Tree Position

R-M269 > L23 > Z2103 > Z2106 > BY41458 > 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
28804542-T-G 26658395-T-G +
23255668-CA-C 21093782-CA-C 10×A+
23488864-AC-A 21326978-AC-A +
59004463-AAAAGAAAG-A 56858316-AAAAGAAAG-A 15×AAAG+
28804537-T-G 26658390-T-G +
16050913-T-C 13939033-T-C M2869 YY+
19293800-G-A 17181920-G-A FTA12541 YY+
13294872-A-T 11139196-A-T +
13294920-C-CCTTTT 11139244-C-CCTTTT +
9940489-C-T 10102880-C-T Y+
13798578-N-G 11677872-G-. +
22457249-C-T 20295363-C-T DYZ19 +
13798577-N-T 11677871-T-. +
22353378-T-C 20191492-T-C DYZ19 +
58829147-T-A 56761724-A-T +
13798576-N-A 11677870-A-. +
13798575-N-A 11677869-A-. +
22345998-A-AGT 20184112-A-AGT DYZ19 +
15698757-GACACAC-G 13586877-GACACAC-G 24×AC+
6521551-G-T 6653510-G-T FT40123 17×T+
6617387-C-A 6749346-C-A Y+
13287869-A-G 11132193-A-G +
13287883-A-G 11132207-A-G +
14334341-G-GT 12213636-G-GT +
13798574-N-G 11677868-G-. +
15752638-CCTTCTTCTT-C 13640758-CCTTCTTCTT-C 25×CTT+
22441018-T-G 20279132-T-G BY22974 DYZ19 +
59007959-CAAAAAAAAAA-C 56861812-CAAAAAAAAAA-C 26×A+
13280097-T-A 11124421-T-A +
13280102-T-A 11124426-T-A +
19520875-G-A 17408995-G-A M9299 YY+
16478198-G-A 14366318-G-A YY16×A+
13686909-ACAC-A 11531233-ACAC-A +
5670077-G-T 5802036-G-T +
6599198-T-G 6731157-T-G +
26834536-G-A 24688389-G-A P1_g2 +
3019392-T-A 3151351-T-A +
3185675-C-A 3317634-C-A +
3390366-C-T 3522325-C-T +
3544896-G-GC 3676855-G-GC +
3550573-TC-T 3682532-TC-T +
3653379-C-T 3785338-C-T +
3755416-C-T 3887375-C-T +
4778008-AT-A 4909967-AT-A +
5043420-C-T 5175379-C-T +
6013651-A-T 6145610-A-T +
6698853-G-T 6830812-G-T YY+
7417576-C-T 7549535-C-T S10255 YY+
8119069-TG-T 8251028-TG-T +
8119070-G-T 8251029-G-T YY+
8888611-AAC-A 9020570-AAC-A +
9030386-AG-A 9192777-AG-A +
9909040-A-T 10071431-A-T Y+
13213845-GGAT-G 11058169-GGAT-G +
13213848-TGGA-T 11058172-TGGA-T +
13222611-G-A 11066935-G-A +
13258359-A-T 11102683-A-T 9×T+
13258558-CTTTTTT-C 11102882-CTTTTTT-C 20×T+
13280044-C-CTATCTTTCT 11124368-C-CTATCTTTCT +
13280048-C-CTTTCCTATT 11124372-C-CTTTCCTATT +
13280119-C-T 11124443-C-T +
13347932-T-C 11192256-T-C 21×AC+
13384756-A-G 11229080-A-G +
13384768-T-C 11229092-T-C +
13500366-A-T 11344690-A-T +
13500608-T-C 11344932-T-C +
13509296-G-C 11353620-G-C +
13572807-G-A 11417131-G-A +
13620795-T-A 11465119-T-A +
13798573-N-C 11677867-C-. +
14334340-G-GT 12213635-G-GT +
15279261-T-G 13167360-T-G YY+
15733905-G-A 13622025-G-A Y+
15733908-G-A 13622028-G-A Y+
16071852-C-A 13959972-C-A A12119 Y+
16809371-GTGAT-G 14697491-GTGAT-G +
16809379-TAGA-T 14697499-TAGA-T +
17029465-G-A 14917585-G-A YY15×A+
17568445-C-G 15456565-C-G YY+
17784121-C-A 15672241-C-A M12018 Y15×A+
17946919-G-GTTT 15835039-G-GTTT 24×T+
18182191-A-C 16070311-A-C A7878 YY+
18735671-TC-T 16623791-TC-T +
18735673-TC-T 16623793-TC-T +
19520882-G-A 17409002-G-A YY+
21012235-C-G 18850349-C-G P4_Dst Y+
21149569-GT-G 18987683-GT-G +
21422265-T-G 19260379-T-G YY+
21574704-A-C 19412818-A-C Y+
21579152-T-G 19417266-T-G Y+
21579190-C-T 19417304-C-T Y+
21579191-T-C 19417305-T-C Y+
21809806-AGTT-A 19647920-AGTT-A +
