Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > Z39589 > DF41/S524 > Z43690 > A874

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
9640935-A-G 9803326-A-G IR3_Prx +
14825074-A-C 12713141-A-C YY+
13908362-A-G 11787656-A-G YY+
13930608-C-T 11809902-C-T S3829 Y+
13954127-AAAT-A 11833421-AAAT-A 12×AAT+
13998090-TG-T 11877384-TG-T +
14061383-TG-T 11940677-TG-T +
14198069-C-CAT 12077363-C-CAT +
14253770-T-G 12133064-T-G YY+
14493173-A-C 12381370-A-C Y+
15083558-A-C 12971648-A-C Y+
15124832-T-A 13012919-T-A S3824 YY+
15209565-C-A 13097651-C-A YY+
15209610-A-T 13097696-A-T YY+
15240761-G-A 13128847-G-A Y687 Y+
15255761-TGTGG-T 13143847-TGTGG-T +
15340401-T-TTTG 13228520-T-TTTG +
15683059-A-G 13571179-A-G Y+
15865598-A-T 13753718-A-T YY+
13888392-A-C 11767686-A-C YY+
13686910-CACGAA-C 11531234-CACGAA-C +
16003275-G-A 13891395-G-A Y+
13311960-G-C 11156284-G-C +
13267775-C-CTCT 11112099-C-CTCT +
13269567-C-T 11113891-C-T +
13269591-AAAC-A 11113915-AAAC-A +
13269592-AAC-A 11113916-AAC-A +
13269593-AC-A 11113917-AC-A +
13269594-C-A 11113918-C-A +
13269957-A-T 11114281-A-T +
13288448-A-AT 11132772-A-AT +
13354558-G-T 11198882-G-T +
13641224-A-T 11485548-A-T +
13362100-C-T 11206424-C-T +
13364246-G-C 11208570-G-C +
13388297-T-C 11232621-T-C A5035 +
13415016-A-T 11259340-A-T +
13415041-T-A 11259365-T-A +
13500741-C-T 11345065-C-T +
13507841-T-C 11352165-T-C +
13530217-A-C 11374541-A-C +
13621660-A-C 11465984-A-C +
16003268-A-C 13891388-A-C Y+
16059286-A-C 13947406-A-C Y+
13241224-G-A 11085548-G-A +
22297589-G-A 20135703-G-A DYZ19 +
21953550-TA-T 19791664-TA-T +
22014995-C-A 19853109-C-A M1972 Y+
22023194-C-T 19861308-C-T YY+
22040900-AG-A 19879014-AG-A +
22040933-C-A 19879047-C-A YY+
22263224-T-A 20101338-T-A DYZ19 +
22297173-C-A 20135287-C-A DYZ19 +
22297546-C-T 20135660-C-T DYZ19 +
22665237-T-G 20503351-T-G S3813 YY+
21273500-A-C 19111614-A-C Z5675 Y+
22684225-A-C 20522339-A-C YY+
22876958-G-A 20715072-G-A Y+
23773311-C-T 21611425-C-T Y+
23807603-G-A 21645717-G-A Y+
26834299-C-T 24688152-C-T P1_g2 +
28588044-C-G 26441897-C-G +
28598170-A-C 26452023-A-C +
28726933-G-T 26580786-G-T +
58975877-C-A 56829730-C-A +
21273503-G-A 19111617-G-A Z5676 Y+
21262846-C-T 19100960-C-T FGC33086 YY+
16305989-C-T 14194109-C-T YY+
18134140-C-CT 16022260-C-CT 9×T+
16345137-C-CCTCTTCTTT 14233257-C-CCTCTTCTTT +
16354883-G-A 14243003-G-A Y9×A+
16354893-G-A 14243013-G-A Y+
16656658-C-CTT 14544778-C-CTT 14×T+
16714835-T-C 14602955-T-C CTS6184 YY+
16908477-G-A 14796597-G-A YY+
17403996-A-G 15292116-A-G YY+
17720094-T-G 15608214-T-G YY+
18165126-C-A 16053246-C-A YY13×A+
21084436-TA-T 18922550-TA-T +
18354219-A-AAAGG 16242339-A-AAAGG P6_Prx +
18966122-T-C 16854242-T-C YY+
19183843-G-T 17071963-G-T Y+
19319878-ATATC-A 17207998-ATATC-A +
19339986-C-T 17228106-C-T YY31×T+
19359990-G-T 17248110-G-T YY+
19520866-AG-A 17408986-AG-A +
19552861-T-G 17440981-T-G Y+
20603841-G-A 18441955-G-A P5_Dst 18×GA+
13241296-T-C 11085620-T-C +
13241208-A-G 11085532-A-G +
