Tree Position

R-M269 > L23 > Z2103 > Z2106 > Z2108 > Z2110 > CTS7556 > Y5589 > 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
HG01515
Manual
Edits
13453104-T-C 11297428-T-C +
7079831-C-T 7211790-C-T Z34574 YP5955 YY+
5439078-T-G 5571037-T-G +
5504101-C-T 5636060-C-T +
5532646-C-T 5664605-C-T 15×T+
5532656-T-G 5664615-T-G +
5865929-C-T 5997888-C-T FT325323 +
5906355-G-C 6038314-G-C +
5999383-ACT-A 6131342-ACT-A +
6498633-C-T 6630592-C-T +
6613906-G-A 6745865-G-A +
6672014-C-G 6803973-C-G Y5586 YY+
6708195-T-C 6840154-T-C CTS359 PF5410 YY+
7158307-T-C 7290266-T-C YY+
5231160-C-A 5363119-C-A +
7218209-G-A 7350168-G-A CTS1121 YY+
7685979-G-A 7817938-G-A FT300213 YY+
7723925-G-A 7855884-G-A Y+
7783503-G-A 7915462-G-A YY+
8178727-C-T 8310686-C-T YY+
8229832-G-A 8361791-G-A YY+
8270705-T-C 8402664-T-C YY+
8413612-G-T 8545571-G-T YY+
8481198-A-AT 8613157-A-AT +
9757387-T-A 9919778-T-A Y+
13296198-TC-T 11140522-TC-T +
5349400-G-A 5481359-G-A FT136541 +
4937386-T-C 5069345-T-C FT322177 +
13494487-C-A 11338811-C-A +
28569292-G-A 26423145-G-A +
17788245-A-T 15676365-A-T Y+
19312777-T-G 17200897-T-G YY+
19386785-TA-T 17274905-TA-T +
20025429-T-C 17913549-T-C P5_Prx +
21579245-C-A 19417359-C-A Y+
21966565-TC-T 19804679-TC-T +
22014995-C-A 19853109-C-A M1972 Y+
22167919-T-C 20006033-T-C YY+
26440573-C-T 24294426-C-T P1_Y1 +
27454144-G-C 25307997-G-C P1_Y2 +
27521864-G-A 25375717-G-A P1_Y2 +
28604285-T-G 26458138-T-G +
4426085-A-G 4558044-A-G +
28604288-A-G 26458141-A-G +
28604299-G-A 26458152-G-A +
28642809-G-C 26496662-G-C 22×AC+
28803488-G-T 26657341-G-T +
58901504-C-G 56689367-G-C +
58906054-T-C 56684817-A-G +
3302783-TTG-T 3434742-TTG-T +
3620095-A-T 3752054-A-T +
3859286-A-G 3991245-A-G FT318742 +
3976433-T-C 4108392-T-C +
4095607-G-C 4227566-G-C +
4426081-C-T 4558040-C-T +
13312887-G-T 11157211-G-T +
13521087-A-T 11365411-A-T +
17160359-G-A 15048479-G-A Y+
22785632-T-C 20623746-T-C YY+
19379478-G-A 17267598-G-A CTS10297 YY+
19561233-A-G 17449353-A-G CTS10593 Y+
20832780-T-A 18670894-T-A P4_Gap +
21273676-C-T 19111790-C-T Y18960 Y+
21987083-A-G 19825197-A-G Y5587 YY+
22013780-T-C 19851894-T-C FT314462 Y+
22244459-C-T 20082573-C-T DYZ19 +
22487131-A-T 20325245-A-T BY224901 DYZ19 +
22511470-T-C 20349584-T-C DYZ19 +
22542629-G-A 20380743-G-A FGC47903 Y+
22767495-C-A 20605609-C-A YY+
23095780-G-T 20933894-G-T Y+
19130975-G-T 17019095-G-T CTS9906 YY+
23191296-G-A 21029410-G-A Y5588 Y+
23257041-G-T 21095155-G-T CTS11767 YY+
23276756-A-G 21114870-A-G Y+
23414903-T-A 21253017-T-A YY+
