Tree Position

A0-T-YP2191 > P305 > L413/PF1409/V31 > M168/PF1416 > P143 > M89/PF2746 > F1329/M3658 > F929 > IJK > IJ > J > J2 > 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
HG01619
13683026-C-T 11527350-C-T BY40877 +
18083935-C-T 15972055-C-T YP110 YY+
17348061-T-C 15236181-T-C PF7334 YY+
17873573-C-T 15761693-C-T YY+
17920515-G-A 15808635-G-A YP101 YY+
17965444-G-A 15853564-G-A CTS8377 Y+
17983183-G-A 15871303-G-A YP105 Y+
18074276-A-G 15962396-A-G CTS8539 YY+
18149582-G-C 16037702-G-C YY+
17295550-A-G 15183670-A-G CTS7112 YY+
18160999-A-G 16049119-A-G YP111 YY+
18606434-T-G 16494554-T-G YY+
18675779-T-C 16563899-T-C CTS9100 YY+
19027792-G-T 16915912-G-T Z28764 Y+
19268635-G-A 17156755-G-A Y132579 YY+
19311571-T-C 17199691-T-C CTS10179 YY+
19429124-C-T 17317244-C-T Y+
17297024-A-G 15185144-A-G YP90 YY+
17241976-G-A 15130096-G-A Y22525 YY+
21178859-A-G 19016973-A-G YP134 YY+
15900270-G-A 13788390-G-A CTS4915 YY+
14822341-T-C 12710408-T-C CTS3310 YY+
15123573-T-A 13011660-T-A YP58 YY+
15127519-T-A 13015606-T-A CTS3722 YY+
15197944-G-A 13086030-G-A CTS3810 YY+
15216701-A-C 13104787-A-C CTS3833 Y+
15839900-A-T 13728020-A-T YY+
16214089-G-A 14102209-G-A CTS5338 Y+
17160888-T-C 15049008-T-C Y+
16341539-A-G 14229659-A-G Y22037 YY+
16435397-G-A 14323517-G-A PF7324 YY+
16650768-C-A 14538888-C-A YP84 YY+
16871968-G-A 14760088-G-A YP85 YY+
16913725-C-T 14801845-C-T YY+
17050431-A-C 14938551-A-C YP87 YY+
17126239-G-T 15014359-G-T CTS6823 Y+
19430762-T-A 17318882-T-A CTS10387 YY+
21364637-T-C 19202751-T-C YP140 YY+
14771925-G-A 12659994-G-A PF7306 YY+
23471983-T-G 21310097-T-G YP184 YY+
22734720-A-G 20572834-A-G CTS10731 PF7319 YY+
23064137-A-G 20902251-A-G CTS11307 YY+
23093441-A-C 20931555-A-C YP172 Y+
23131051-C-T 20969165-C-T PF7331 YY+
23197176-C-G 21035290-C-G YP175 Y+
23436447-G-A 21274561-G-A YP183 YY+
23574580-T-G 21412694-T-G Y3163 YY+
22629712-G-T 20467826-G-T Y+
23733441-C-T 21571555-C-T Y3162 +
23808852-T-C 21646966-T-C Y3161 Y+
23963077-C-T 21816930-C-T Y3160 Y+
24004530-T-A 21858383-T-A Y38239 Y+
24418427-A-T 22272280-A-T Y3165 Y+
26404712-G-A 24258565-G-A P1_Y1 +
28616600-T-A 26470453-T-A CTS12568 +
22670079-A-G 20508193-A-G YP166 YY+
22593727-A-C 20431841-A-C YP163 Y+
21544124-T-C 19382238-T-C YP144 Y+
22081463-G-A 19919577-G-A Y22524 YY+
21544794-A-G 19382908-A-G PF7377 Y+
21569683-A-C 19407797-A-C PF7376 YY+
21691673-C-T 19529787-C-T YP149 YY+
21777517-A-G 19615631-A-G PF7316 YY+
21857161-A-T 19695275-A-T PF7321 YY+
22007004-A-G 19845118-A-G YP159 YY+
22015258-G-A 19853372-G-A Y+
22088872-G-T 19926986-G-T YY+
22484383-G-A 20322497-G-A Y3166 YFS3166 DYZ19 +
22189193-G-A 20027307-G-A Y3167 YY+
22271500-T-G 20109614-T-G PF7314 DYZ19 +
22316832-T-G 20154946-T-G DYZ19 +
22317318-G-T 20155432-G-T DYZ19 +
