Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z198 > Z46513 > ZS312 > Z262 > M167 > Z264 > Z205 > ~22224168-A-C > Z206/S235 > Z208/S362 > Z207/S251 > CTS9762 > CTS4299 > ZZ42 > 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
14453708-AG-A 12332981-AG-A +
15983912-T-G 13872032-T-G YY+
6917371-G-A 7049330-G-A FT289244 Y+
7539599-G-GA 7671558-G-GA 9×A+
15016964-T-C 12905053-T-C BY99117 YY+
15535367-G-T 13423487-G-T BY102332 YY+
15875703-C-A 13763823-C-A CTS4863 YY+
17289395-G-T 15177515-G-T CTS7099 YY+
17706869-C-T 15594989-C-T BY116812 YY+
18042835-A-C 15930955-A-C YY+
22045643-A-G 19883757-A-G FT292178 YY+
23417452-A-G 21255566-A-G CTS12011 YY+
23499372-C-T 21337486-C-T FGC14714 YY+
28688278-T-C 26542131-T-C FT292764 Y+
19127667-T-C 17015787-T-C YY18×AC+
13285136-T-C 11129460-T-C +
22974074-T-A 20812188-T-A YY+
9075227-G-T 9237618-G-T Y+
18982873-T-C 16870993-T-C Z30199 YY+
2855483-TG-T 2987442-TG-T +
2898576-A-G 3030535-A-G Y+
3036366-T-A 3168325-T-A +
3374871-G-A 3506830-G-A +
3930696-TTA-T 4062655-TTA-T +
4416738-G-A 4548697-G-A +
4503526-G-T 4635485-G-T +
5035602-GTT-G 5167561-GTT-G +
5138569-C-A 5270528-C-A +
5155094-C-T 5287053-C-T FT322919 +
5430834-G-A 5562793-G-A +
5430844-T-A 5562803-T-A +
6141809-A-C 6273768-A-C IR3_Dst +
6347862-A-AAGAG 6479821-A-AAGAG +
6775434-T-A 6907393-T-A YY+
6776566-G-T 6908525-G-T YY+
7159463-A-G 7291422-A-G Y27875 YY+
7223229-C-T 7355188-C-T Y+
7528152-C-T 7660111-C-T BY65673 YY+
7617848-G-T 7749807-G-T Y24389 YY+
7723896-C-A 7855855-C-A Y+
8452220-C-A 8584179-C-A YY+
8666722-AGT-A 8798681-AGT-A +
8718065-C-A 8850024-C-A BY75410 YY+
9063859-C-T 9226250-C-T Y16×T+
9132606-G-C 9294997-G-C BY206349 Y+
13241296-T-C 11085620-T-C +
13241341-C-A 11085665-C-A +
13241355-A-G 11085679-A-G +
13258579-C-T 11102903-C-T +
13285142-G-T 11129466-G-T +
13311809-C-T 11156133-C-T +
13418209-G-T 11262533-G-T +
13486863-A-T 11331187-A-T +
13494277-A-T 11338601-A-T +
13502954-G-T 11347278-G-T +
13526853-G-A 11371177-G-A +
13569052-T-C 11413376-T-C +
13655763-A-G 11500087-A-G BY87221 +
14200754-A-AT 12080048-A-AT +
14295777-C-T 12175071-C-T BY94640 YY+
14331128-TTTC-T 12210422-TTTC-T +
14458584-G-A 12337857-G-A YY+
14533046-A-C 12421247-A-C HU508 Y+
14602056-TG-T 12490258-TG-T +
15022841-GA-G 12910929-GA-G +
15161280-T-G 13049366-T-G YY+
15557123-TAATATA-T 13445243-TAATATA-T +
15794242-C-A 13682362-C-A M12013 Y+
15815325-A-AG 13703445-A-AG +
15865944-G-GTTTTTTTTT 13754064-G-GTTTTTTTTT +
17069522-T-G 14957642-T-G Y+
17731014-C-CAAAA 15619134-C-CAAAA 35×A+
17818107-T-A 15706227-T-A BY117634 YY+
17818108-C-A 15706228-C-A BY117635 YY+
18067930-G-A 15956050-G-A BY119639 YY+
18537877-T-A 16425997-T-A CTS8897 Y+
18756817-T-TTG 16644937-T-TTG +
18843971-C-A 16732091-C-A YY+
19314707-CTA-C 17202827-CTA-C +
19377209-AGAGG-A 17265329-AGAGG-A 4×GAGG+
21435138-T-A 19273252-T-A YY+
21896481-C-A 19734595-C-A BY136290 YY+
21978368-T-G 19816482-T-G S23811 YY+
22028433-T-C 19866547-T-C FT292164 YY+
22228168-A-T 20066282-A-T DYZ19 +
22445581-T-A 20283695-T-A BY219657 DYZ19 +
22464172-G-A 20302286-G-A BY221266 DYZ19 +
22484530-A-T 20322644-A-T DYZ19 +
22537614-A-G 20375728-A-G BY138822 Y+
22686453-G-T 20524567-G-T BY140057 YY+
22699706-C-T 20537820-C-T FT292308 YY+
22768257-G-T 20606371-G-T YY+
22829643-TC-T 20667757-TC-T +
22962392-A-T 20800506-A-T YY+
23168500-G-T 21006614-G-T FT292458 Y+
23168969-A-G 21007083-A-G CTS11586 Y+
23168971-C-T 21007085-C-T CTS11587 Y+
23316060-A-ATTTT 21154174-A-ATTTT +
23415304-GTATGTA-G 21253418-GTATGTA-G +
23446195-G-T 21284309-G-T BY145343 YY+
23498116-C-T 21336230-C-T YY+
23777994-T-G 21616108-T-G Y+
23891147-G-T 21729261-G-T Y15×T+
28552532-C-A 26406385-C-A FT292732 +
28663105-A-C 26516958-A-C +
28804636-T-A 26658489-T-A +
28804674-G-T 26658527-G-T +
27337312-C-A 25191165-C-A ZZ42_3 P1_g3 *

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:

Manual6459988-GA-G6591947-GA-GAll 4 reads show the deletion.
Manual3443764-TTTATTA-T3575723-TTTATTA-TJust one read covers the region, but it does have the deletion.
Manual27337312-C-A25191165-C-A1A 1C