
5620287-T-C 5752246-T-C **
5644698-C-T 5776657-C-T **
5702620-CAAA-C 5834579-CAAA-C 25×A**
5817757-C-A 5949716-C-A **
5979213-G-T 6111172-G-T **
6092948-CTT-C 6224907-CTT-C 39×T**
6435174-C-T 6567133-C-T **
6575005-C-A 6706964-C-A **
6592269-C-A 6724228-C-A **
7201630-C-A 7333589-C-A 11×T**
7428128-C-A 7560087-C-A **
7436250-C-T 7568209-C-T **
2858904-T-C 2990863-T-C **
8679383-A-C 8811342-A-C **
2785254-T-G 2917213-T-G **
21476390-C-A 19314504-C-A **
6283109-T-G 6415068-T-G IR3_Dst **
5194678-G-T 5326637-G-T **
19686221-CTTT-C 17574341-CTTT-C P5_Prx 16×T**
6714666-C-A 6846625-C-A **
20645829-C-A 18483943-C-A P4_Prx **
23425330-C-A 21263444-C-A **
5586751-C-A 5718710-C-A **
18121862-C-A 16009982-C-A **
10692527-C-G **
27967276-GTATATA-G 25821129-GTATATA-G P1_Y2 9×TA**
11033879-T-A **
28621362-C-A 26475215-C-A **
2740414-C-A 2872373-C-A **
21512309-C-A 19350423-C-A **
11031433-C-A **
10887410-T-C **
6384596-G-T 6516555-G-T **
6516338-C-A 6648297-C-A **
18747000-C-T 16635120-C-T FT227193 ***
27967351-TATAT-T,TATAG 25821204-TATAT-T,TATAG P1_Y2 ***
11031491-C-A ***
10807280-T-C ***
10801001-A-G ***
17143891-ATTTTTTTTT-A,ATTTTT 15032011-ATTTTTTTTT-A,ATTTTT 35×T***
13463295-G-T 11307619-G-T ***
13405720-T-C 11250044-T-C ***
10682552-CATTCC-C,CATTCT ***
7706472-C-A 7838431-C-A ***
10686633-TT-T,TC ***
13811067-AGGAAT-A 11690361-AGGAAT-A 11×GGAAT******
13489519-A-G 11333843-A-G ***
21162703-C-A 19000817-C-A ***
7160894-C-CT,CTT 7292853-C-CT,CTT 16×T***
15380682-A-G 13268802-A-G ***
11643768-G-GGAAAC ***
13194505-C-A 11038829-C-A ***
22288252-G-T 20126366-G-T DYZ19 ******
15279206-GT-G,GTT 13167305-GT-G,GTT 13×T***
13842770-A-G 11722064-A-G ***
10925541-T-G ***
18816988-C-A 16705108-C-A ***
56836250-C-A ***
10764576-A-C ***
10989104-C-A,G ***
10796677-C-T ***
3804817-G-A 3936776-G-A ***
13466094-C-A 11310418-C-A ***
17118395-CTTT-C,CT 15006515-CTTT-C,CT 16×T***
13696601-A-G 11540925-A-G ***
4936053-CAAA-C,CAA 5068012-CAAA-C,CAA 26×A***
5784601-AA-A,AAT 5916560-AA-A,AAT ***
10925552-T-G ***

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: 66616983454980391037930597
Kit: 666161518821795135518380231
Used in age calculations1518821795135518380231
Counts of SNPs2723
Variant counts last updated 2020-11-24 02:48:00.



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