Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > ZZ12 > YP4695 > BY3327 > Y24801

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
13439897-T-C 11284221-T-C +
13504796-G-T 11349120-G-T +
15194942-C-T 13083028-C-T YY+
15098351-C-CG 12986439-C-CG +
15098347-G-A 12986435-G-A Y+
14904873-C-T 12792940-C-T YY+
14179183-G-T 12058477-G-T Y+
13994326-G-A 11873620-G-A CTS1626 Y+
13852065-T-A 11731359-T-A +
13616769-C-A 11461093-C-A +
13592314-C-G 11436638-C-G +
13588309-C-T 11432633-C-T +
13451591-AT-A 11295915-AT-A +
16074966-C-G 13963086-C-G Y+
13450505-ACTCCACTCC-A 11294829-ACTCCACTCC-A +
13407110-C-G 11251434-C-G +
13387195-C-T 11231519-C-T +
13379781-G-A 11224105-G-A +
10064587-A-G 10226978-A-G +
9728203-G-A 9890594-G-A FGC40721 IR3_Prx +
9515818-C-T 9678209-C-T +
8722345-G-A 8854304-G-A YY+
8672551-C-T 8804510-C-T YY+
8035143-C-A 8167102-C-A YY+
15506598-A-G 13394718-A-G YY+
16638994-C-A 14527114-C-A YY+
13439904-T-A 11284228-T-A +
21600568-G-A 19438682-G-A Y+
28587197-C-T 26441050-C-T +
28581734-G-T 26435587-G-T CTS12360 +
28581716-C-T 26435569-C-T CTS12359 +
25025268-C-T 22879121-C-T g1 +
24413865-T-A 22267718-T-A Y+
23895419-C-G 21733533-C-G Y+
23823606-T-C 21661720-T-C Y+
23632401-G-C 21470515-G-C YY+
23262974-G-A 21101088-G-A YY+
22447365-G-C 20285479-G-C DYZ19 +
21467995-C-T 19306109-C-T YY+
16896669-G-A 14784789-G-A YY+
21442107-C-A 19280221-C-A YY+
20063809-G-A 17951929-G-A P5_Gap +
19507082-T-A 17395202-T-A YY+
19453438-C-T 17341558-C-T YY+
19377516-G-A 17265636-G-A YY+
18810636-C-G 16698756-C-G YY+
18749977-G-A 16638097-G-A Y+
18544798-T-G 16432918-T-G Y+
18161201-TC-T 16049321-TC-T +
17324270-A-T 15212390-A-T YY+
16915547-G-T 14803667-G-T YY+
7654224-G-C 7786183-G-C YY+
7428278-C-T 7560237-C-T FT61120 YY+
7282151-C-T 7414110-C-T YY+
14627597-G-A 12515665-G-A BY22401 YY+
17893683-G-A 15781803-G-A YY+
17843630-A-G 15731750-A-G YY+
17612685-T-A 15500805-T-A BY122CTS7678 S3935 YY+
17371538-G-T 15259658-G-T YY+
17364443-G-T 15252563-G-T YY+
17282915-T-G 15171035-T-G YY+
15153129-T-C 13041216-T-C YY+
14919081-G-A 12807148-G-A YY+
14737233-A-G 12625301-A-G Y+
14694024-T-C 12582090-T-C YY+
8434158-C-T 8566117-C-T BY17746 YY+
7148742-G-A 7280701-G-A Y+
8107633-T-A 8239592-T-A YY+
8068485-C-G 8200444-C-G YY+
8042174-T-A 8174133-T-A YY+
7776092-C-T 7908051-C-T YY+
7574727-G-A 7706686-G-A Y+
7127156-T-C 7259115-T-C M8158 YY+
7127109-A-G 7259068-A-G CTS989 YY+
6983629-G-C 7115588-G-C YY+
6829173-C-T 6961132-C-T Y+
6676826-C-A 6808785-C-A YY+
2831778-G-T 2963737-G-T YY+
18131910-T-C 16020030-T-C Y+
18656325-A-G 16544445-A-G BY55093 YY10×TG+
18997651-T-A 16885771-T-A YY+
19414790-T-C 17302910-T-C YY+
7127173-A-C 7259132-A-C YY+
6942289-G-T 7074248-G-T YY+
6867678-TTG-T 6999637-TTG-T +
6623709-C-T 6755668-C-T Y+
6609129-A-T 6741088-A-T +
6402783-A-G 6534742-A-G +
5954186-A-G 6086145-A-G +
5818187-T-TAGAG 5950146-T-TAGAG +
5544671-G-A 5676630-G-A +
5522226-C-G 5654185-C-G +
3724215-G-A 3856174-G-A +
3138819-G-A 3270778-G-A +
3112863-A-T 3244822-A-T +
3047071-G-A 3179030-G-A +
3035388-C-T 3167347-C-T +
9955949-A-C 10118340-A-C Y+
28496407-A-C 26350260-A-C Y+
24412133-G-A 22265986-G-A Y+
21445328-G-A 19283442-G-A Z25149 YY+
21204681-T-C 19042795-T-C F23998 YY+
21195497-C-T 19033611-C-T YY+
21096828-G-A 18934942-G-A Y+
19445403-G-A 17333523-G-A YY+
28151806-T-C 26005659-T-C Y24801 P1_b4 *
24677835-T-C 22531688-T-C Y24801 P3_b2 *
25810564-A-G 23664417-A-G P1_b3 *

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:

Manual19736631-T-C17624751-T-COne read, a C.
Manual22311956-G-C20150070-G-C3G 1C
Manual22302922-G-C20141036-G-C4G 4C
Manual19790829-A-T17678949-A-T1A 2T
Manual9229314-A-C9391705-A-C8A 2C
Manual28151806-T-C26005659-T-C1T 1C
Manual24677835-T-C22531688-T-C2T 3C
Manual25810564-A-G23664417-A-G11A 2G. The 2G are mates of one paired end read. Some of the 11A may be mates.

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