23787904-T-A 21626018-T-A +
24388240-CTA-C 22242093-CTA-C +
24873557-C-T 22727410-C-T g1 +
27546078-T-C 25399931-T-C P1_Y2 +
28569275-G-A 26423128-G-A +
28687298-T-A 26541151-T-A +
28752878-T-A 26606731-T-A +
19253014-G-A 17141134-G-A CTS10097 Y+
19073869-TAC-T 16961989-TAC-T 10×AC+
13639899-C-A 11484223-C-A +
15967501-T-TC 13855621-T-TC +
13686866-T-C 11531190-T-C +
13688239-A-T 11532563-A-T +
13820330-G-A 11699624-G-A FT328504 +
13831727-C-T 11711021-C-T FT328593 +
14248631-T-C 12127925-T-C YY+
14266331-ATATG-A 12145625-ATATG-A +
14388605-T-C 12267901-T-C YY+
14868202-T-A 12756272-T-A YY+
14869230-C-A 12757300-C-A YY+
15530115-G-T 13418235-G-T YY+
15688461-C-T 13576581-C-T YY+
16272499-A-C 14160619-A-C Y+
19010395-A-G 16898515-A-G YY+
16388423-TTG-T 14276543-TTG-T +
16512997-A-T 14401117-A-T YY+
16926238-C-A 14814358-C-A FT301504 Y+
17026197-A-G 14914317-A-G CTS6641 Y+
17427183-A-G 15315303-A-G CTS7334 YY+
17653947-T-C 15542067-T-C YY+
17764622-A-T 15652742-A-T CTS7959 YY+
17829781-C-A 15717901-C-A Y+
18385663-G-A 16273783-G-A Y11923 FGC10794 P6_Gap +
18633441-A-G 16521561-A-G YY+
18760768-G-T 16648888-G-T CTS9230 YY+
18872288-T-C 16760408-T-C YY+
17304914-TTAA-T 15193034-TTAA-T +
16938208-TC-T 14826328-TC-T +
13686864-C-A 11531188-C-A BY998 +
6036859-T-G 6168818-T-G +
14609822-AT-A +
58910951-G-T 56679920-C-A +
15491908-G-T 13380028-G-T YY+
6498648-A-G 6630607-A-G +
9735605-G-GTTT 9897996-G-GTTT IR3_Prx 30×T+
58823340-C-T 56767531-G-A +
3902256-A-T 4034215-A-T PF66 +
16739069-G-A 14627189-G-A Y17×A+
10091895-A-C 10254286-A-C +
58823338-T-A 56767533-A-T +
8546027-C-G 8677986-C-G BY73892 YY+
6036864-C-T 6168823-C-T +
58881774-C-T 56709097-G-A +
22015014-C-G 19853128-C-G Y+
58877533-T-C 56713338-A-G +
13388629-T-C 11232953-T-C +
13441590-T-A 11285914-T-A Z11552 +
58823337-A-C 56767534-T-G +
9877903-T-G 10040294-T-G A12120 YY+
58976110-T-TACTCC 56829963-T-TACTCC +
3035361-T-C 3167320-T-C +
3080515-A-AT 3212474-A-AT +
3186017-A-G 3317976-A-G +
3250107-G-A 3382066-G-A +
15320655-AGAG-A 13208761-AGAG-A +
58881805-C-T 56709066-G-A +
3420167-C-T 3552126-C-T +
14512004-A-G 12400209-A-G CTS2836 Y+
16772453-C-T 14660573-C-T FT231730 YY+
22507126-G-T 20345240-G-T BY225315 DYZ19 +
15320661-AGAG-A 13208767-AGAG-A +
9478312-A-C 9640703-A-C +
9478313-A-C 9640704-A-C +
28604359-T-C 26458212-T-C CTS12540 +
28604360-T-C 26458213-T-C CTS12541 +
7723948-C-T 7855907-C-T FT426388 Y25×T+
14242413-A-G 12121707-A-G CTS2264 YY+
26538868-TTA-T 24392721-TTA-T P1_g2 16×TA+
13736210-T-A 11580534-T-A +
58824721-A-T 56766150-T-A +
