Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > BY3332

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
361579
3898737-G-C 4030696-G-C A+
28024685-A-G 25878538-A-G P1_Y2 A+
26389930-G-A 24243783-G-A P1_Y1 A+
25937690-T-C 23791543-T-C P1_Y1 A+
58976349-A-C 56830202-A-C A*
22304558-C-G 20142672-C-G DYZ19 A*
19733361-G-A 17621481-G-A P5_Prx A*
19735813-G-T 17623933-G-T P5_Prx A*
19789356-A-G 17677476-A-G P5_Prx A*
19847022-T-C 17735142-T-C P5_Prx A*
20015544-A-G 17903664-A-G P5_Prx A*
56827268-A-G A*
13687664-A-G 11531988-A-G A*
13448296-A-T 11292620-A-T A*
13687467-G-C 11531791-G-C A*
56846837-C-T A*
10868980-T-C A*
13451650-A-AG 11295974-A-AG A*
19635543-C-T 17523663-C-T P5_Prx A*
14994941-T-A 12883026-T-A BY98963 YY+
14263805-C-T 12143099-C-T BY94411 YY+
14233842-G-A 12113136-G-A BY54604 YY+
6347818-A-G 6479777-A-G A9040BY53560 +
15015065-T-A 12903153-T-A BY99103 YY+
15064411-G-A 12952503-G-A BY99522 YY+
13846006-G-A 11725300-G-A BY91289 +
13925569-A-C 11804863-A-C FT239460 Y+
15709350-G-A 13597470-G-A FT239770 YY+
13818102-G-A 11697396-G-A FT239422 +
13811801-TGGAATGGAATCGAATGGAATGGAGTCAAAA-T 11691095-TGGAATGGAATCGAATGGAATGGAGTCAAAA-T +
11670657-C-A FT451169 +
13650243-G-A 11494567-G-A BY87037 +
13542682-A-T 11387006-A-T BY86388 +
13214665-G-T 11058989-G-T +
15386249-G-T 13274369-G-T FT239720 YY+
19430263-T-C 17318383-T-C BY128991 YY+
16186711-A-C 14074831-A-C FT2995 Y+
21258495-G-T 19096609-G-T BY131506 YY+
28593855-A-G 26447708-A-G FT240897 +
28556146-G-GTACC 26409999-G-GTACC +
24475355-C-T 22329208-C-T FT240863 Y+
23861582-G-A 21699696-G-A BY148497 Y+
22528995-G-A 20367109-G-A FT240640 Y+
22445464-T-A 20283578-T-A BY219630 DYZ19 +
21894072-G-T 19732186-G-T YY+
21297756-A-G 19135870-A-G FT240449 YY+
21122062-C-T 18960176-C-T FT240420 Y+
17022352-A-T 14910472-A-T FT239973 YY+
21073645-T-C 18911759-T-C BY130252 YY+
19462450-G-T 17350570-G-T FT240384 Y+
10956411-T-C +
18983737-T-C 16871857-T-C BY125259 YY+
18253653-C-T 16141773-C-T BY121217 Y+
18088904-T-C 15977024-T-C FT240182 Y+
17131039-C-G 15019159-C-G BY112508 YY+
17088017-G-A 14976137-G-A FT239979 Y+
13214658-C-T 11058982-C-T +
13965264-C-A 11844558-C-A FT239469 Y+
4999559-T-C 5131518-T-C FT238661 +
5977169-G-T 6109128-G-T FT238864 +
4076542-A-G 4208501-A-G FT238497 +
10962882-C-A FT438370 +
4068669-A-T 4200628-A-T FT238496 +
3726567-C-T 3858526-C-T FT238427 +
3093205-GCAAAA-T 3225164-GCAAAA-T +
17158968-CTTTTTTTTTT-C 15047088-CTTTTTTTTTT-C 26×T+
4790328-C-T 4922287-C-T FT238624 +
6656452-C-T 6788411-C-T BY60559 YY+
6773370-G-A 6905329-G-A FT238977 Y+
4999998-A-C 5131957-A-C BY58502 +
