Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > FGC11134 > A353 > Z16250 > A114 > CTS4466/S1136 > S1115 > A541 > S1121 > Z16251 > A159 > Z17981 > A6507 > S27124 > 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
NA20278
Manual
Edits
22739741-G-A 20577855-G-A YY+
13298698-C-T 11143022-C-T +
13386219-C-T 11230543-C-T +
13383123-G-A 11227447-G-A +
13373487-G-A 11217811-G-A +
13309130-T-C 11153454-T-C +
13306419-A-T 11150743-A-T +
13306386-A-G 11150710-A-G +
13298427-G-A 11142751-G-A +
13392768-CA-C 11237092-CA-C 11×A+
13295471-T-C 11139795-T-C +
13294965-A-G 11139289-A-G +
13294960-T-C 11139284-T-C +
13263647-G-A 11107971-G-A +
13261289-T-A 11105613-T-A +
13261275-G-A 11105599-G-A +
13387195-C-T 11231519-C-T +
13423471-G-T 11267795-G-T Z11551 +
13259839-T-A 11104163-T-A +
13475187-G-A 11319511-G-A +
13538672-A-C 11382996-A-C +
13533709-G-T 11378033-G-T +
13521412-T-A 11365736-T-A +
13507055-C-G 11351379-C-G +
13502853-T-A 11347177-T-A +
13482531-G-C 11326855-G-C +
13472458-C-T 11316782-C-T +
13435066-A-G 11279390-A-G +
13464789-C-T 11309113-C-T BY85702 +
13448850-A-ATTCCATTCCT 11293174-A-ATTCCATTCCT +
13448847-T-TCCATACCATA 11293171-T-TCCATACCATA +
13448846-T-TTCCATTCCAC 11293170-T-TTCCATTCCAC +
13448844-C-CATTCCATTCA 11293168-C-CATTCCATTCA +
13448734-C-CATTCG 11293058-C-CATTCG +
13445381-G-GAAA 11289705-G-GAAA +
13261255-G-C 11105579-G-C +
13259808-G-C 11104132-G-C +
13612029-C-A 11456353-C-A +
7428503-C-T 7560462-C-T CTS1473 YY+
8034824-G-A 8166783-G-A YY+
7915372-A-C 8047331-A-C YY+
7717676-CT-C 7849635-CT-C +
7717632-TCCC-T 7849591-TCCC-T +
7657669-GCA-G 7789628-GCA-G +
7604553-T-C 7736512-T-C YY+
7417492-G-A 7549451-G-A YY+
8534777-C-G 8666736-C-G YY+
7320854-AAC-A 7452813-AAC-A +
7317603-T-C 7449562-T-C CTS1295 YY+
7053358-AAAAGAAAGAAAGAAAGAAAG-A 7185317-AAAAGAAAGAAAGAAAGAAAG-A 17×AAAG+
6786748-C-T 6918707-C-T YY+
6515573-A-ATTT 6647532-A-ATTT 10×T+
6438073-G-A 6570032-G-A +
6403110-A-T 6535069-A-T +
8093696-G-A 8225655-G-A YY+
8774154-G-A 8906113-G-A YY+
13258359-A-T 11102683-A-T 9×T+
13194504-C-T 11038828-C-T +
13257817-A-T 11102141-A-T +
13254614-TC-T 11098938-TC-T +
13252941-G-T 11097265-G-T +
13243352-G-A 11087676-G-A +
13241598-G-C 11085922-G-C +
13241593-T-C 11085917-T-C +
13194502-T-C 11038826-T-C +
9009910-A-G 9172301-A-G Y+
10068759-C-A 10231150-C-A +
10068675-C-G 10231066-C-G +
9958851-C-T 10121242-C-T Y+
9958801-G-T 10121192-G-T Y+
9859556-A-C 10021947-A-C YY+
9674996-T-C 9837387-T-C IR3_Prx +
9307402-G-GTT 9469793-G-GTT +
13579340-C-T 11423664-C-T +
13690097-ATGGAG-A 11534421-ATGGAG-A +
6150000-G-T 6281959-G-T IR3_Dst +