6756935-G-A 6888894-G-A Y+
9398567-G-T 9560958-G-T BY65178F1541 YY+
3279698-A-AAAAT 3411657-A-AAAAT 9×AAAT+
22258848-A-T 20096962-A-T DYZ19 +
58837733-G-A 56753138-C-T +
22273206-G-C 20111320-G-C BY31013 DYZ19 +
13712902-A-T 11557226-A-T +
28588053-C-T 26441906-C-T +
28604465-C-G 26458318-C-G CTS12543 +
17667239-A-G 15555359-A-G CTS7791 YY+
27127602-A-C 24981455-A-C BY226822 P1_g3 14×TTTC+
13639861-A-C 11484185-A-C FGC78075 +
28787610-A-G 26641463-A-G +
3301831-C-T 3433790-C-T +
3420807-T-G 3552766-T-G +
16904729-A-AGT 14792849-A-AGT +
13504349-G-A 11348673-G-A +
13271216-AG-A 11115540-AG-A +
13278499-A-T 11122823-A-T +
13295768-T-G 11140092-T-G +
13309455-A-G 11153779-A-G +
13431640-A-G 11275964-A-G +
13440850-C-T 11285174-C-T +
13440910-C-A 11285234-C-A +
13440911-A-G 11285235-A-G +
13500003-C-T 11344327-C-T +
13500074-C-A 11344398-C-A +
13500181-G-A 11344505-G-A +
13504405-A-G 11348729-A-G +
13261275-G-A 11105599-G-A +
13616462-A-T 11460786-A-T +
13690097-ATGGAG-A 11534421-ATGGAG-A +
13691802-G-GAATGC 11536126-G-GAATGC +
13691813-A-AATGGC 11536137-A-AATGGC +
13898753-TG-T 11778047-TG-T +
14709272-C-CT 12597338-C-CT +
14709281-A-AC 12597348-A-AC +
14886421-G-A 12774487-G-A YY+
14981870-CTTCCT-C 12869938-CTTCCT-C +
15047298-TA-T 12935388-TA-T +
15374426-C-T 13262546-C-T YY+
16889955-A-ATAAC 14778075-A-ATAAC +
13261289-T-A 11105613-T-A +
13261255-G-C 11105579-G-C +
3567565-GCA-G 3699524-GCA-G +
7197568-G-T 7329527-G-T YY+
3736996-A-T 3868955-A-T +
3902277-A-AT 4034236-A-AT +
4021899-G-T 4153858-G-T 12×T+
5227087-C-CAAAA 5359046-C-CAAAA 21×A+
5403289-A-T 5535248-A-T +
5552404-T-G 5684363-T-G +
5661422-A-G 5793381-A-G +
5962150-G-A 6094109-G-A +
6521568-TG-T 6653527-TG-T +
6756952-T-A 6888911-T-A YY9×A+
7124832-G-A 7256791-G-A FT300068 Y+
7545011-T-TC 7676970-T-TC +
13256166-C-T 11100490-C-T +
7723917-G-A 7855876-G-A Y+
7758508-TC-T 7890467-TC-T +
7915372-A-C 8047331-A-C YY+
9414414-C-CTG 9576805-C-CTG 17×TG+
9789274-ACG-A 9951665-ACG-A +
9955964-A-C 10118355-A-C Y+
13138217-ATTCC-A 10627703-ATTCC-A +
13138390-CACCAT-C 10627876-CACCAT-C +
13140970-A-AT 10630456-A-AT +
13223340-G-A 11067664-G-A +
13223592-A-T 11067916-A-T +
13252192-A-C 11096516-A-C +
28805028-C-A 26658881-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
Manual15275092-G-A13163181-G-A3A
Manual15689304-A-G13577424-A-G1G
Manual17713385-A-T15601505-A-T1T
Manual21481015-T-G19319129-T-G1G
Manual23183253-A-G21021367-A-G1A 2G
Manual16050529-T-G13938649-T-G1G



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