22362090-T-A 20200204-T-A BY40905 DYZ19 +
22446293-G-T 20284407-G-T DYZ19 +
22480075-T-G 20318189-T-G BY40909 DYZ19 +
14776132-C-G 12664201-C-G PF7357 YY+
14722795-A-G 12610863-A-G PF7368 YY+
13680835-G-A 11525159-G-A BY88216 +
6795563-G-A 6927522-G-A CTS494 YY+
5528090-T-C 5660049-T-C +
5549944-C-T 5681903-C-T +
5987564-G-A 6119523-G-A +
6355463-C-T 6487422-C-T BY40873 +
6376932-A-G 6508891-A-G BY40874 +
6761978-C-T 6893937-C-T YP8 YY+
6844984-G-T 6976943-G-T CTS560 YY+
4992499-C-T 5124458-C-T +
7308226-C-T 7440185-C-T CTS1282 YY+
7395505-G-A 7527464-G-A Y22526 YY+
7449560-C-T 7581519-C-T Z28759 IR1_L +
7508352-C-CTT 7640311-C-CTT +
7518040-G-T 7649999-G-T Y12196 Y+
7542914-A-G 7674873-A-G Y22527 YY+
7604736-T-C 7736695-T-C PF7294 YY+
5255396-G-A 5387355-G-A +
4646193-C-T 4778152-C-T +
7774205-C-A 7906164-C-A YY+
3038640-C-A 3170599-C-A +
7869092-G-A 8001051-G-A Y12198 YY+
16617481-A-G 14505601-A-G Y+
22670292-G-A 20508406-G-A A4632 YY+
2730419-G-A 2862378-G-A Y3180 YY+
2788565-G-A 2920524-G-A PF7356 Y+
2903922-T-C 3035881-T-C PF7347 YY+
3173598-G-A 3305557-G-A +
4317554-T-A 4449513-T-A +
3308400-G-C 3440359-G-C +
3320980-T-C 3452939-T-C PF7367 +
3487393-T-G 3619352-T-G +
3823953-T-C 3955912-T-C +
3968929-T-C 4100888-T-C +
4069151-T-C 4201110-T-C PF7345 +
4083909-C-G 4215868-C-G +
7647202-T-C 7779161-T-C YSC0000302 YY+
7844023-T-C 7975982-T-C PF7301 YY+
14593938-T-C 12482138-T-C Y22521 YY+
13933783-A-G 11813077-A-G YP21 Y+
9908976-G-A 10071367-G-A Y+
9977088-A-T 10139479-A-T Y+
10022291-C-T 10184682-C-T BY40875 Y+
13235818-A-C 11080142-A-C +
13609895-T-A 11454219-T-A +
13684801-G-C 11529125-G-C BY54326 +
13994300-G-A 11873594-G-A Y+
9442891-C-T 9605282-C-T Y3169 YY+
14073956-G-C 11953250-G-C YP28 YY+
14083214-C-T 11962508-C-T PF7308 YY+
14136163-G-T 12015457-G-T CTS1969 YY+
14137063-A-G 12016357-A-G YP31 YY+
14178291-C-A 12057585-C-A YP34 Y+
14178714-G-T 12058008-G-T YP35 Y+
14493787-G-A 12381984-G-A YP46 YY+
9846835-G-A 10009226-G-A Y3164 YY+
9399174-G-A 9561565-G-A Y38247 YY+
7975150-A-G 8107109-A-G PF7354 YY+
8333752-T-G 8465711-T-G PF7364 YY+
8059228-G-A 8191187-G-A Y3179 YY+
8064348-G-A 8196307-G-A Y+
8067892-C-T 8199851-C-T YY+
8181475-A-G 8313434-A-G Y3178 YY+
8193207-C-T 8325166-C-T Y3177 YY+
8203555-C-G 8335514-C-G Y3176 YY+
8314932-A-T 8446891-A-T Y3175 YY+
8352913-C-T 8484872-C-T Y22529 YY+
9084785-G-C 9247176-G-C PF7353 Y+
8425847-A-G 8557806-A-G Y3174 YY+
8452783-C-G 8584742-C-G Y3173 YY+
8540917-T-C 8672876-T-C Y22520 YY+
8675266-G-A 8807225-G-A PF7344 YY+
8709112-G-A 8841071-G-A Y3172 YY+
8710700-A-G 8842659-A-G YY+
8858289-C-A 8990248-C-A Y3171 YY+
59017912-A-T 56871765-A-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.




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