7606841-A-G 7738800-A-G BY66238 YY+
7652539-T-C 7784498-T-C BY66563 YY+
2962990-T-C 3094949-T-C FT238282 +
8185927-T-C 8317886-T-C BY70534 YY+
8357323-C-T 8489282-C-T BY71946 YY+
17003352-G-A 14891472-G-A FGC1058FGC1058 YY+
2681341-G-C 2813300-G-C BY55777 YY+
8842184-G-A 8974143-G-A BY76284 YY+
9141506-G-T 9303897-G-T BY78451 Y+
9377794-C-G 9540185-C-G BY78929 Y+
10828925-C-A FT433053 +
22257809-T-C 20095923-T-C DYZ19 *
11018773-TCTCCACTCCA-T,TCTCCA *
10898332-CCACACCACTC-C,CCACTCCACTG *
16739273-T-TG 14627393-T-TG *
3718160-G-T 3850119-G-T *
3013661-A-C 3145620-A-C *
10672091-C-G *
22299036-C-T 20137150-C-T DYZ19 *
8465934-T-TTGTG 8597893-T-TTGTG 20×TG*
56832066-CCCACTCCA-C *
3006196-G-T 3138155-G-T *
22275108-G-T 20113222-G-T DYZ19 *
14286784-CTTTTTTTT-C,CT 12166078-CTTTTTTTT-C,CT 22×T*
16973346-G-T 14861466-G-T **
26228689-C-CTT 24082542-C-CTT P1_Y1 27×T**
23289213-G-A 21127327-G-A **
22239230-T-C 20077344-T-C BY49256 DYZ19 **
23289215-G-A 21127329-G-A **
21746812-C-T 19584926-C-T **
7280950-TC-T 7412909-TC-T **
21789639-C-T 19627753-C-T **
27593063-G-A 25446916-G-A P1_Y2 **
22271259-T-A 20109373-T-A BY215157 DYZ19 **
9337-C-T **
22269538-C-T 20107652-C-T DYZ19 **
18892196-A-G 16780316-A-G **
9340-C-A **
4428347-A-G 4560306-A-G **
14161303-A-G 12040597-A-G **
15931853-G-A 13819973-G-A FT204724 **
15959336-C-A 13847456-C-A **
16101996-C-CTTTT 13990116-C-CTTTT P8_Prx 19×T**
6459788-A-T 6591747-A-T **
7008252-A-G 7140211-A-G **
16422268-G-A 14310388-G-A **
3941045-A-T 4073004-A-T **
8062863-C-T 8194822-C-T **
8556351-C-A 8688310-C-A **
13640454-C-T 11484778-C-T **
28566048-TTA-T 26419901-TTA-T ***
28814828-C-T 26668681-C-T ***
13455773-C-T 11300097-C-T ***
14178595-A-G 12057889-A-G ***
6494984-C-T 6626943-C-T FT395292 ***
23802229-A-G 21640343-A-G ***
23289221-G-A 21127335-G-A ***
23289220-G-A 21127334-G-A ***
56841368-T-C ***
14342024-G-T 12221319-G-T ***
14673654-T-C 12561720-T-C ***
14682825-G-A 12570891-G-A ***
6405898-G-A 6537857-G-A ***
22302812-T-C 20140926-T-C DYZ19 ***
14682839-G-A 12570905-G-A ***
22274884-T-G 20112998-T-G DYZ19 ***
5231216-C-T 5363175-C-T ***
15059802-C-A 12947894-C-A ***
21887993-A-G 19726107-A-G ***
18875228-C-A 16763348-C-A ***
22551603-TAGTATA-T 20389717-TAGTATA-T ***
3628709-GAAA-G 3760668-GAAA-G 26×A***
7671341-CA-C 7803300-CA-C ***
13463834-A-C 11308158-A-C ***
14682827-G-A 12570893-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: 3615791060000077000007800000
Used in age calculations1494220993793008303022
Counts of SNPs3327
Variant counts last updated 2021-12-29 04:00:48.



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