22893304-CCTTTCTTTCTTTCTTT-C 20731418-CCTTTCTTTCTTTCTTT-C 17×CTTT+
24485667-C-CA 22339520-C-CA +
24388225-CTA-C 22242078-CTA-C +
23271510-G-C 21109624-G-C CTS11786 YY+
23148744-TC-T 20986858-TC-T +
22938826-T-TTG 20776940-T-TTG +
22893384-C-T 20731498-C-T BY163170 YY+
22489700-G-T 20327814-G-T DYZ19 +
24886464-C-A 22740317-C-A PF4400 g1 13×A+
22489691-G-A 20327805-G-A DYZ19 +
22260993-A-T 20099107-A-T DYZ19 +
21946479-G-A 19784593-G-A YY+
21722694-A-T 19560808-A-T YY+
21616829-C-G 19454943-C-G YY+
21502811-C-T 19340925-C-T S23175 Y+
24485671-A-AT 22339524-A-AT +
25200847-C-A 23054700-C-A g1 15×AAAG+
21423453-T-A 19261567-T-A YY+
58906054-T-C 56684817-A-G +
59028960-G-A 56882813-G-A +
59025553-C-A 56879406-C-A +
59024715-T-C 56878568-T-C +
59002708-A-G 56856561-A-G +
58986296-C-G 56840149-C-G +
58970942-G-A 56824795-G-A +
58901504-C-G 56689367-G-C +
26508182-C-T 24362035-C-T FGC8528 P1_Y1 +
58873959-T-C 56716912-A-G +
58872987-C-G 56717884-G-C +
58819361-NG-N +
28724418-C-G 26578271-C-G Y+
28698666-GT-G 26552519-GT-G 9×T+
28661410-T-C 26515263-T-C Y+
28638611-T-C 26492464-T-C +
21502807-G-T 19340921-G-T M4411 Y+
21347063-A-G 19185177-A-G Y+
13714700-G-T 11559024-G-T +
14881732-GTA-G 12769800-GTA-G +
17275757-A-G 15163877-A-G M9206 YY+
16892590-A-C 14780710-A-C M9186 YY+
16244821-GTGTA-G 14132941-GTGTA-G +
16244790-AGGGT-A 14132910-AGGGT-A +
16218835-C-A 14106955-C-A Z36112 YY+
15159251-T-A 13047337-T-A YY+
14419573-C-G 12298848-C-G CTS2672 YY+
17302264-T-A 15190384-T-A YY+
14296437-T-C 12175731-T-C CTS2414 YY+
13949032-C-A 11828326-C-A Y+
13888692-T-TTG 11767986-T-TTG 9×TG+
13873378-A-G 11752672-A-G Y+
13738889-A-G 11583213-A-G +
13714760-C-CGGAAG 11559084-C-CGGAAG +
13714756-C-CGAACG 11559080-C-CGAACG +
17275758-A-G 15163878-A-G M9207 YY10×AAGGG+
17385419-T-A 15273539-T-A YY+
21189054-T-A 19027168-T-A YY+
19050397-G-A 16938517-G-A S21692 YY+
21149581-GGT-G 18987695-GGT-G +
19386785-TA-T 17274905-TA-T +
19187413-TGCAC-T 17075533-TGCAC-T +
19128804-AG-A 17016924-AG-A +
19073921-TAC-T 16962041-TAC-T +
19056770-A-T 16944890-A-T CTS9750 S3651 YY+
18891480-T-C 16779600-T-C YY+
17543973-AT-A 15432093-AT-A +
18872262-CTTT-C 16760382-CTTT-C +
18872258-CTTTCT-C 16760378-CTTTCT-C +
18564313-A-T 16452433-A-T YY+
18550523-A-G 16438643-A-G CTS8921 S3648 Y+
18409093-T-G 16297213-T-G P6_Gap +
18230822-G-T 16118942-G-T +
17948277-A-C 15836397-A-C YY+
6398637-A-AAC 6530596-A-AAC 23×AC+
6084038-T-C 6215997-T-C +
14612404-G-C 12500610-G-C KMS46 YY+
13888652-T-C 11767946-T-C YY+
17836391-A-G 15724511-A-G Y+
17230162-T-A 15118282-T-A Y14×A+
16348383-G-A 14236503-G-A S3646 CTS5536 YY+
15987060-A-T 13875180-A-T YY13×T+
