Tree Position

R-M269 > L23 > L51 > P310 > L151 > S1194 > S1200 > S14328 > A8469 > S1196 > S6868 > S9254

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
HG00148
Manual
Edits
9577017-C-A 9739408-C-A IR3_Prx 15×A+
23476059-C-A 21314173-C-A YY+
22330847-A-T 20168961-A-T DYZ19 +
22423580-A-T 20261694-A-T DYZ19 +
22445947-A-G 20284061-A-G DYZ19 +
22816400-T-G 20654514-T-G YY+
22852198-A-C 20690312-A-C Y+
23199757-CA-C 21037871-CA-C +
23476053-C-T 21314167-C-T FTB13455 YY+
26499952-ATTTT-A 24353805-ATTTT-A P1_Y1 20×T+
22228067-G-A 20066181-G-A DYZ19 +
28539194-AG-A 26393047-AG-A +
58870507-CATCG-C 56720357-AATCG-A +
58871118-C-T 56719753-G-A +
2795554-TA-T 2927513-TA-T +
3662716-CAT-C 3794675-CAT-C +
3727669-A-G 3859628-A-G +
4067149-G-C 4199108-G-C FT319407 +
5298492-A-G 5430451-A-G +
22262435-GATTTAGTCCTTC-G 20100549-GATTTAGTCCTTC-G DYZ19 +
22127974-TC-T 19966088-TC-T +
5857921-T-C 5989880-T-C +
18688498-T-TA 16576618-T-TA +
15047302-TG-T 12935393-TG-T +
15842560-T-TCTTTC 13730680-T-TCTTTC +
16374685-AG-A 14262805-AG-A +
17543973-AT-A 15432093-AT-A +
17664818-G-C 15552938-G-C YY+
17678618-T-C 15566738-T-C YY+
18036544-T-G 15924664-T-G YY+
18036576-T-G 15924696-T-G YY+
19052414-C-CAAA 16940534-C-CAAA 24×A+
22127973-TTC-T 19966087-TTC-T +
19187375-A-C 17075495-A-C Y+
19411998-G-GA 17300118-G-GA +
21096483-C-A 18934597-C-A FT314001 Y+
21435138-T-A 19273252-T-A YY+
21464171-AAAGGAC-A 19302285-AAAGGAC-A +
21502798-TG-T 19340912-TG-T +
21919374-G-T 19757488-G-T YY+
22011582-C-A 19849696-C-A Y+
5662434-T-C 5794393-T-C FT324675 +
5870121-T-C 6002080-T-C +
14639057-G-T 12527126-G-T YY+
21697079-C-G 19535193-C-G YY+
18405678-T-C 16293798-T-C FT291394 P6_Gap +
18870106-A-G 16758226-A-G M1946 YY+
19304904-T-A 17193024-T-A YY+
20804334-T-C 18642448-T-C P4_Gap +
21342964-C-T 19181078-C-T FT291898 YY+
21394711-A-C 19232825-A-C YY+
21500881-G-C 19338995-G-C FT291971 Y+
21797814-G-T 19635928-G-T S23564 YY+
17190122-C-G 15078242-C-G FT291001 YY+
22129713-T-A 19967827-T-A FT292203 Y+
22460096-C-A 20298210-C-A DYZ19 +
22486216-T-A 20324330-T-A DYZ19 +
22486649-A-C 20324763-A-C BY224833 DYZ19 +
23796049-G-A 21634163-G-A Y+
26325480-G-A 24179333-G-A P1_Y1 +
26325491-T-C 24179344-T-C P1_Y1 +
26325493-A-C 24179346-A-C P1_Y1 +
18223723-G-T 16111843-G-T CTS8818 Y+
17026035-T-G 14914155-T-G CTS6640 Y+
5962146-ATATG-A 6094105-ATATG-A +
13566946-TAC-T 11411270-TAC-T +
5973990-G-C 6105949-G-C FT39942 +
6751613-C-G 6883572-C-G Y+
7106210-C-A 7238169-C-A FT289296 YY+
7440419-C-A 7572378-C-A CTS1495 Y+
7885982-C-G 8017941-C-G FT289514 Y+
13383248-C-T 11227572-C-T +
13477390-G-T 11321714-G-T +
13494804-C-T 11339128-C-T +
13585072-AG-A 11429396-AG-A +
17025924-A-C 14914044-A-C Y+
14135112-T-C 12014406-T-C Y+
14152716-G-T 12032010-G-T YY+
14212035-G-T 12091329-G-T YY+
14214685-T-C 12093979-T-C FT290124 YY+
14234793-A-C 12114087-A-C YY+
14579564-T-G 12467764-T-G FT290265 YY+
15981155-T-C 13869275-T-C FT290649 YY+
16819331-A-T 14707451-A-T FT290895 YY+
14738430-TG-T 12626498-TG-T +
14493181-A-C 12381378-A-C Y+
22768819-C-T 20606933-C-T YY20×T+
13441588-A-T 11285912-A-T +
22300856-A-T 20138970-A-T DYZ19 +