22238369-G-T 20076483-G-T DYZ19 +
22271623-C-A 20109737-C-A DYZ19 +
22520811-AG-A 20358925-AG-A +
22568342-C-T 20406456-C-T M4919 YY+
24600424-CTCTG-C 22454277-CTCTG-C P3_t2 +
24895715-G-T 22749568-G-T g1 +
25273809-TG-T 23127662-TG-T P2_r1 +
28680954-G-GC 26534807-G-GC +
28726597-C-T 26580450-C-T Y+
59021932-T-TTTC 56875785-T-TTTC +
28804531-A-G 26658384-A-G +
22271624-T-A 20109738-T-A DYZ19 +
2713342-G-A 2845301-G-A CTS76 YY+
2925410-A-AT 3057369-A-AT +
2925422-A-G 3057381-A-G +
3042626-C-A 3174585-C-A +
3076638-C-T 3208597-C-T FT315977 +
3111010-T-C 3242969-T-C FT158541 +
3444141-G-A 3576100-G-A FT317266 +
3682885-A-G 3814844-A-G FT318122 +
4414185-TG-T 4546144-TG-T +
4558065-T-C 4690024-T-C +
5108354-C-T 5240313-C-T FT159088 +
5275721-A-G 5407680-A-G BY21628FGC7777 YFS032832 +
5486696-C-A 5618655-C-A FT1209 +
6496657-G-A 6628616-G-A +
6702153-A-T 6834112-A-T CTS347 YY+
6822605-C-G 6954564-C-G CTS521 YY+
6848047-T-A 6980006-T-A CTS563 YY+
6981070-T-G 7113029-T-G YY+
8131958-G-A 8263917-G-A F16670 YY+
8297724-C-G 8429683-C-G F16881 YY+
8785238-C-T 8917197-C-T Y87997 YY+
8793199-T-A 8925158-T-A FGC22331 YY+
9004414-G-A 9166805-G-A F17631 Y+
10015410-G-A 10177801-G-A BY82918 Y+
13135711-G-A 10625197-G-A +
13222622-G-GGA 11066946-G-GGA +
13455773-C-A 11300097-C-A +
13620821-C-T 11465145-C-T FT53820 +
14213797-A-AAG 12093091-A-AAG +
14213799-GAA-G 12093093-GAA-G +
14304362-C-T 12183656-C-T CTS2437 Y+
14616879-A-C 12505077-A-C M5141 Y+
14705563-C-T 12593629-C-T F19188 YY+
14981450-G-A 12869526-G-A CTS3508 YY+
15000833-T-C 12888918-T-C F19455 YY+
15486542-C-T 13374662-C-T YY+
15872622-A-C 13760742-A-C F20230 YY+
16132476-GAT-G 14020596-GAT-G +
16658637-A-G 14546757-A-G FT301439 Y+
16992724-T-C 14880844-T-C YY+
17127836-G-A 15015956-G-A F21405 YY+
17322850-G-A 15210970-G-A YY+
17415731-C-T 15303851-C-T CTS7312 YY+
17428936-A-T 15317056-A-T FT301635 Y+
17432033-C-T 15320153-C-T Y+
17618712-G-A 15506832-G-A CTS7693 Y+
18087488-G-T 15975608-G-T CTS8568 YY+
18553548-G-A 16441668-G-A FT301904 Y+
18570650-C-A 16458770-C-A FT301911 YY+
18756411-G-A 16644531-G-A CTS9226 YY+
18763200-C-T 16651320-C-T CTS9232 YY+
19205773-A-G 17093893-A-G F23428 YY+
19279124-C-T 17167244-C-T FT302115 YY+
19353913-A-G 17242033-A-G CTS10258 Y+
21402650-C-T 19240764-C-T F24270 YY+
21464308-A-G 19302422-A-G FT302381 YY+
21693523-C-G 19531637-C-G F24594 YY+
21695532-A-G 19533646-A-G BY38978 YY+
21890496-G-A 19728610-G-A FT302516 YY+
22271848-G-C 20109962-G-C FT454367 DYZ19 +
22487919-G-C 20326033-G-C DYZ19 +
23130092-G-T 20968206-G-T CTS11481 YY+
23207312-C-T 21045426-C-T FT302840 Y+
23429537-G-A 21267651-G-A CTS12026 YY+
23970617-C-A 21824470-C-A F26536 Y+
26371786-G-C 24225639-G-C P1_Y1 +
28744956-T-G 26598809-T-G Y+
58986236-A-G 56840089-A-G +

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:

Manual28795350-A-T26649203-A-TFrom an hg19 aligned BAM, all 4 reads which look to belong there are positive. Many other reads which should be aligned elsewhere are negative.
Manual5064056-A-G5196015-A-G1G. There is also 1A with mapping quality 0.