15753706-G-A 13641826-G-A S3649 CTS4655 YY+
14033930-G-A 11913224-G-A YY+
2894227-T-C 3026186-T-C Z9905 YY+
18763472-C-T 16651592-C-T CTS9233 S3643 YY+
18606854-G-T 16494974-G-T YY13×T+
8119489-G-T 8251448-G-T BY70093 YY14×T+
15023555-A-C 12911643-A-C S16678 F11578 YY+
21502799-G-T 19340913-G-T M8115 Y+
28698742-GCTT-ACTC 26552595-GCTT-ACTC +
7270276-C-T 7402235-C-T YY25×T+
18231477-A-G 16119597-A-G CTS8832 +
21434334-T-C 19272448-T-C YY+
22319023-GT-G 20157137-GT-G DYZ19 +
13741945-A-T 11586269-A-T +
13570558-C-T 11414882-C-T +
14467033-ATCTG-A 12346302-ATCTG-A +
13508902-A-G 11353226-A-G +
13276363-T-C 11120687-T-C +
5408786-A-C 5540745-A-C +
13270036-A-G 11114360-A-G +
13276016-T-C 11120340-T-C +
28672335-AAAAAAG-TAAAAAA 26526188-AAAAAAG-TAAAAAA +
13272929-C-T 11117253-C-T +
17385421-C-A 15273541-C-A YY15×A+
6417344-C-CT 6549303-C-CT +
4489540-C-T 4621499-C-T FGC65994 +
6417359-A-G 6549318-A-G +
13502822-A-T 11347146-A-T +
5634005-C-A 5765964-C-A +
13387250-A-G 11231574-A-G +
13392883-G-A 11237207-G-A +
13489486-G-T 11333810-G-T +
16990247-AG-A 14878367-AG-A +
58884655-T-A 56706216-A-T +
59017984-C-T 56871837-C-T +
5905918-G-A 6037877-G-A +
13306346-T-G 11150670-T-G +
13306805-A-C 11151129-A-C +
58871385-T-C 56719486-A-G +
58867513-C-T 56723358-G-A +
4682322-C-T 4814281-C-T +
59012707-T-G 56866560-T-G +
7105709-CGT-C 7237668-CGT-C +
17836401-T-G 15724521-T-G CTS8102 Y+
28638522-G-A 26492375-G-A CTS12611 +
13727671-A-G 11571995-A-G +
13704923-A-G 11549247-A-G +
16833655-TAC-T 14721775-TAC-T 17×AC+
13241287-G-A 11085611-G-A +
58836907-C-T 56753964-G-A +
13392904-G-A 11237228-G-A +
22457517-G-A 20295631-G-A DYZ19 +
13302779-G-A 11147103-G-A +
19130738-C-T 17018858-C-T YY33×T+
19130731-C-T 17018851-C-T 17018851-C-T YY+
4682288-A-G 4814247-A-G YFS032810 +
3440990-C-T 3572949-C-T +
13298423-A-C 11142747-A-C +
13243326-T-C 11087650-T-C +
13252913-G-A 11097237-G-A +
59002734-A-C 56856587-A-C +
4682281-C-A 4814240-C-A YFS032809 +
59030791-G-GA 56884644-G-GA 10×A+
19073838-GTA-G 16961958-GTA-G 16×TA+
13258354-G-A 11102678-G-A +
13276278-C-G 11120602-C-G +
13392858-A-C 11237182-A-C +
13570555-A-T 11414879-A-T +
13462413-G-C 11306737-G-C +
5999363-C-CAAAAAA 6131322-C-CAAAAAA 20×A+
4453852-T-A 4585811-T-A +
5130488-G-T 5262447-G-T +
5032237-A-ATT 5164196-A-ATT 13×T+
4826402-A-T 4958361-A-T +
4548351-T-C 4680310-T-C +
4493229-T-C 4625188-T-C FGC37865 +
4473474-A-AT 4605433-A-AT +
4442072-C-T 4574031-C-T +
5168875-A-G 5300834-A-G +
4442069-T-C 4574028-T-C +
4442007-C-T 4573966-C-T +
4438834-C-T 4570793-C-T +
4425057-G-A 4557016-G-A +
4425052-A-T 4557011-A-T +
4419752-G-C 4551711-G-C +
