Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > ZZ45 > Z36/S206

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
B257635
13687277-C-G 11531601-C-G DYZ17 A*
16104263-G-A 13992383-G-A P8_Prx A*
18343360-T-C 16231480-T-C P6_Prx A*
19938338-G-A 17826458-G-A BY16342 P5_Prx A*
20000745-A-T 17888865-A-T P5_Prx 11×TA*
20019234-T-G 17907354-T-G P5_Prx A*
20027641-A-G 17915761-A-G P5_Prx A*
20683164-T-C 18521278-T-C P4_Prx A*
20779772-C-G 18617886-C-G P4_Prx A*
25564637-G-A 23418490-G-A P1_gr1 A*
26334203-G-C 24188056-G-C P1_Y1 A*
7251243-C-T 7383202-C-T FGC20124 ZS7719 YY+
8568410-GT-G 8700369-GT-G 9×T+
24381475-T-C 22235328-T-C FT32844 Y+
6846070-G-A 6978029-G-A Y81895Y82677 YY+
6926922-G-T 7058881-G-T FT32269 Y+
9883501-C-T 10045892-C-T FT32386 YY+
2907494-G-A 3039453-G-A BY57220 YY+
3168917-T-A 3300876-T-A FT31950 +
3172002-A-G 3303961-A-G FT31951 +
4068651-A-T 4200610-A-T FT32019 +
4071777-C-T 4203736-C-T FT32021 +
4319014-C-A 4450973-C-A FT32046 +
4355606-C-T 4487565-C-T FT32051 +
4443885-A-C 4575844-A-C FT32058 +
5263848-G-A 5395807-G-A FT32135 +
5385593-TTGTC-T 5517552-TTGTC-T +
5393231-GA-G 5525190-GA-G +
5444564-A-T 5576523-A-T FT32157 +
6788074-T-C 6920033-T-C FT32262 YY+
7747400-A-AT 7879359-A-AT +
7812455-C-TGTT 7944414-C-TGTT +
8115209-C-T 8247168-C-T FT32320 YY+
9452932-A-G 9615323-A-G FT32373 YY+
9893047-G-A 10055438-G-A FT32388 YY+
10838611-C-A FT433524 +
13576116-T-C 11420440-T-C FT445647 +
13684645-C-T 11528969-C-T FT448333 DYZ17 +
13711105-G-A 11555429-G-A FT449352 DYZ17 +
14594482-A-C 12482682-A-C FT32446 YY+
14985451-T-C 12873519-T-C FT32468 YY+
15195883-G-A 13083969-G-A FT32478 YY+
15877315-T-G 13765435-T-G FT32516 YY+
16002374-C-T 13890494-C-T FT32521 Y+
16296872-C-T 14184992-C-T FT32536 Y+
16417624-T-C 14305744-T-C FT32543 YY+
16779475-A-T 14667595-A-T FT32569 YY+
18126810-A-G 16014930-A-G FT32641 YY+
18415784-C-G 16303904-C-G FT32657 P6_Gap +
18598997-T-A 16487117-T-A FT32662 YY+
18598998-C-T 16487118-C-T FT32663 YY+
19121252-T-C 17009372-T-C FT32690 YY+
19159368-C-T 17047488-C-T FT32694 YY+
19163877-A-C 17051997-A-C FT32695 YY+
19200493-T-C 17088613-T-C FT32697 YY+
19423427-C-G 17311547-C-G FT32710 YY+
21367723-T-A 19205837-T-A FT32729 YY+
21837397-T-G 19675511-T-G FT32750 Y+
22465669-C-A 20303783-C-A FT458578 DYZ19 +
22771842-T-C 20609956-T-C FT32785 YY+
23440890-T-C 21279004-T-C FT32823 Y+
23454186-T-C 21292300-T-C FT32824 YY+
24393992-G-A 22247845-G-A FT32846 Y+
27823661-C-G 25677514-C-G P1_Y2 +
28813480-G-C 26667333-G-C BY152143 +
28807197-A-G 26661050-A-G *
22113187-CAAAAAAA-C 19951301-CAAAAAAA-C 23×A**
16711107-C-CAT 14599227-C-CAT **
22640280-G-GA 20478394-G-GA 9×A**
6410965-TAAATAAATAAATAAATAAATAAATAATAA-T 6542924-TAAATAAATAAATAAATAAATAAATAATAA-T **
19048412-C-G 16936532-C-G FT283374 **
3563051-C-T 3695010-C-T FTB84871 **
5505962-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-A 5637921-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-A 53×T**
9410135-T-C 9572526-T-C **
13623556-G-A 11467880-G-A **
15573028-AGAAG-A 13461148-AGAAG-A **
15628667-C-T 13516787-C-T **
19625896-A-C 17514016-A-C P5_Prx **
20797952-G-T 18636066-G-T P4_Prx **
21109590-G-T 18947704-G-T **
24256537-C-A 22110390-C-A P3_b1 **
12683-T-A **
2888870-CAAAAAAAAAA-C 3020829-CAAAAAAAAAA-C 32×A***
6931642-T-C 7063601-T-C BY62271 ***
3540810-G-T 3672769-G-T ***
7275525-G-A 7407484-G-A ***
8702818-T-G 8834777-T-G ***
15904168-A-AC,C 13792288-A-AC,C 8×AC***
15928396-TTG-T,TG 13816516-TTG-T,TG ***
15940306-CAAAAA-C,CAAA 13828426-CAAAAA-C,CAAA 24×A***
18612759-GTA-G,GTATATA 16500879-GTA-G,GTATATA 15×TA***
22151642-C-T 19989756-C-T ***
22345423-A-G 20183537-A-G DYZ19 ***
22505738-A-T 20343852-A-T DYZ19 ***

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.