Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z272 > S450 > ZZ40 > S21184 > FGC13557 > A7066 > BY32727

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
20636061-C-A 18474175-C-A P4_Prx A*
58979669-C-T 56833522-C-T A*
56833827-T-C A*
56836250-C-T A*
13687786-G-A 11532110-G-A A*
3416300-G-A 3548259-G-A A*
13687421-C-T 11531745-C-T A*
13451224-C-G 11295548-C-G A*
19803372-T-A 17691492-T-A P5_Prx A*
19803414-T-C 17691534-T-C P5_Prx A*
20066949-C-T 17955069-C-T P5_Dst A*
20376366-A-G 18214480-A-G P5_Dst A*
20376408-A-T 18214522-A-T P5_Dst A*
20979250-C-CGT 18817364-C-CGT P4_Dst A*
21008110-G-T 18846224-G-T P4_Dst YA*
24265802-G-A 22119655-G-A P3_b1 A*
24272064-A-G 22125917-A-G P3_b1 A*
26221434-C-G 24075287-C-G P1_Y1 A*
28816836-T-C 26670689-T-C A*
13280464-C-T 11124788-C-T FT442248 +
8386583-T-TA 8518542-T-TA 9×A+
18110280-C-A 15998400-C-A Z10889 YY+
8835331-CTTCT-C 8967290-CTTCT-C 4×TTCT+
24518027-T-C 22371880-T-C FT171544 +
19109975-C-T 16998095-C-T FT170298 YY+
5003732-C-T 5135691-C-T FT96142FT95571 +
5339523-G-A 5471482-G-A FT166543 +
5389891-A-G 5521850-A-G FT166567 +
5738509-A-G 5870468-A-G FT166751 +
5873777-G-A 6005736-G-A FT166820 +
6848620-G-T 6980579-G-T FT167168 YY+
8209700-G-A 8341659-G-A FT167663 YY+
8245979-G-A 8377938-G-A BY71085 YY+
8589353-C-T 8721312-C-T FT167853 YY+
8980855-C-T 9143246-C-T FT168000 Y+
9088588-C-T 9250979-C-T FT168040 Y+
9156859-A-G 9319250-A-G FT168061 +
10988186-C-T FT439342 +
11653740-T-A FT450390 +
15073335-G-A 12961425-G-A FT168810 YY+
15106993-A-T 12995080-A-T FT168819 YY+
15534561-G-A 13422681-G-A FT168957 YY+
15689174-C-G 13577294-C-G FT169004 YY+
16473219-C-T 14361339-C-T FT169302 YY+
16658927-G-T 14547047-G-T FT169369 YY+
17886085-C-A 15774205-C-A FT169853 Y+
18382842-G-A 16270962-G-A FT170049 P6_Gap +
18524053-T-C 16412173-T-C FT170072 P6_Dst +
18646657-T-G 16534777-T-G FT170119 YY+
19319616-G-A 17207736-G-A FT170387 YY+
22468793-C-G 20306907-C-G FT458937 DYZ19 +
28480877-G-A 26334730-G-A FT171562 +
28685154-T-G 26539007-T-G FT171663 +
13445955-A-C 11290279-A-C *
22237837-A-G 20075951-A-G BY213733 DYZ19 *
21371746-C-T 19209860-C-T Z23388 AM00277 AMM232 K619 **
18095757-A-AAT 15983877-A-AAT **
6273855-CA-C 6405814-CA-C IR3_Dst **
26153962-G-GAA 24007815-G-GAA P1_Y1 15×A**
22445212-A-G 20283326-A-G BY188441BY219575 DYZ19 **
6359095-C-A 6491054-C-A 30×A**
6901325-G-C 7033284-G-C **
8111244-CA-C 8243203-CA-C **
13516424-C-A 11360748-C-A **
19018046-A-G 16906166-A-G **
21287968-T-C 19126082-T-C **
21392697-G-A 19230811-G-A **
21958185-A-G 19796299-A-G **
22263511-A-G 20101625-A-G DYZ19 **
22438630-G-C 20276744-G-C DYZ19 **
22458841-G-T 20296955-G-T DYZ19 **
23036544-G-A 20874658-G-A **
23171644-G-C 21009758-G-C **
23316182-G-A 21154296-G-A **
56824722-CT-C **
56878652-A-G **
9429665-TAC-T 9592056-TAC-T ***
27699878-G-T 25553731-G-T P1_Y2 ***
23439905-G-GTT 21278019-G-GTT 15×T***
10776114-T-C,G ***
16710763-GTATA-G,GTA 14598883-GTATA-G,GTA 14×TA***
13458052-ATTCCT-A 11302376-ATTCCT-A ***
3640539-CC-C,CT 3772498-CC-C,CT ***
16050950-CTT-C,CTTTCTT 13939070-CTT-C,CTTTCTT ***
5088451-CTTTTTT-C 5220410-CTTTTTT-C 27×T***
22876964-TA-T,TAA 20715078-TA-T,TAA 20×A***
18841242-T-G 16729362-T-G ***
15109427-CT-C 12997514-CT-C 8×T***
4360906-AC-AG,G 4492865-AC-AG,G ***
13222419-C-A,G 11066743-C-A,G ***
13337528-C-A 11181852-C-A ***
13349492-C-G 11193816-C-G ***
13449314-GCATT-G 11293638-GCATT-G ***
13466792-A-C 11311116-A-C ***
14312045-G-T 12191339-G-T ***
28679879-G-C 26533732-G-C ***
56869837-T-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.