Tree Position

R-P312/S116 > Y18209 > BY12148

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
13698057-T-C 11542381-T-C BY25120 A+
20725185-A-C 18563299-A-C P4_Prx A+
20918990-T-G 18757104-T-G P4_Dst A+
19997762-C-T 17885882-C-T FGC69351 P5_Prx A*
19600641-T-C 17488761-T-C P5_Prx YA*
13450712-A-C 11295036-A-C A*
13447057-G-T 11291381-G-T A*
3572472-T-C 3704431-T-C A*
6174896-C-T 6306855-C-T IR3_Dst A*
9705492-G-A 9867883-G-A IR3_Prx A*
18308572-G-A 16196692-G-A P6_Prx A*
19732534-G-A 17620654-G-A P5_Prx A*
20636027-C-T 18474141-C-T P4_Prx A*
20724658-C-T 18562772-C-T P4_Prx A*
20732542-G-A 18570656-G-A P4_Prx A*
20796346-C-T 18634460-C-T P4_Prx A*
20801880-A-C 18639994-A-C P4_Prx A*
20842280-T-G 18680394-T-G P4_Dst A*
20847826-G-A 18685940-G-A P4_Dst A*
20852320-C-T 18690434-C-T P4_Dst A*
20911633-C-T 18749747-C-T P4_Dst A*
23175078-C-A 21013192-C-A YA*
23178593-C-T 21016707-C-T YA*
24336321-G-A 22190174-G-A P3_t1 A*
25940653-C-G 23794506-C-G P1_Y1 A*
26413308-G-A 24267161-G-A P1_Y1 A*
21370350-G-A 19208464-G-A Y56588 YY+
19609399-C-T 17497519-C-T FT218742 P5_Prx Y+
2690515-G-A 2822474-G-A BY55814 YY+
3043910-C-T 3175869-C-T FT191294 +
3504442-A-G 3636401-A-G FT191412 +
4230257-G-A 4362216-G-A FT191620 +
4807693-T-C 4939652-T-C FT191776 +
5041529-CAGG-C 5173488-CAGG-C +
5092293-A-G 5224252-A-G FT114142 +
5439470-A-T 5571429-A-T FT114406 +
5827134-T-C 5959093-T-C FT192039 +
6052303-T-C 6184262-T-C FT114906 +
6882893-A-G 7014852-A-G BY61959 YY+
7368874-C-A 7500833-C-A FT192342 YY+
7410621-G-A 7542580-G-A BY65069 YY+
7688133-C-T 7820092-C-T BY66918 YY+
7836361-A-G 7968320-A-G BY68072 YY+
8431819-A-T 8563778-A-T BY72681 YY+
8530856-G-T 8662815-G-T BY73725 YY+
8580759-T-G 8712718-T-G BY74217 YY+
8665949-T-C 8797908-T-C BY75054 YY+
8831470-A-G 8963429-A-G BY76172 YY+
8854505-T-C 8986464-T-C FT192661 YY+
10956402-T-C FT218735 +
13841973-G-A 11721267-G-A BY91149 +
14627534-A-C 12515602-A-C BY96845 YY+
14877966-G-A 12766036-G-A BY98194 YY+
15499134-TATACAA-T 13387254-TATACAA-T +
15660188-C-A 13548308-C-A BY103164 YY+
15775973-G-A 13664093-G-A Y+
15785869-T-C 13673989-T-C FT193209 YY+
15828819-T-C 13716939-T-C FT196202 YY+
16055283-A-G 13943403-A-G FT196233 Y+
16803649-T-G 14691769-T-G FT196360 YY+
17587695-G-A 15475815-G-A FT193541 YY+
17751757-C-T 15639877-C-T BY117136 YY+
17883308-C-A 15771428-C-A FT193608 YY+
17908533-C-T 15796653-C-T BY118337 YY+
18225666-T-C 16113786-T-C BY121024 Y+
18784963-C-T 16673083-C-T BY123879 YY+
18907472-A-C 16795592-A-C BY124700 YY+
19539499-C-T 17427619-C-T BY129903 YY+
21050074-A-G 18888188-A-G BY130125 YY+
21258140-C-T 19096254-C-T BY131495 YY+
21362027-C-T 19200141-C-T FT194030 YY+
21766962-A-G 19605076-A-G BY135301 YY+
22462477-T-A 20300591-T-A FT457996 DYZ19 +
22610188-G-A 20448302-G-A BY139495 YY+
22712275-C-T 20550389-C-T BY140238 YY+
22755865-T-C 20593979-T-C BY140578 YY+
22798418-C-T 20636532-C-T FT194290 Y+
23456266-T-A 21294380-T-A BY145415 YY+
23852470-C-A 21690584-C-A BY148391 Y+
23979159-GT-G 21833012-GT-G +
13447089-C-A 11291413-C-A *
22317551-T-C 20155665-T-C BY217292 DYZ19 *
10997107-CTCCAC-C,CTCCAT *
6861290-C-CTTT 6993249-C-CTTT *
8768612-T-TACAC 8900571-T-TACAC 17×AC*
17136931-CTTTTTT-C 15025051-CTTTTTT-C 18×T**
6240502-T-C 6372461-T-C IR3_Dst **
3930938-C-G 4062897-C-G **
4917745-G-A 5049704-G-A FT114000 **
6767930-C-T 6899889-C-T FT192201 **
9955292-G-A 10117683-G-A FT218744 **
13320964-T-A 11165288-T-A **
13320966-AC-A 11165290-AC-A **
13414840-CT-C 11259164-CT-C **
17702580-C-G 15590700-C-G FTB37331 **
18250029-T-G 16138149-T-G BY121185 **
19689606-A-T 17577726-A-T P5_Prx **
26460252-G-GCA 24314105-G-GCA P1_Y1 **
26460262-G-A 24314115-G-A P1_Y1 **
26460273-T-G 24314126-T-G P1_Y1 **
28682950-A-T 26536803-A-T FT194600 **
28700790-CAT-C 26554643-CAT-C **
28780217-A-T 26634070-A-T FT218743 **
7723948-C-CTT 7855907-C-CTT 25×T***
13485657-G-C 11329981-G-C ***
22287875-C-G 20125989-C-G DYZ19 ***
22287881-G-T 20125995-G-T BY216194 DYZ19 ***
18340489-T-TACAC 16228609-T-TACAC P6_Prx 12×AC***
18883233-CTT-C,CT 16771353-CTT-C,CT 14×T***
13485649-T-C 11329973-T-C ***
22974348-C-G 20812462-C-G ***
22974349-A-T 20812463-A-T ***
22974350-C-G 20812464-C-G ***
3926006-T-C 4057965-T-C ***
4573136-T-C 4705095-T-C ***
6861289-TC-T 6993248-TC-T ***
13414833-A-T 11259157-A-T ***
13459243-T-A 11303567-T-A ***
13606222-T-G 11450546-T-G ***
14796172-T-C 12684243-T-C ***
16973743-A-G 14861863-A-G ***
17865768-A-G 15753888-A-G ***
19223242-A-T 17111362-A-T ***
20824598-T-C 18662712-T-C P4_Gap ***
21969743-A-G 19807857-A-G ***
22319860-A-G 20157974-A-G DYZ19 ***
22858148-T-C 20696262-T-C ***
28561180-G-C 26415033-G-C ***

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.