Tree Position

R-P312/S116 > Z40481 > FGC84729 > DF99/S11987 > Z29643 > FGC16982 > S23540 > FGC16979 > ZZ73 > Y31433 > BY15485 > BY15487

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
20498990-C-T 18337104-C-T P5_Dst A+
20816924-C-CA 18655038-C-CA P4_Gap 22×AA*
7475612-T-A 7607571-T-A IR1_L A*
26133997-C-T 23987850-C-T P1_Y1 A*
28817409-T-G 26671262-T-G A*
13687818-A-T 11532142-A-T A*
28816795-G-A 26670648-G-A A*
28817347-A-G 26671200-A-G A*
56858628-G-T A*
18280304-G-A 16168424-G-A P6_Prx A*
19587171-C-T 17475291-C-T BY15485 P5_Prx YA*
26084246-G-A 23938099-G-A P1_Y1 A*
19696433-T-TA 17584553-T-TA P5_Prx 14×AA*
25617175-T-TTG 23471028-T-TTG P1_gr1 19×TGA*
26351915-C-T 24205768-C-T P1_Y1 A*
19680787-G-A 17568907-G-A P5_Prx A*
16013103-T-G 13901223-T-G YA*
19631612-A-C 17519732-A-C P5_Prx A*
14641193-C-T 12529262-T-. L52 PF6541 YY+
22157311-A-. 19995425-A-. P312 +
17844018-C-. 15732138-C-. +
16751825-A-. 14639945-A-. +
8502236-A-. 8634195-A-. +
6912992-G-. 7044951-G-. +
6753511-A-. 6885470-A-. +
22739367-C-. 20577481-C-. +
6032961-G-. 6164920-G-. +
19418178-C-. 17306298-C-. +
8829491-C-A 8961450-C-A DF99/S11987DF99 S11987 Z6001 YY+
4404325-G-A 4536284-G-A Z29643Z29643 +
2784645-C-G 2916604-C-G Y31433Y31433 YY+
8023548-C-T 8155507-C-T Y31433BY15482 Y31434 YY+
17688792-G-T 15576912-G-T FGC16982Y5049 FGC16982 YY+
17879816-A-G 15767936-A-G FGC16979Y5046 FGC16979 YY+
18883425-A-G 16771545-A-G Y31433CTS9423 S4249 YY+
21783578-A-C 19621692-A-C S23540S23540 YY+
24425801-G-A 22279654-G-A Y31433BY15483 Y31435 Y+
14539162-G-A 12427363-G-A S23540S16136 YY+
4585565-A-G 4717524-A-G S23540FGC16988 +
6286963-GCACACA-G 6418922-GCACACA-G FT67050 IR3_Dst +
5465148-A-. 5597107-A-. +
7242725-C-A 7374684-C-A BY15485BY183855 Y+
15375766-G-A 13263886-G-A BY11781Y16635 YY+
4943495-A-G 5075454-A-G FGC43638 +
10973221-G-A +
10934009-T-G FGC84729FGC84729 +
8614401-A-G 8746360-A-G BY15485BY15485 YY+
8906656-G-A 9038615-G-A BY15485BY15486 +
9448171-A-G 9610562-A-G BY15487BY15487 YY+
10766771-G-A BY15487FT310232 +
13213911-G-A 11058235-G-A BY15487FT310231 +
13485237-G-A 11329561-G-A BY15485BY43128 +
13681255-C-A 11525579-C-A BY15487BY38505 +
13717027-A-T 11561351-A-T BY15487BY38506 +
14114952-C-T 11994246-C-T FT304304 YY+
14604773-C-T 12492975-C-T BY15485BY43358 YY+
14696563-G-A 12584629-G-A BY15488 YY+
14883725-A-C 12771791-A-C BY15487BY15489 YY+
15346493-T-C 13234612-T-C BY15485BY15490 YY+
15670909-T-C 13559029-T-C BY15487BY15484 Y+
15704942-T-G 13593062-T-G BY15487BY15491 YY+
16337455-A-C 14225575-A-C BY15485BY15492 YY+
17018466-A-C 14906586-A-C BY15485BY15493 YY+
17113039-TA-T 15001159-TA-T BY15487 +
17225598-T-A 15113718-T-A BY15485BY15494 YY+
18398343-T-C 16286463-T-C BY15485BY15495 P6_Gap +
18645296-C-T 16533416-C-T BY15485BY15496 YY+
