Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > DF13 > FGC5494 > Exact position not yet finalized.

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 STR1kG
8403300-AG-A 8535259-AG-A +
15260679-C-T 13148763-C-T YY+
13143956-N-A 10633442-N-A +
13143957-N-C 10633443-N-C +
13143958-N-T 10633444-N-T +
14630493-A-C 12518562-A-C YY+
22294800-G-C 20132914-G-C DYZ19 +
13253182-C-T 11097506-C-T +
14307953-C-A 12187247-C-A Y15×A+
2682558-G-T 2814517-G-T A7846 YY+
2742828-C-G 2874787-C-G PH38 YY+
2910890-G-T 3042849-G-T PH109 YY+
6728388-G-T 6860347-G-T A7848 Y+
6777060-T-C 6909019-T-C CTS478 YY+
6914803-T-C 7046762-T-C A7849 YY+
6946246-G-T 7078205-G-T A7851 YY+
7070804-A-T 7202763-A-T S6304 YY+
7201118-T-C 7333077-T-C PH514 Y+
7783724-T-C 7915683-T-C A7854 YY+
8310182-A-C 8442141-A-C A7855 YY+
8358159-G-T 8490118-G-T S7343 YY+
9006627-C-T 9169018-C-T Y+
9014563-C-T 9176954-C-T A11340 Y+
14118875-C-G 11998169-C-G Y+
14256021-G-T 12135315-G-T A7858 Y+
14624151-T-A 12512349-T-A A7860 YY+
15010490-G-A 12898575-G-A A7863 YY+
15275438-C-A 13163527-C-A A7864 YY+
15277425-A-C 13165514-A-C PH1650 YY+
15348949-G-A 13237068-G-A A7865 YY+
15635691-A-G 13523811-A-G M7477 YY+
15730942-C-T 13619062-C-T A7867 Y+
15977517-G-A 13865637-G-A CTS5037 YY+
16492320-G-A 14380440-G-A S6321 YY+
16579100-G-C 14467220-G-C S7357 YY+
16876192-C-T 14764312-C-T Y49938S6317 YY+
16903186-T-A 14791306-T-A S6308 YY+
17012745-T-C 14900865-T-C Z11600 YY+
17034718-A-G 14922838-A-G A7872 YY+
17239677-T-C 15127797-T-C PH2906 YY+
17444038-G-C 15332158-G-C PH3073 YY+
17620997-C-A 15509117-C-A A7877 Y+
21534566-C-A 19372680-C-A A7883 YY+
21708540-C-T 19546654-C-T A7884 Y+
21948481-C-T 19786595-C-T A7885 YY+
22660336-T-C 20498450-T-C A7888 YY+
22832020-A-G 20670134-A-G A7890 YY+
23078199-C-T 20916313-C-T FT292416 Y+
23294325-G-A 21132439-G-A A7891 YY+
23601350-G-T 21439464-G-T A7893 Y+
28724466-G-A 26578319-G-A A7896 Y+
13222655-C-G 11066979-C-G +
5273207-C-T 5405166-C-T +
13143961-N-A 10633447-N-A +
13530113-G-A 11374437-G-A +
16533469-CAT-C 14421589-CAT-C +
13265038-G-A 11109362-G-A +
14664252-G-GA 12552317-G-GA +
3072856-A-G 3204815-A-G FT315963 +
3318710-C-T 3450669-C-T A7847 +
3572202-C-T 3704161-C-T +
3728329-T-C 3860288-T-C FT318282 +
3824389-G-A 3956348-G-A FT77969 +
3834016-T-C 3965975-T-C S7352 +
3949498-A-C 4081457-A-C FT319025 +
4096465-C-T 4228424-C-T FT319493 +
4124584-G-A 4256543-G-A FT319595 +
4334648-A-G 4466607-A-G +
4896649-C-A 5028608-C-A 16×A+
4941487-TC-T 5073446-TC-T +
4986492-A-G 5118451-A-G +
5095840-C-T 5227799-C-T +
5130488-G-T 5262447-G-T +
5130492-G-T 5262451-G-T +
5140966-C-T 5272925-C-T FT235528 +
5178049-C-T 5310008-C-T +
5184164-C-T 5316123-C-T FT323016 +
5748614-C-T 5880573-C-T FT4401 +
5807122-G-A 5939081-G-A FT159264 +
5921255-T-C 6053214-T-C FT325508 +
6017175-C-T 6149134-C-T +
6044012-G-T 6175971-G-T +
6044320-G-T 6176279-G-T FT325961 +
6604082-TTC-T 6736041-TTC-T +
6858590-TTC-T 6990549-TTC-T +
6863782-A-C 6995741-A-C YY+
6915783-G-T 7047742-G-T YY+
6918598-G-A 7050557-G-A A7850 YY+
7124470-T-C 7256429-T-C S6318 Y+
7223216-AG-A 7355175-AG-A +
