Tree Position

A0-T-YP2191 > P305[A1] > A1b > BT/A1b2 > M168/PF1416[CT] > P143[CF] > M89/PF2746[F] > F1329/M3658[GHI > F929[HIJK] > 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
NA21130
3513343-C-A 3645302-C-A FGC35376 +
3543999-C-G 3675958-C-G FGC28800 F8735 +
3672050-A-G 3804009-A-G Z44875 +
4072344-A-C 4204303-A-C FGC35375 +
4090408-G-A 4222367-G-A Z44876 +
4252900-T-C 4384859-T-C Z44877 +
4643319-G-T 4775278-G-T FGC35360 +
4686234-A-C 4818193-A-C Z44878 +
4790174-C-A 4922133-C-A Z44880 +
4815972-C-T 4947931-C-T FGC35346 +
5075424-G-A 5207383-G-A FGC35383 +
5979761-C-T 6111720-C-T FGC35374 +
6010584-T-C 6142543-T-C Z44881 +
6367173-T-A 6499132-T-A FGC35348 +
6871199-C-A 7003158-C-A FGC35372 YY+
7040606-C-T 7172565-C-T FGC35351 Y+
7152161-T-C 7284120-T-C FGC35362 Z32166 A5360 YY+
7682862-G-T 7814821-G-T FGC35382 YY+
7915606-G-A 8047565-G-A FGC35371 YY+
7956150-A-C 8088109-A-C Y15907 Z36242 YY+
8022965-C-G 8154924-C-G Z44886 YY+
8023660-G-T 8155619-G-T FGC35347 YY+
8202202-T-C 8334161-T-C Y15908 FGC35356 YY+
8249632-G-A 8381591-G-A Y15598 Z36243 YY+
8250217-G-A 8382176-G-A FGC35380 YY+
8463471-G-C 8595430-G-C Y15599 FGC35354 YY+
8473032-C-T 8604991-C-T Y15600 FGC35373 YY+
9429897-A-C 9592288-A-C Z44889 Y+
9476166-G-T 9638557-G-T Z44890 +
9891649-T-C 10054040-T-C Z44891 YY+
9919566-G-C 10081957-G-C Z44892 Y+
13210274-G-A 11054598-G-A Z44893 +
13291222-C-A 11135546-C-A FGC35352 +
13404717-G-A 11249041-G-A FGC35345 +
13651728-A-C 11496052-A-C FGC35361 +
13685007-C-T 11529331-C-T FGC35368 +
13946693-C-T 11825987-C-T FGC35370 YY+
14165659-G-A 12044953-G-A FGC35384 Y+
14271313-G-A 12150607-G-A Z44894 Y+
14282310-T-C 12161604-T-C Y15602 FGC35343 YY+
14736860-A-G 12624928-A-G FGC35367 Y+
14908349-G-T 12796416-G-T Y15909 FGC35386 YY+
15100799-G-T 12988887-G-T FGC35363 Y+
15139740-A-G 13027827-A-G Y15603 FGC35385 YY+
15222012-C-G 13110098-C-G Z44895 Y+
15505635-C-T 13393755-C-T Z44896 YY+
15798404-C-T 13686524-C-T Y15604 FGC35344 Z32167 YY+
16039008-A-G 13927128-A-G Z44898 YY+
16257282-A-C 14145402-A-C Z44899 YY+
16821066-C-G 14709186-C-G FGC35349 YY+
16919863-A-G 14807983-A-G Y15605 FGC35369 YY+
16995056-G-C 14883176-G-C Z44900 Y+
17421640-G-C 15309760-G-C FGC35355 YY+
17473367-C-G 15361487-C-G FGC35364 YY+
17980068-G-A 15868188-G-A Z44901 Y+
18079270-C-A 15967390-C-A Z44902 YY+
18171223-G-A 16059343-G-A FGC35029 YY+
18554260-G-A 16442380-G-A Z44903 YY+
18602746-C-T 16490866-C-T Z44904 YY+
18940714-C-T 16828834-C-T Z28740 YY+
19058119-C-G 16946239-C-G Z44906 YY+
19123916-C-A 17012036-C-A Y15607 FGC35379 YY+
19192530-T-G 17080650-T-G Z44907 YY+
19192862-T-C 17080982-T-C Z44908 YY+
19260680-G-A 17148800-G-A Y15608 Z36248 YY+
19453172-C-T 17341292-C-T FGC35357 YY+
20817095-G-C 18655209-G-C FGC35353 P4_Gap +
21210788-G-A 19048902-G-A Y15911 FGC35350 YY+
21348537-A-G 19186651-A-G FGC35358 Y+
21844795-C-G 19682909-C-G FGC35341 YY+
22051889-G-C 19890003-G-C FGC35365 Y+
22090193-A-G 19928307-A-G FGC35366 Y+
22678173-A-C 20516287-A-C Y15609 FGC35378 YY+
23251318-T-A 21089432-T-A Z44909 YY+
23344857-T-C 21182971-T-C Y15610 FGC35381 YY+
23461351-C-T 21299465-C-T Y15611 Z32169 YY+
23592376-C-A 21430490-C-A FGC35359 YY+
23969996-C-T 21823849-C-T Z44911 Y+
28668068-C-G 26521921-C-G FGC35377 +
28788845-T-G 26642698-T-G FGC35342 +

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.