Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > DF21/S192 > S5488

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
4005957-A-AT 4137916-A-AT 12×TA*
8662707-T-TA 8794666-T-TA L1/S26 10×AA*
19798785-C-A 17686905-C-A P5_Prx A*
28796403-G-A 26650256-G-A A*
4803315-C-CT 4935274-C-CT 13×TA*
20724340-C-T 18562454-C-T P4_Prx A*
5434294-G-A 5566253-G-A A*
23175619-G-T 21013733-G-T YA*
3509015-T-A 3640974-T-A A*
22291261-T-A 20129375-T-A DYZ19 A*
6291804-G-C 6423763-G-C IR3_Dst A*
3509031-T-G 3640990-T-G A*
3509030-G-A 3640989-G-A A*
26366276-G-C 24220129-G-C P1_Y1 A*
7339420-G-A 7471379-G-A YY+
7078936-C-T 7210895-C-T FT36406 YY+
7833150-T-C 7965109-T-C FT36525 YY+
7940964-G-T 8072923-G-T FT36537 YY+
7378356-T-C 7510315-T-C YY+
6404315-C-T 6536274-C-T FT36304 +
6850952-C-T 6982911-C-T FT36375 YY+
6792269-T-G 6924228-T-G FT36368 YY+
6630748-C-T 6762707-C-T FT36345 YY+
8356327-C-T 8488286-C-T FT36584 YY+
5601908-T-C 5733867-T-C FT36183 +
5323284-A-G 5455243-A-G FT36120 +
4877921-T-G 5009880-T-G FT36010 +
4754292-T-TG 4886251-T-TG +
4734605-C-A 4866564-C-A FT35979 +
8207637-T-G 8339596-T-G FT36567 YY+
10022863-G-A 10185254-G-A Y+
8788382-T-C 8920341-T-C FT36631 YY+
15634424-T-C 13522544-T-C FT36996 YY+
17414474-C-G 15302594-C-G YY+
17049710-C-T 14937830-C-T FT37199 YY+
16757295-A-T 14645415-A-T FT37151 YY+
19207474-G-A 17095594-G-A FT37506 YY+
16496166-C-T 14384286-C-T BY108211 YY+
16436565-G-A 14324685-G-A FT37099 YY+
16392115-C-T 14280235-C-T FT37091 YY+
16071693-G-C 13959813-G-C FT37058 Y+
15340886-T-C 13229005-T-C FT36952 YY+
8817911-G-T 8949870-G-T FT36636 YY+
19237040-T-C 17125160-T-C FT37513 YY+
15248524-A-AT 13136610-A-AT +
14720623-T-TG 12608691-T-TG +
14288202-C-A 12167496-C-A FT36820 YY+
13666515-G-A 11510839-G-A +
10847708-G-A +
9647072-G-A 9809463-G-A FT36689 IR3_Prx +
9142256-G-A 9304647-G-A Y+
19119494-C-T 17007614-C-T FT37494 YY+
4713856-A-C 4845815-A-C FT35968 +
4366108-C-A 4498067-C-A FT35913 +
14264291-G-A 12143585-G-A FGC63373 YY+
28470598-C-A 26324451-C-A +
4380192-T-C 4512151-T-C FT35917 +
17534376-G-T 15422496-G-T PH3160 YY12×T+
28788076-T-A 26641929-T-A +
24391671-A-G 22245524-A-G FT37963 Y+
23546427-C-T 21384541-C-T FT37919 YY+
23249414-G-A 21087528-G-A FT37883 YY+
23233211-G-C 21071325-G-C FT37880 Y+
21090150-C-T 18928264-C-T YY+
22990666-G-T 20828780-G-T FT37841 Y+
22831703-C-T 20669817-C-T YY+
10870824-CTCCAT-C +
18021860-T-A 15909980-T-A FT37348 Y+
21814035-A-G 19652149-A-G FT37702 YY+