18959922-A-G 16848042-A-G BY15485BY15497 YY+
18979358-C-A 16867478-C-A BY15485BY15498 YY+
19232967-A-G 17121087-A-G BY15485BY183856 YY+
19281778-G-A 17169898-G-A BY15499 YY+
19482038-G-A 17370158-G-A BY15485BY183857 YY+
22707971-T-C 20546085-T-C BY15501 YY+
23293367-C-T 21131481-C-T BY15485BY15502 YY+
23485752-T-C 21323866-T-C BY15487BY15503 YY+
23608303-T-C 21446417-T-C BY15504 YY+
24401518-G-C 22255371-G-C BY15487BY15505 Y+
26153823-G-C 24007676-G-C BY15487 P1_Y1 +
18636727-G-A 16524847-G-A FT202086 YY+
28582021-G-C 26435874-G-C FT202721 +
13839536-A-. 11718830-A-. +
3605699-G-A 3737658-G-A FT200332 +
3900675-C-G 4032634-C-G FT200384 +
4797381-A-G 4929340-A-G FT200573 +
5746411-A-T 5878370-A-T FT200755 +
5918961-G-A 6050920-G-A FT200787 +
5955621-T-C 6087580-T-C FT200796 +
6481340-A-G 6613299-A-G FT200861 +
13890249-G-A 11769543-G-A FT126586 Y+
18411661-C-T 16299781-C-T FT202072 P6_Gap +
21269346-T-C 19107460-T-C FT202294 Y+
21526094-G-A 19364208-G-A FT202341 Y+
28704418-A-G 26558271-A-G FT202740 +
9787962-C-A 9950353-C-A FTB14629 Y+
13336576-T-C 11180900-T-C +
17115541-T-G 15003661-T-G YY+
19104658-G-C 16992778-G-C YY+
21346628-G-C 19184742-G-C Y+
5170248-GAGGA-G 5302207-GAGGA-G 11×AGGA*
3249466-TTGTG-T 3381425-TTGTG-T 17×TG*
10781676-A-AATTCC *
3721207-T-C 3853166-T-C BY15485BY42622 *
22301884-C-T 20139998-C-T DYZ19 *
28796049-G-C 26649902-G-C FT462009 *
3713579-A-G 3845538-A-G *
5268561-GC-G 5400520-GC-G *
9587513-CT-C 9749904-CT-C IR3_Prx *
5568497-G-A 5700456-G-A FT83105 **
24293019-T-G 22146872-T-G P3_t1 **
11651885-CGAATG-C **
13453306-T-G 11297630-T-G **
23825772-AAAT-A 21663886-AAAT-A **
24517283-G-A 22371136-G-A BY15487BY15506 **
13453278-C-G 11297602-C-G **
19377420-A-G 17265540-A-G **
24291383-A-T 22145236-A-T P3_t1 **
20448893-G-GGTGTGT 18287007-G-GGTGTGT P5_Dst **
19792501-T-C 17680621-T-C P5_Prx **
4163583-T-G 4295542-T-G **
19597206-TTATTA-T 17485326-TTATTA-T P5_Prx **
19788333-C-A 17676453-C-A P5_Prx **
22548342-C-A 20386456-C-A **
22882961-C-A 20721075-C-A **
24291391-A-C 22145244-A-C P3_t1 **
25592447-T-A 23446300-T-A P1_gr1 **
26019729-C-A 23873582-C-A P1_Y1 **
22420062-C-G 20258176-C-G BY23368 DYZ19 ***
17669700-CAT-C 15557820-CAT-C 15×AT***
20989104-TAC-T 18827218-TAC-T P4_Dst 25×AC***
19537901-C-CAA 17426021-C-CAA 17×A***
4997519-CAG-C 5129478-CAG-C 16×AG***
9416722-C-A 9579113-C-A ***
15070614-CAAAAAAAA-C 12958705-CAAAAAAAA-C 20×A***
23792029-C-CTTT 21630143-C-CTTT 15×T***
13470032-C-A 11314356-C-A ***
13260592-CTT-C,CT 11104916-CTT-C,CT 14×T***
6131927-G-C 6263886-G-C ***
8901182-A-T 9033141-A-T ***
13427974-T-C 11272298-T-C ***
13606495-T-A 11450819-T-A ***
17859649-G-A 15747769-G-A ***
21680438-G-A 19518552-G-A ***
23484315-T-A 21322429-T-A ***
23484317-T-A 21322431-T-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.