21691554-CT-C 19529668-CT-C 15×T+
13433830-A-AT 11278154-A-AT +
22610705-G-A 20448819-G-A S3700 YY+
28767411-C-T 26621264-C-T S3805 Y+
14523372-A-G 12411573-A-G YY+
13530026-A-G 11374350-A-G +
58910959-G-C 56679912-C-G +
19472669-A-C 17360789-A-C YY+
5179928-T-G 5311887-T-G +
13507437-G-C 11351761-G-C F10876 +
9142153-T-G 9304544-T-G M4663 Y+
22203606-C-T 20041720-C-T PH5091 YY+
9798080-TC-T 9960471-TC-T +
2810364-G-T 2942323-G-T YY+
3079580-G-A 3211539-G-A +
3126786-A-G 3258745-A-G Z8495 +
3301243-TTA-T 3433202-TTA-T 8×TA+
3394307-G-T 3526266-G-T +
3412038-GTGT-G 3543997-GTGT-G +
3412039-TGTGG-T 3543998-TGTGG-T +
22542074-G-A 20380188-G-A Y+
22055789-G-A 19893903-G-A FGC945 S3817 Z6929 YY+
3467021-T-C 3598980-T-C +
8792293-A-G 8924252-A-G YY+
8562865-C-A 8694824-C-A YY17×A+
6673834-TA-T 6805793-TA-T 10×A+
2749355-G-GT 2881314-G-GT 6643898-A-G 9×T+
2866480-C-G 2998439-C-G CTS275 YY+
2892335-A-T 3024294-A-T S3808 YY+
6697544-T-G 6829503-T-G S3814 YY+
7177065-T-G 7309024-T-G S3819 YY+
7390128-G-A 7522087-G-A S3807 YY+
13956073-C-A 11835367-C-A Y+
21706225-C-T 19544339-C-T S3706 YY+
15435237-T-C 13323357-T-C S3818 YY+
15739036-G-A 13627156-G-A S3703 CTS4623 YY+
15879290-A-G 13767410-A-G S3831 V3206 YY+
16328203-G-A 14216323-G-A S3827 YY+
16907088-A-G 14795208-A-G Z10778 YY+
16995307-C-A 14883427-C-A Y+
17299929-G-C 15188049-G-C YY+
21081876-T-C 18919990-T-C S3806 YY+
21326380-A-C 19164494-A-C PH4769 YY+
3412041-TGG-T 3544000-TGG-T +
3609639-G-T 3741598-G-T +
13223577-A-G 11067901-A-G +
7451294-C-CTTT 7583253-C-CTTT IR1_L 29×T+
6502955-G-A 6634914-G-A +
7100949-C-T 7232908-C-T Y+
7113260-TG-T 7245219-TG-T +
7113261-G-T 7245220-G-T YY+
7125241-T-G 7257200-T-G Y+
7135368-G-T 7267327-G-T YY+
7160192-T-G 7292151-T-G YY+
7199179-A-C 7331138-A-C YY+
7608434-T-TCC 7740393-T-TCC +
6346123-TAG-T 6478082-TAG-T +
7608436-C-CCT 7740395-C-CCT 15×CT+
7965574-T-A 8097533-T-A Y+
8119690-T-G 8251649-T-G Z31279 YY+
8398857-AG-A 8530816-AG-A +
8826678-C-CAAAAA 8958637-C-CAAAAA 29×A+
9063235-A-C 9225626-A-C Z12147 Y+
9931513-CTT-C 10093904-CTT-C +
13140854-T-C 10630340-T-C +
13222368-A-G 11066692-A-G +
6385618-G-A 6517577-G-A +
6094931-G-T 6226890-G-T +
3619422-T-C 3751381-T-C +
4917601-C-T 5049560-C-T 16×T+
3878659-A-AAG 4010618-A-AAG +
3916934-CAAA-C 4048893-CAAA-C 20×A+
3950995-G-A 4082954-G-A Z7378 +
4200039-T-A 4331998-T-A +
4345751-C-A 4477710-C-A +
4502530-A-G 4634489-A-G F9063 +
4574082-C-T 4706041-C-T +
4614006-A-C 4745965-A-C +
5179541-T-C 5311500-T-C Z38491 8×AC+
6019246-C-T 6151205-C-T +
5259908-T-A 5391867-T-A +
5259932-C-G 5391891-C-G +
5287279-T-C 5419238-T-C +
5366445-A-G 5498404-A-G +
5458485-A-G 5590444-A-G +
5786630-T-A 5918589-T-A +
5786634-C-A 5918593-C-A +
5872838-A-C 6004797-A-C +
6019240-A-C 6151199-A-C +
59007432-CTT-C 56861285-CTT-C 18×T+

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. 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.

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