2710753-A-G 2842712-A-G FT35595 YY+
2663375-C-T 2795334-C-T FT35590 YY+
21519511-CTT-A 19357625-CTT-A +
22300011-T-C 20138125-T-C DYZ19 *
3477851-GGTGT-G 3609810-GGTGT-G 17×GT*
13447474-G-T 11291798-G-T *
28790867-T-C 26644720-T-C *
15698757-G-GAC 13586877-G-GAC 24×AC*
10761260-TTTCCATTCCA-T *
8377909-TACAC-T 8509868-TACAC-T 16×AC*
10849819-T-TCATTC *
22279207-GT-G 20117321-GT-G DYZ19 *
10990086-TACTCC-T *
18067401-TAGAAAGAA-T 15955521-TAGAAAGAA-T 15×AGAA*
56871623-T-TA 9×A*
13820775-T-TATGGA 11700069-T-TATGGA 11×ATGGA*
17180153-A-AACAC 15068273-A-AACAC 23×AC*
5308799-T-G 5440758-T-G 19×AG**
3630979-T-C 3762938-T-C **
17081305-A-T 14969425-A-T **
20676268-G-T 18514382-G-T P4_Prx **
21745900-C-A 19584014-C-A **
26101856-C-A 23955709-C-A P1_Y1 **
13467993-T-G 11312317-T-G **
19692692-T-G 17580812-T-G P5_Prx **
20676213-C-A 18514327-C-A P4_Prx **
19906893-A-G 17795013-A-G P5_Prx **
13467963-T-C 11312287-T-C **
13466191-A-C 11310515-A-C **
13347944-C-T 11192268-C-T **
13337058-TG-T 11181382-TG-T **
26416274-CA-C 24270127-CA-C P1_Y1 24×A**
9917783-G-A 10080174-G-A **
22269421-T-C 20107535-T-C DYZ19 **
22461325-A-T 20299439-A-T DYZ19 **
13407141-CT-C 11251465-CT-C 13×T**
56685536-C-G 4×AATGG**
9160320-A-AAC 9322711-A-AAC 17×AC***
16531083-CAAA-C,CAAAA 14419203-CAAA-C,CAAAA 24×A***
4067369-TAAA-T 4199328-TAAA-T 26×A***
23825773-A-T 21663887-A-T A13801 11×AT***
26477922-AAC-A 24331775-AAC-A P1_Y1 14×AC***
6401942-A-G 6533901-A-G ***
18817019-C-CTAAA 16705139-C-CTAAA 10×TAAA***
13465914-T-A 11310238-T-A ***
4630151-TTGTG-T 4762110-TTGTG-T 18×TG***
13447123-ATTCCATTC-A 11291447-ATTCCATTC-A ***
28526659-T-TA 26380512-T-TA 12×A***
10744298-A-C ***
10744305-T-A ***
10744287-CA-T ***
13480445-C-A 11324769-C-A ***
15296963-CA-C 13185062-CA-C ***
10776407-T-C ***
2856782-CTTTTT-C 2988741-CTTTTT-C 24×T***
16723259-C-CT 14611379-C-CT 11×T***
3270924-ATT-A,AT 3402883-ATT-A,AT 25×T***
4082712-C-T 4214671-C-T ***
4082732-C-T 4214691-C-T ***
4424377-GTTT-G 4556336-GTTT-G 18×T***
5088451-CT-C,CTT 5220410-CT-C,CTT 27×T***
5904031-CAAAAAAA-C 6035990-CAAAAAAA-C 27×A***
7643558-GA-G 7775517-GA-G ***
14088301-A-G 11967595-A-G ***
14835327-ATT-A,AT 12723394-ATT-A,AT 14×T***
56879484-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)

Kit: N2078271516804595081288376544
Used in age calculations1516804595081288376544
Counts of SNPs3935
Variant counts last updated 2019-07-03 01:26:17.

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