3215414-G-A 3347373-G-A +
8288850-G-A 8420809-G-A YY+
2866480-C-G 2998439-C-G CTS275 YY+
7464057-G-A 7596016-G-A IR1_L +
13633047-A-C 11477371-A-C BY40838S3202 FGC8047 +
2987520-T-C 3119479-T-C +
6998016-A-C 7129975-A-C YY+
26325267-T-A 24179120-T-A Z5834 P1_Y1 +
2795559-G-T 2927518-G-T YY24×T+
15967518-G-T 13855638-G-T M5002 YY8×T+
17662052-GTT-G 15550172-GTT-G +
23315713-C-CTTT 21153827-C-CTTT 20×T+
7723973-T-TTTG 7855932-T-TTTG +
2764940-T-G 2896899-T-G F14899 YY+
3229174-AG-A 3361133-AG-A +
3754539-T-TG 3886498-T-TG +
22300858-G-A 20138972-G-A DYZ19 +
19202953-AG-A 17091073-AG-A +
4134484-C-A 4266443-C-A 18×A+
13259068-T-C 11103392-T-C +
28787560-G-T 26641413-G-T AM01977 +
19513143-C-T 17401263-C-T FTA27036 YY20×T+
19412008-G-A 17300128-G-A BY47823 YY+
28779795-T-A 26633648-T-A CTS13011 +
28779802-T-C 26633655-T-C CTS13012 +
26325233-TGA-T 24179086-TGA-T P1_Y1 +
17319880-GAAGAAAGAAAGA-G 15208000-GAAGAAAGAAAGA-G 16×AAGA+
58885322-G-A 56705549-C-T +
22268251-C-G 20106365-C-G DYZ19 +
58870508-A-AT 56720361-G-GA +
58862960-C-A 56727911-G-T +
22366863-G-A 20204977-G-A DYZ19 +
22457319-G-GT 20295433-G-GT DYZ19 +
4976809-G-A 5108768-G-A +
26325528-T-C 24179381-T-C P1_Y1 +
14612382-TAGAC-T 12500588-TAGAC-T 6×AGAC+
13193950-N-T 11038274-T-. +
23505495-C-CAAA 21343609-C-CAAA 23×A+
4021930-C-T 4153889-C-T 15×T+
4175942-T-G 4307901-T-G +
14493173-A-C 12381370-A-C Y+
13306419-A-T 11150743-A-T +
9398653-G-GC 9561044-G-GC +
13193949-N-A 11038273-A-. +
13222251-T-G 11066575-T-G +
13222255-A-G 11066579-A-G +
13233337-G-A 11077661-G-A +
13257983-G-C 11102307-G-C +
13292600-C-T 11136924-C-T +
13306386-A-G 11150710-A-G +
13309574-T-C 11153898-T-C +
8785009-C-T 8916968-C-T YY+
13309588-A-C 11153912-A-C +
13312545-A-C 11156869-A-C +
13328789-C-T 11173113-C-T +
13328819-TG-T 11173143-TG-T +
13330312-T-TTA 11174636-T-TTA +
13452069-A-ACTCCACTCCC 11296393-A-ACTCCACTCCC +
13566948-C-T 11411272-C-T 12×AT+
13606604-C-G 11450928-C-G +
8977029-C-A 9139420-C-A Y16×A+
8218011-CTTTT-C 8349970-CTTTT-C +
4377969-C-T 4509928-C-T 19×T+
5350037-C-CTT 5481996-C-CTT 21×T+
4462151-T-C 4594110-T-C +
4978408-T-G 5110367-T-G +
4983763-T-A 5115722-T-A +
5017610-CACAA-C 5149569-CACAA-C +
5035602-GTT-G 5167561-GTT-G +
5127018-A-G 5258977-A-G +
5130488-G-T 5262447-G-T +
5316970-G-C 5448929-G-C FT191894 +
5706227-T-G 5838186-T-G +
7573242-A-C 7705201-A-C Y+
5962108-TCATA-T 6094067-TCATA-T +
5998402-A-G 6130361-A-G +
6149989-G-A 6281948-G-A IR3_Dst +
6150000-G-T 6281959-G-T IR3_Dst +
6579301-T-G 6711260-T-G +
6604084-C-T 6736043-C-T 17×T+
7453565-CAG-C 7585524-CAG-C IR1_L +
7508384-T-TTCCA 7640343-T-TTCCA +
28574057-C-G 26427910-C-G CTS12318 +

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
Manual3161667-A-G3293626-A-G3G
Manual6167116-T-G6299075-T-G3G
Manual13815638-AAATGGAATGGACAGG-A11694932-AAATGGAATGGACAGG-AMessy region. Looks like at least one good read shows the deletion.
Manual18701465-ATATT-A16589585-ATATT-A4 reads, all positive.
Manual22315571-C-A20153685-C-A2C 4A
Manual23244049-C-A21082163-C-A8A
Manual22483094-G-C20321208-G-C4C



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