7235929-C-T 7367888-C-T A7853 YY+
7518489-AT-A 7650448-AT-A +
7545015-G-GC 7676974-G-GC +
7758509-C-T 7890468-C-T Y+
8432274-G-A 8564233-G-A S6319 YY+
9429709-C-A 9592100-C-A Y+
9920844-A-G 10083235-A-G A7856 Y+
10006912-C-T 10169303-C-T A7857 Y+
13220656-C-T 11064980-C-T ZS8461 +
13222611-G-A 11066935-G-A +
13222619-G-A 11066943-G-A +
13256877-C-T 11101201-C-T +
13265088-C-T 11109412-C-T +
13267776-C-CCCCA 11112100-C-CCCCA +
13267779-C-CCCCT 11112103-C-CCCCT +
13280025-G-A 11124349-G-A +
13291461-G-A 11135785-G-A +
13433088-TAA-T 11277412-TAA-T +
13531776-AC-A 11376100-AC-A +
13545811-C-T 11390135-C-T +
13617064-T-C 11461388-T-C +
13624344-A-ATG 11468668-A-ATG +
13923845-T-C 11803139-T-C Y+
13931993-T-C 11811287-T-C Y+
14329730-G-T 12209024-G-T A7859 YY+
14442333-G-T 12321606-G-T PH1232 Y+
14661436-C-A 12549501-C-A A7861 YY+
14709281-A-AC 12597348-A-AC +
14784690-A-T 12672760-A-T A7862 YY+
15070475-T-G 12958566-T-G YY+
15092766-AT-A 12980854-AT-A +
15290972-GA-G 13179071-GA-G +
15358761-G-GAAAAA 13246880-G-GAAAA 26×A+
15491941-G-GTA 13380061-G-GTA 19×TA+
15556992-A-C 13445112-A-C A7866 YY+
15815397-C-T 13703517-C-T YY+
15832213-C-T 13720333-C-T YY+
15956886-T-G 13845006-T-G YY+
16072160-T-C 13960280-T-C PH2024 Y+
16305949-G-A 14194069-G-A A7868 YY+
16397707-G-T 14285827-G-T A7869 Y+
16435955-T-TTTA 14324075-T-TTTA +
16435956-G-T 14324076-G-T A7871 YY+
16692791-G-A 14580911-G-A YY+
16897689-T-G 14785809-T-G YY+
17299917-GATAC-G 15188037-GATAC-G +
17441209-TATATATAC-T 15329329-TATATATAC-T +
17495908-A-T 15384028-A-T A7876 YY+
17564937-C-A 15453057-C-A YY+
17817386-TTC-T 15705506-TTC-T +
17868560-G-C 15756680-G-C S7358 YY+
17934763-A-C 15822883-A-C YY+
17946902-TG-T 15835022-TG-T +
18182191-A-C 16070311-A-C A7878 YY+
18392973-CTCCT-C 16281093-CTCCT-C P6_Gap +
18688482-A-T 16576602-A-T YY+
19128109-T-G 17016229-T-G YY+
19192046-A-G 17080166-A-G S3835 YY+
19237112-A-T 17125232-A-T A7879 YY+
19432428-G-A 17320548-G-A A7880 YY+
20685195-G-A 18523309-G-A P4_Prx +
21236238-A-C 19074352-A-C A7881 YY+
21318496-AG-A 19156610-AG-A +
21965736-T-A 19803850-T-A A7886 Y+
22262434-G-GGA 20100548-G-GGA DYZ19 +
22289550-T-C 20127664-T-C DYZ19 +
22293301-T-C 20131415-T-C DYZ19 +
22293305-G-A 20131419-G-A DYZ19 +
22293315-T-A 20131429-T-A DYZ19 +
22444323-T-C 20282437-T-C BY219369 DYZ19 +
22445947-A-G 20284061-A-G DYZ19 +
22516363-C-T 20354477-C-T A7887 Y+
22769297-TC-T 20607411-TC-T +
22852215-TA-T 20690329-TA-T +
22876992-C-A 20715106-C-A Y+
22877007-G-A 20715121-G-A Y+
23885869-T-A 21723983-T-A Y+
24242347-AG-A 22096200-AG-A P3_b1 +
24388253-CTA-C 22242106-CTA-C +
24404239-T-G 22258092-T-G A7894 +
25273809-TG-T 23127662-TG-T P2_r1 +
26391561-C-CACAG 24245414-C-CACAG P1_Y1 +
28461869-G-C 26315722-G-C +
28592617-G-A 26446470-G-A S7355 +
28661351-G-C 26515204-G-C M10417 Y10×ATCC+
28761414-G-A 26615267-G-A A7897 +
28761439-C-T 26615292-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.

Mutation Notes:

HG0011522231381-G-A20069495-G-AChecked BAM File.
HG001153445114-A-G3577073-A-GChecked BAM File.
Manual22231381-G-A20069495-G-A5 reads - 3G and 2A.