Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13

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
58979700-C-T 56833553-C-T A*
13449466-T-A 11293790-T-A A*
6328463-A-G 6460422-A-G IR3_Dst A*
13687524-A-G 11531848-A-G A*
19623095-A-T 17511215-A-T P5_Prx A*
19814193-G-A 17702313-G-A P5_Prx A*
19901630-T-G 17789750-T-G P5_Prx A*
19933260-G-A 17821380-G-A P5_Prx A*
20722990-T-A 18561104-T-A P4_Prx A*
20791434-A-C 18629548-A-C P4_Prx A*
20921184-A-T 18759298-A-T P4_Dst A*
22305313-A-G 20143427-A-G DYZ19 A*
22438392-C-T 20276506-C-T DYZ19 A*
26170242-G-A 24024095-G-A P1_Y1 A*
26397262-C-G 24251115-C-G P1_Y1 A*
26524217-G-T 24378070-G-T P1_Y1 A*
21216619-TCA-T 19054733-TCA-T +
21925513-TA-T 19763627-TA-T +
3109923-C-G 3241882-C-G FT191321FT90816 +
2774140-G-A 2906099-G-A FT287223 YY+
3234177-A-G 3366136-A-G FT287279 +
3622603-T-C 3754562-T-C FT238402 +
3693861-A-C 3825820-A-C FT287341 +
4301318-A-G 4433277-A-G FT238545 +
4876550-C-G 5008509-C-G FT238640 +
4968222-G-A 5100181-G-A FT238653 +
5025315-G-A 5157274-G-A FT287508 +
5151186-T-C 5283145-T-C FT287527 +
5170818-G-A 5302777-G-A FT287530 +
5252616-A-T 5384575-A-T FT287540 +
5495119-C-T 5627078-C-T FT287568 +
5849939-A-G 5981898-A-G FT238836 +
5946610-A-T 6078569-A-T FT100813 +
6379016-G-A 6510975-G-A FT287651 +
7367279-C-A 7499238-C-A FT287737 YY+
7377386-C-T 7509345-C-T FT287741 YY+
7379246-G-A 7511205-G-A FT287743 Y+
8196249-T-G 8328208-T-G FT287833 YY+
8872275-T-C 9004234-T-C FT287924 Y+
9070576-G-C 9232967-G-C FT287940 Y+
9484698-G-A 9647089-G-A BY79806 +
9841545-T-C 10003936-T-C BY81355 YY+
10093082-T-C 10255473-T-C FT292848 +
14117282-G-T 11996576-G-T YY+
14689471-C-T 12577537-C-T FT288153 Y+
14854608-CA-C 12742674-CA-C +
14880362-G-A 12768432-G-A BY197279 YY+
15746288-C-T 13634408-C-T FT288264 Y+
16315179-T-C 14203299-T-C FT288325 YY+
16458512-G-A 14346632-G-A BY107969 YY+
16646697-A-G 14534817-A-G FT288374 YY+
16670340-G-A 14558460-G-A YY+
17048922-C-T 14937042-C-T BY112006 YY+
17130892-G-A 15019012-G-A FT288420 YY+
17477321-G-A 15365441-G-A BY115093 YY+
17500711-G-A 15388831-G-A FT288474 Y+
17581405-A-G 15469525-A-G YY+
17586978-T-A 15475098-T-A FT288484 YY+
17831359-A-G 15719479-A-G FT288515 YY+
17976293-A-G 15864413-A-G BY118875 Y+
18405372-A-G 16293492-A-G BY121764 P6_Gap +
18591905-C-T 16480025-C-T FT288604 YY+
18818400-A-C 16706520-A-C FT5906 Y+
18937210-C-A 16825330-C-A FT288646 YY+
19213453-G-A 17101573-G-A FT288678 YY+
19256266-A-T 17144386-A-T FT288686 YY+
19288346-T-G 17176466-T-G FT288692 YY+
21139212-G-A 18977326-G-A FT288742 YY+
21298992-C-T 19137106-C-T BY197676 YY+
21399210-G-C 19237324-G-C BY18783 YY+
21408696-A-C 19246810-A-C FT288776 Y+
21460600-C-A 19298714-C-A FT288781 YY+
22025025-C-A 19863139-C-A FT288865 YY+
22073302-TGAA-T 19911416-TGAA-T +
22188954-G-A 20027068-G-A FT240628 YY+
23583719-T-C 21421833-T-C BY146488 YY+
23956478-C-G 21810331-C-G BY148736 +
24004570-G-A 21858423-G-A FT289049 Y+
11006084-C-CTCCAT *
20105758-CT-C,CATCTATCT 17993878-CT-C,CATCTATCT P5_Dst *
22274755-T-A 20112869-T-A DYZ19 *
27022296-T-A 24876149-T-A BY30073 A19358 P1_r4 **
22467168-C-T 20305282-C-T FT310311 DYZ19 **
27397017-A-G 25250870-A-G P1_g3 **
8751101-T-C 8883060-T-C **
19686596-A-T 17574716-A-T P5_Prx **
14302898-T-C 12182192-T-C **
18095769-T-C 15983889-T-C **
5244350-GC-G 5376309-GC-G **
7372029-C-T 7503988-C-T **
10083431-G-C 10245822-G-C **
13963943-C-T 11843237-C-T **
14153345-A-G 12032639-A-G **
19529219-C-G 17417339-C-G **
20659330-G-C 18497444-G-C BY154937 P4_Prx **
22478787-C-A 20316901-C-A BY196888 DYZ19 **
22694801-G-A 20532915-G-A **
27266455-G-A 25120308-G-A P1_g3 **
28438209-AAAAAAAAAAAG-A 26292062-AAAAAAAAAAAG-A P1_gr2 **
9057382-G-GT ***
27423940-C-A 25277793-C-A P1_g3 ***
13457725-C-G 11302049-C-G ***
13898366-C-CAA 11777660-C-CAA 15×A***
18035665-CTTTTTTT-C 15923785-CTTTTTTT-C 30×T***
3076069-CTTTTTTT-C,CT 3208028-CTTTTTTT-C,CT 25×T***
18712393-T-A 16600513-T-A ***
3522984-AAAAAAAAAT-A 3654943-AAAAAAAAAT-A ***
5338112-A-G 5470071-A-G FT2634 ***
6784476-GAAA-G,GAA 6916435-GAAA-G,GAA 23×A***
9075188-CTTTT-C,CTT 9237579-CTTTT-C,CTT 20×T***
13446541-AT-A 11290865-AT-A ***
13469281-T-C 11313605-T-C ***
13469283-G-C 11313607-G-C ***
13689858-A-G 11534182-A-G ***
21367863-C-CATATATAT 19205977-C-CATATATAT 9×AT***
21540758-C-T 19378872-C-T ***
21561516-TA-T 19399630-TA-T ***
21754457-GA-G,GAA ***
23952171-A-AATG 21806024-A-AATG ***
56877556-C-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.