Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > L513/S215/DF1 > S6365 > Z16361 > CTS750 > FGC13411 > FGC32363 > BY11280 > A11235 > BY87746

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
HG00103
Manual
Edits
5905918-G-A 6037877-G-A +
15123165-C-A 13011252-C-A YY+
13840815-C-G 11720109-C-G Y133466 9×GAATG+
13873187-G-T 11752481-G-T Y+
14101407-C-T 11980701-C-T CTS1863 YY+
14729321-A-T 12617389-A-T YY+
14760882-C-T 12648951-C-T Y+
14848351-G-A 12736417-G-A CTS3340 YY+
15047302-TG-T 12935393-TG-T +
15353851-G-T 13241970-G-T CTS4044 YY+
13691811-G-GGAATT 11536135-G-GGAATT +
15554944-G-A 13443064-G-A YY+
15737506-A-C 13625626-A-C YY+
16242401-GCT-G 14130521-GCT-G +
16248072-A-C 14136192-A-C YY+
16257958-T-C 14146078-T-C YY+
16710922-A-G 14599042-A-G YY+
16729170-A-T 14617290-A-T M12048 YY+
13691813-A-AATGGC 11536137-A-AATGGC +
13691802-G-GAATGC 11536126-G-GAATGC +
16786235-TC-T 14674355-TC-T +
13338555-A-G 11182879-A-G +
9954392-C-T 10116783-C-T Y+
9997062-C-A 10159453-C-A F10492 Y+
13256166-C-T 11100490-C-T +
13267454-G-A 11111778-G-A +
13273818-A-G 11118142-A-G +
13305685-G-A 11150009-G-A +
13307070-G-T 11151394-G-T +
13379781-G-A 11224105-G-A +
13636145-C-T 11480469-C-T +
13382987-C-T 11227311-C-T +
13500003-C-T 11344327-C-T +
13500318-T-G 11344642-T-G +
13508867-T-C 11353191-T-C +
13539334-G-A 11383658-G-A +
13621171-G-C 11465495-G-C +
13636131-A-G 11480455-A-G +
16729171-CGTT-C 14617291-CGTT-C +
16813105-ACG-A 14701225-ACG-A +
8730021-G-A 8861980-G-A YY+
28522394-TG-T 26376247-TG-T +
23584011-C-T 21422125-C-T YY+
23901432-N-G 21739546-N-G +
24386328-T-C 22240181-T-C +
24480646-A-T 22334499-A-T Y+
26508182-C-T 24362035-C-T FGC8528 P1_Y1 +
28485487-C-T 26339340-C-T +
28490934-G-A 26344787-G-A +
28571435-CTT-C 26425288-CTT-C +
23479934-A-T 21318048-A-T BY145589 YY+
28571474-C-T 26425327-C-T +
28595390-C-G 26449243-C-G CTS12491 +
28595406-A-G 26449259-A-G CTS12492 +
28595450-C-A 26449303-C-A CTS12493 +
28595452-A-G 26449305-A-G CTS12494 +
28726834-C-T 26580687-C-T Y+
28802738-G-C 26656591-G-C +
23541400-G-A 21379514-G-A YY+
23128622-C-T 20966736-C-T CTS11477 YY+
17322927-G-A 15211047-G-A Y1090 YY+
21146297-C-A 18984411-C-A YY+
17872656-TG-T 15760776-TG-T +
17923152-C-T 15811272-C-T YY+
19272160-AG-A 17160280-AG-A +
19387017-A-ATGTAT 17275137-A-ATGTAT +
20803192-G-C 18641306-G-C P4_Gap +
21012234-A-T 18850348-A-T P4_Dst Y+
21089752-T-C 18927866-T-C YY+
21459021-C-A 19297135-C-A Y+
23112705-C-G 20950819-C-G CTS11438 YY+
21502775-G-T 19340889-G-T Y+
21662606-A-G 19500720-A-G YY+
21908671-C-T 19746785-C-T YY+
22325240-C-G 20163354-C-G DYZ19 +
22458007-T-A 20296121-T-A DYZ19 +
22879397-G-A 20717511-G-A Y34532 FGC75764 Y+
22981818-G-A 20819932-G-A Y+
23106031-A-T 20944145-A-T Y+
8971407-C-T 9133798-C-T +
8696020-G-T 8827979-G-T YY+
20574931-G-T 18413045-G-T P5_Dst +
3342287-A-T 3474246-A-T 10×T+
8445984-CC-GAAA 8577943-CC-GAAA CTS750 +
13339812-G-A 11184136-G-A +
2664162-C-T 2796121-C-T YY+
2718877-C-T 2850836-C-T YY+
3147666-C-T 3279625-C-T Z8497 +
3226995-C-T 3358954-C-T +
3272097-C-T 3404056-C-T +
3342316-A-C 3474275-A-C +
23507296-C-G 21345410-C-G YY+
3554057-C-A 3686016-C-A 8×A+
3554062-A-G 3686021-A-G +
3554125-C-G 3686084-C-G +
3604675-T-G 3736634-T-G +
3829722-C-T 3961681-C-T +
3830334-C-A 3962293-C-A 9×A+
3830343-A-C 3962302-A-C FGC7560 +
5354745-TACAC-T 5486704-TACAC-T +
21889540-A-G 19727654-A-G YY+
4152013-C-A 4283972-C-A +
28490956-C-T 26344809-C-T CTS12136 +
22715167-AG-A 20553281-AG-A +
28630057-T-C 26483910-T-C CTS12593 +
2898521-C-G 3030480-C-G Y+
2898533-G-T 3030492-G-T Y+
7218538-GAC-CAG 7350497-GAC-CAG +
28491035-T-C 26344888-T-C +
14737352-C-T 12625420-C-T Y+
2702974-A-AGTTTTTTTTTTTT 2834933-A-AGTTTTTTTTTTTT +
18846444-G-A 16734564-G-A CTS9358 Y+
19452278-A-T 17340398-A-T CTS10428 YY+
19452295-G-T 17340415-G-T CTS10429 YY+
2659133-T-G 2791092-T-G CTS9 S3199 YY+
2803921-T-C 2935880-T-C CTS197 S3200 YY+
7996735-C-T 8128694-C-T B53 YY+
13995496-C-T 11874790-C-T FGC75765 Y+
14366294-A-T 12245589-A-T CTS2563 YY+
15654923-A-G 13543043-A-G YY+
3902277-A-AT 4034236-A-AT +
4165240-C-T 4297199-C-T +
8616588-C-T 8748547-C-T YY+
7218538-G-C 7350497-G-C YY+
6042007-T-A 6173966-T-A 18×A+
6042023-A-T 6173982-A-T +
6075821-C-T 6207780-C-T Z3804 +
6438063-T-A 6570022-T-A +
6992927-C-T 7124886-C-T BY62773 YY+
7105122-C-A 7237081-C-A YY+
7218477-G-C 7350436-G-C YY+
7218540-C-G 7350499-C-G YY+
6006845-C-T 6138804-C-T +
7581573-T-C 7713532-T-C Z40735 YY+
7774813-T-G 7906772-T-G YY+
8085460-G-A 8217419-G-A YY+
8359497-A-G 8491456-A-G YY+
8369847-G-A 8501806-G-A Y+
8467454-G-A 8599413-G-A Z20313 YY+
8505964-G-A 8637923-G-A YY+
6013651-A-T 6145610-A-T +
6006838-G-T 6138797-G-T +
4293806-A-G 4425765-A-G +
5495433-TG-T 5627392-TG-T +
4571872-G-A 4703831-G-A +
4580751-C-T 4712710-C-T +
4640648-A-C 4772607-A-C +
4742852-T-A 4874811-T-A +
4814245-G-C 4946204-G-C FGC75769 +
5092265-T-C 5224224-T-C +
5254263-G-A 5386222-G-A FGC29365 +
5495454-T-G 5627413-T-G +
5966753-A-C 6098712-A-C +
5497431-G-A 5629390-G-A +
5497590-A-G 5629549-A-G Y138293 +
5512992-T-C 5644951-T-C +
5539342-T-A 5671301-T-A +
5754647-A-T 5886606-A-T +
5768635-A-G 5900594-A-G +
5831298-G-A 5963257-G-A +
5964425-T-C 6096384-T-C +
58985194-C-A 56839047-C-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.