5130492-G-T 5262451-G-T +
5240050-A-G 5372009-A-G +
4368476-A-G 4500435-A-G +
5570756-G-C 5702715-G-C +
5905922-C-T 6037881-C-T +
5862139-T-C 5994098-T-C +
5833627-C-CT 5965586-C-CT 9×T+
5680232-C-G 5812191-C-G +
5680174-A-C 5812133-A-C +
5680164-T-G 5812123-T-G +
5506037-G-A 5637996-G-A +
5240155-G-A 5372114-G-A +
5462508-CCA-C 5594467-CCA-C +
5458918-A-G 5590877-A-G +
5421275-A-T 5553234-A-T +
5411321-A-C 5543280-A-C +
5381817-A-G 5513776-A-G +
5317042-T-C 5449001-T-C +
5308974-G-A 5440933-G-A +
4416300-A-G 4548259-A-G +
4353990-T-C 4485949-T-C +
5670077-G-T 5802036-G-T +
3302904-TTTTA-T 3434863-TTTTA-T 11×TTTA+
3440982-T-G 3572941-T-G +
3430154-T-A 3562113-T-A +
3427775-C-T 3559734-C-T FGC48408 +
3427606-C-T 3559565-C-T +
3425715-A-G 3557674-A-G +
3410398-A-T 3542357-A-T +
3297535-A-G 3429494-A-G +
3496479-C-A 3628438-C-A +
3279696-TAA-T 3411655-TAA-T +
3146573-C-A 3278532-C-A S3554 +
3110476-G-A 3242435-G-A +
3110401-C-T 3242360-C-T +
3072315-T-A 3204274-T-A +
2775139-C-T 2907098-C-T M8138 Y+
18872246-TTCTC-T 16760366-TTCTC-T +
3475896-G-A 3607855-G-A +
3706791-T-G 3838750-T-G +
4329086-G-A 4461045-G-A +
4191420-A-C 4323379-A-C +
4329083-C-G 4461042-C-G +
4293744-T-C 4425703-T-C +
4226185-G-A 4358144-G-A +
4217428-T-C 4349387-T-C +
4217408-A-G 4349367-A-G +
4217141-G-A 4349100-G-A +
4177137-TAC-T 4309096-TAC-T 18×AC+
3706829-A-G 3838788-A-G +
3923136-C-G 4055095-C-G +
3923120-A-T 4055079-A-T +
3923086-G-A 4055045-G-A +
3899405-G-C 4031364-G-C +
3899386-T-G 4031345-T-G +
3756315-C-T 3888274-C-T +
3706839-G-A 3838798-G-A +
59028981-C-T 56882834-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:

Kit POSITION-REF-ALT (hg19) POSITION-REF-ALT (hg38) Note
NA2027822229264-C-A20067378-C-AChecked BAM File. Just one read, but it is an A.
Manual25133527-C-T22987380-C-T1C 1T
Manual6172699-G-C6304658-G-CJust one read, but is a C.
Manual14710233-A-G12598300-A-G1G
Manual15540246-T-C13428366-T-C1C
Manual16452022-C-T14340142-C-T3T
Manual19237370-C-T17125490-C-TJust one read, a T. Oddly, the mate doesn't look to belong here, or anywhere else.
Manual23894624-G-C21732738-G-C1C
Manual17868583-TAC-T15756703-TAC-TJust one read, but it has the deletion.
Manual14435052-A-T12314325-A-T3A 2T
Manual19690217-T-A17578337-T-A2 reads cover the necessary area, and both show the T to A replacement.
Manual14583239-G-A12471439-G-A1A
Manual21316002-C-A19154116-C-A1A
Manual6517053-TC-T6649012-TC-T3 reads all show the deletion.
Manual3898943-G-A4030902-G-A1A
Manual14161650-G-A12040944-G-A1A
Manual25972245-T-C23826098-T-C4C 1T
Manual8420708-T-C8552667-T-C1C



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