Tree Position

R-P312/S116 > Z40481 > ZZ11 > U152/S28 > L2/S139 > Z258 > Z367/S255 > L20/S144 > Z1909 > 38:26092490T>TA > Y22248 > Y22958 > 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
HG01356
Manual
Edits
13143284-G-C 10632770-G-C +
6000954-C-T 6132913-C-T +
13462731-C-T 11307055-C-T BY47068 +
13703199-C-T 11547523-C-T +
22298369-G-C 20136483-G-C BY48236 DYZ19 +
28777831-T-C 26631684-T-C CTS12994 +
28777847-T-C 26631700-T-C CTS12995 +
21980030-T-G 19818144-T-G YY+
13908917-A-C 11788211-A-C Y+
13956770-G-A 11836064-G-A Y310 Z3297 Y+
14656179-G-A 12544244-G-A YY+
9072404-G-T 9234795-G-T Y+
13928633-A-G 11807927-A-G Y+
14151436-T-C 12030730-T-C CTS2004 YY+
14659381-A-G 12547446-A-G CTS3091 YY+
14918815-T-C 12806882-T-C CTS3432 YY+
15740371-G-A 13628491-G-A CTS4629 Y+
16058058-A-G 13946178-A-G FT296734 YY+
18993414-G-A 16881534-G-A Y22957 YY+
19261866-T-G 17149986-T-G FT298001 YY+
19300140-T-G 17188260-T-G CTS10161 Y+
22573589-C-T 20411703-C-T FT298981 YY+
22684209-G-A 20522323-G-A CTS10658 YY+
23056404-G-A 20894518-G-A CTS11289 YY+
23345288-C-T 21183402-C-T FT299321 YY+
28515511-A-C 26369364-A-C FT299611 Y+
7573180-G-A 7705139-G-A ZS7884 Y+
28799002-G-A 26652855-G-A +
2759997-T-C 2891956-T-C A18079 YY+
2934185-T-C 3066144-T-C 6792625-T-C +
3035510-C-T 3167469-C-T +
3250694-CA-C 3382653-CA-C +
3301818-T-G 3433777-T-G +
4072018-ACG-A 4203977-ACG-A +
4072019-CGG-C 4203978-CGG-C +
4480240-A-C 4612199-A-C +
4480684-T-C 4612643-T-C +
4503074-C-G 4635033-C-G BY58196 +
4583234-C-G 4715193-C-G FT321113 +
4917618-C-T 5049577-C-T +
4965207-T-A 5097166-T-A +
4965215-T-A 5097174-T-A +
5035558-T-TTG 5167517-T-TTG 22×TG+
5035602-GTT-G 5167561-GTT-G +
5400489-TC-T 5532448-TC-T +
5541674-A-G 5673633-A-G FT324258 +
5653464-T-C 5785423-T-C FT93785 +
5702618-AAC-A 5834577-AAC-A +
6010263-T-C 6142222-T-C +
6087659-A-G 6219618-A-G FT326110 +
6231281-C-A 6363240-C-A IR3_Dst +
6434941-AC-A 6566900-AC-A +
6863815-CA-C 6995774-CA-C +
7025790-T-C 7157749-T-C CTS805 Y+
7201646-C-T 7333605-C-T Y+
7204844-A-G 7336803-A-G FT294807 YY+
7218297-GAC-G 7350256-GAC-G +
7590696-T-G 7722655-T-G YY+
8232960-A-AT 8364919-A-AT +
8731915-C-G 8863874-C-G Y+
9831596-CAT-C 9993987-CAT-C +
9909040-A-T 10071431-A-T Y+
9909073-G-C 10071464-G-C Y+
9909097-G-A 10071488-G-A Y+
13143267-T-A 10632753-T-A +
13143274-C-A 10632760-C-A +
13143276-C-A 10632762-C-A +
13143280-A-C 10632766-A-C +
13143319-C-T 10632805-C-T +
13241208-A-G 11085532-A-G +
13245577-C-CA 11089901-C-CA +
13257652-G-A 11101976-G-A +
13257895-A-G 11102219-A-G +
13275524-G-T 11119848-G-T +
13308888-C-G 11153212-C-G +
13351168-C-A 11195492-C-A +
13351172-G-A 11195496-G-A +
13383230-A-G 11227554-A-G +
13384541-T-G 11228865-T-G +
13402662-T-A 11246986-T-A +
13415167-G-A 11259491-G-A +
13415169-G-A 11259493-G-A +
13435795-C-T 11280119-C-T +
13441433-T-TG 11285757-T-TG 10×G+
13441881-C-T 11286205-C-T +
13462744-C-T 11307068-C-T +
13521212-A-G 11365536-A-G +
13531132-T-A 11375456-T-A FT425868 +
13545564-T-C 11389888-T-C +
13940892-AGG-A 11820186-AGG-A +
14082092-T-TCTATC 11961386-T-TCTATC +
14106962-T-C 11986256-T-C M3099 YY+
14600808-A-AAC 12489008-A-AAC +
14612378-TAGATAGAC-T 12500584-TAGATAGAC-T +
14642440-G-T 12530509-G-T YY+
14642453-GGT-G 12530522-GGT-G +
15128119-GC-G 13016206-GC-G +
17861959-TC-T 15750079-TC-T +
18147506-A-T 16035626-A-T YY+
18343627-TC-T 16231747-TC-T P6_Prx +
18959341-A-T 16847461-A-T YY+
19209822-A-C 17097942-A-C YY+
19401618-A-T 17289738-A-T YY+
19449451-AG-A 17337571-AG-A +
21038297-G-A 18876411-G-A FTA6172 Y+
21540226-T-G 19378340-T-G Y+
21540277-T-C 19378391-T-C Y+
22128005-A-T 19966119-A-T YY+
22147325-A-G 19985439-A-G FT298875 YY+
22185813-T-A 20023927-T-A YY+
22229174-T-A 20067288-T-A DYZ19 +
22270390-C-T 20108504-C-T DYZ19 +
22463464-T-G 20301578-T-G DYZ19 +
22476256-G-T 20314370-G-T DYZ19 +
22512681-A-T 20350795-A-T DYZ19 +
22644480-G-C 20482594-G-C Y+
23281340-A-C 21119454-A-C YY+
24127500-C-A 21981353-C-A P3_b1 +
24388080-T-TAA 22241933-T-TAA +
28551836-G-T 26405689-G-T +
28604101-A-G 26457954-A-G +
28604108-C-G 26457961-C-G FTB21967 +
28778101-G-T 26631954-G-T +
28779578-T-C 26633431-T-C +
28779596-T-A 26633449-T-A +
28798982-T-G 26652835-T-G +

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
Manual19829809-T-C17717929-T-CJust one read, a C.
Manual22233129-T-A20071243-T-A4A, 4T
Manual9810794-C-.9973185-C-.6C
Manual14231292-A-.12110586-A-.2A
Manual6732878-G-A6864837-G-A1A
Manual9159791-T-A9322182-T-A1A
Manual18804523-A-G16692643-A-G1A 2G
Manual19773694-A-G17661814-A-G2G
Manual21149509-T-G18987623-T-G1G
Manual22752880-T-C20590994-T-C1C
Manual26092490-T-TA23946343-T-TA4 regions cover the region. 2 are positive, 2 are negative.