Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > ZZ10 > Z253 > BY4086 > FGC17436 > Z17693 > FGC73657 > A505

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
4326739-G-A 4458698-G-A A+
19682983-C-T 17571103-C-T P5_Prx A+
6417359-A-G 6549318-A-G A*
13449728-C-G 11294052-C-G A*
58977176-T-C 56831029-T-C A*
28816688-G-T 26670541-G-T A*
13695465-T-A 11539789-T-A A*
56836032-C-T A*
28817183-A-T 26671036-A-T A*
56833678-C-CA A*
6431332-A-C 6563291-A-C A*
56834167-A-G A*
13450927-A-T 11295251-A-T A*
56836889-C-T A*
19865016-T-G 17753136-T-G P5_Prx A*
6170654-T-A 6302613-T-A IR3_Dst A*
6262193-C-G 6394152-C-G IR3_Dst A*
6324844-T-C 6456803-T-C IR3_Dst A*
13449940-C-A 11294264-C-A A*
19578936-C-A 17467056-C-A P5_Prx YA*
19810775-G-A 17698895-G-A P5_Prx A*
19875317-G-A 17763437-G-A P5_Prx A*
19925001-G-A 17813121-G-A P5_Prx A*
20785275-G-GT 18623389-G-GT P4_Prx A*
26142164-A-G 23996017-A-G P1_Y1 A*
26234108-T-C 24087961-T-C P1_Y1 A*
26403257-C-A 24257110-C-A P1_Y1 A*
26491442-G-T 24345295-G-T P1_Y1 A*
26496044-C-T 24349897-C-T P1_Y1 A*
56831061-C-G A*
3159117-G-A 3291076-G-A BY184431 FGC24833 +
17165252-G-C 15053372-G-C FT405771 YY+
15711064-G-A 13599184-G-A FGC73159 YY+
16364368-T-C 14252488-T-C CTS4861BY187423 YY+
3153545-C-G 3285504-C-G FT404411 +
3164588-A-C 3296547-A-C FT404412 +
3261971-T-C 3393930-T-C FT404426 +
4168527-A-G 4300486-A-G FT404560 +
5049139-G-C 5181098-G-C FT404692 +
6667815-T-G 6799774-T-G FT404891 YY+
6905070-T-G 7037029-T-G FT404924 YY+
7740527-C-T 7872486-C-T FT405039 YY+
7845481-A-G 7977440-A-G FT405054 YY+
8073902-G-A 8205861-G-A FT405078 Y+
8502868-C-T 8634827-C-T FT405148 YY+
8645897-T-C 8777856-T-C FT405181 YY+
8885974-G-T 9017933-G-T FT405217 Y+
9166654-A-T 9329045-A-T FT405253 Y+
9833788-A-G 9996179-A-G FT405287 YY+
13327678-C-G 11172002-C-G FT442951 +
13938366-A-G 11817660-A-G FT405331 Y+
14390390-C-T 12269686-C-T FT405422 Y+
14901191-G-A 12789258-G-A YY+
15066136-C-T 12954228-C-T FT405498 Y+
15975675-T-A 13863795-T-A FT405609 YY+
16003140-C-T 13891260-C-T FT1911 Y+
16004278-T-C 13892398-T-C FT405614 Y+
16678923-G-A 14567043-G-A FT405702 YY+
16797898-G-A 14686018-G-A FT405721 YY+
17146084-G-T 15034204-G-T FT405769 YY+
17273912-T-C 15162032-T-C FT405781 YY+
17405343-A-G 15293463-A-G FT405810 YY+
17407712-C-T 15295832-C-T FT405811 YY+
17506651-T-C 15394771-T-C FT30553 YY+
17731615-C-T 15619735-C-T FT405850 Y+
18826388-G-A 16714508-G-A FT405993 YY+
18958091-T-C 16846211-T-C FT452177 YY+
18979315-C-T 16867435-C-T FT406022 YY+
19221031-C-T 17109151-C-T YY+
21321712-A-G 19159826-A-G FT406166 Y+
21517689-C-T 19355803-C-T FT406201 YY+
21803143-C-T 19641257-C-T FT406240 Y+
22271139-G-C 20109253-G-C FT454274 DYZ19 +
22461563-G-C 20299677-G-C FT457801 DYZ19 +
22510067-C-A 20348181-C-A FT460737 DYZ19 +
22963743-G-T 20801857-G-T FT406366 YY+
23742127-G-A 21580241-G-A FT406462 +
23825851-C-A 21663965-C-A FT406473 Y+
24408207-G-C 22262060-G-C FT406492 +
24426240-AT-A 22280093-AT-A 9×T+
28720685-C-T 26574538-C-T FT406544 +
18580-T-C +
13868409-C-CGGAAT 11747703-C-CGGAAT 10×GGAAT*
10769852-GTTCCA-G *
4964479-C-CGTGT 5096438-C-CGTGT 19×GT*
10754717-C-CTCCAT *
10781037-T-TATTCCATTCC *
22300431-T-C 20138545-T-C DYZ19 *
28792218-T-C 26646071-T-C *
22484614-G-A 20322728-G-A DYZ19 **
22271935-G-A 20110049-G-A DYZ19 **
22484606-G-A 20322720-G-A BY51541 DYZ19 **
22183095-C-T 20021209-C-T **
22271926-G-A 20110040-G-A BY21446 DYZ19 **
3628709-GAAAAAAAAA-G 3760668-GAAAAAAAAA-G 26×A**
13624011-G-T 11468335-G-T **
15795755-T-C 13683875-T-C **
15803640-G-A 13691760-G-A **
16067474-CA-C 13955594-CA-C **
17627928-C-G 15516048-C-G **
18975959-T-C 16864079-T-C **
20067086-T-C 17955206-T-C P5_Dst **
22271912-T-A 20110026-T-A BY21445 DYZ19 **
22271938-A-G 20110052-A-G DYZ19 **
22465047-G-A 20303161-G-A DYZ19 **
22484590-G-C 20322704-G-C DYZ19 **
22484599-T-C 20322713-T-C DYZ19 **
23019043-T-C 20857157-T-C **
26130188-G-T 23984041-G-T P1_Y1 **
19036703-GTT-G 16924823-GTT-G 40×T***
3331462-AAT-A 3463421-AAT-A 8×AT***
13457815-C-T 11302139-C-T ***
7103038-TACAC-T 7234997-TACAC-T 17×AC***
13457780-C-T 11302104-C-T ***
9508531-CTTTT-C 9670922-CTTTT-C 25×T***
9013257-C-CAA 9175648-C-CAA 18×A***
16598984-CAAAA-C 14487104-CAAAA-C 25×A***
13930171-CAAAAAA-C 11809465-CAAAAAA-C 21×A***
7363157-TA-T,TAA 7495116-TA-T,TAA 18×A***
5493431-CTTT-C 5625390-CTTT-C 24×T***
8379577-CTGTGTG-C,CTG 8511536-CTGTGTG-C,CTG 18×TG***
3271601-CTT-C,CTTTT 3403560-CTT-C,CTTTT 14×T***
3558246-TAA-T,TA 3690205-TAA-T,TA 16×A***
4076256-C-CAAA 4208215-C-CAAA 21×A***
4787959-A-G 4919918-A-G ***
6821765-G-A 6953724-G-A ***
13394427-G-T 11238751-G-T ***
13588533-T-C 11432857-T-C ***
14101064-A-G 11980358-A-G ***
15477760-T-C 13365880-T-C ***
19204123-A-T 17092243-A-T ***
22001683-C-T 19839797-C-T ***
22551673-TTA-T 20389787-TTA-T ***

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.