Mutation Notes:

Kit POSITION-REF-ALT (hg19) POSITION-REF-ALT (hg38) Note
Manual3436073-T-C3568032-T-C5 reads, all C.
Manual3436043-G-C3568002-G-C2 C reads, 1 A read.
Manual7080571-C-T7212530-C-T2 good reads, both T.
Manual8445984-CC-GAAA8577943-CC-GAAAIt's an odd situation. I was checking for 8445984-C-A, but that's not what I found. There were two good reads, both showing the CC -> GAAA mutation.
Manual8647188-G-T8779147-G-TOne read, a T.
Manual15713060-A-G13601180-A-GTwo reads, both G.
Manual18405442-G-T16293562-G-TNo coverage.
Manual21834863-A-T19672977-A-T5 reads, all T. This is a nasty junction between an AT repeat and a T repeat.
Manual22462458-A-C20300572-A-C3 reads, all C.
Manual23882406-T-C21720520-T-CNo coverage.
Manual25821433-G-A23675286-G-A2 reads, one A and one G. There's also one third read that seems misaligned.
Manual26144006-G-T23997859-G-TOne good read, a G. There is also one other misaligned read, that looks to be a poor match, but is a G also.
Manual27028447-C-A24882300-C-AOne read, an A.
Manual8445983-T-TGA8577942-T-TGAIn the BigY files, I think the mutations here are recorded as 8445983-T-TGA and 8445984-C-A. But I think it is more correctly reported as 8445984-CC-GAAA.
Manual18090661-C-A15978781-C-A1A
Manual6236579-C-G6368538-C-G2G
Manual17572831-CCT-C15460951-CCT-CAll 4 reads positive.
Manual16718688-C-CAT14606808-C-CAT5 reads
Manual22294679-A-T20132793-A-T4A 2T
Manual27990846-G-C25844699-G-C2C
Manual9028082-CT-C9190473-CT-CJust two reads coverage, but both carry the deletion.
Manual22273433-G-C20111547-G-C2C



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