Tree Position

R-P312/S116 > Z290 > L21/S145 > S552 > 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
22300858-G-A 20138972-G-A DYZ19 +
22300856-A-T 20138970-A-T DYZ19 +
6617230-T-C 6749189-T-C Y+
8562865-C-A 8694824-C-A YY17×A+
2749355-G-GT 2881314-G-GT BY3501 BY18924 9×T+
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+
8792293-A-G 8924252-A-G FT300539 YY+
13956073-C-A 11835367-C-A FT300727 Y+
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 FT301519 Y+
17299929-G-C 15188049-G-C YY+
18167497-G-A 16055617-G-A CTS8729 S3699 YY+
21081876-T-C 18919990-T-C S3806 YY+
21326380-A-C 19164494-A-C PH4769 YY+
21706225-C-T 19544339-C-T S3706 YY+
22055789-G-A 19893903-G-A FGC945 S3817 Z6929 YY+
22203606-C-T 20041720-C-T PH5091 YY+
22542074-G-A 20380188-G-A FT302637 Y+
22610705-G-A 20448819-G-A S3700 YY+
28767411-C-T 26621264-C-T S3805 Y+
58861964-T-TC 56728905-T-TG +
13258549-T-C 11102873-T-C +
14523372-A-G 12411573-A-G YY+
58910959-G-C 56679912-C-G +
13255859-C-T 11100183-C-T +
19472669-A-C 17360789-A-C YY+
5179928-T-G 5311887-T-G +
13507437-G-C 11351761-G-C F10876 +
13433830-A-AT 11278154-A-AT +
9142153-T-G 9304544-T-G M4663 Y+
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 +
3394307-G-T 3526266-G-T +
3412038-GTGT-G 3543997-GTGT-G +
3412039-TGTGG-T 3543998-TGTGG-T +
3412041-TGG-T 3544000-TGG-T +
3467021-T-C 3598980-T-C FT317347 +
3609639-G-T 3741598-G-T +
3619422-T-C 3751381-T-C FT7096 +
3878659-A-AAG 4010618-A-AAG +
3950995-G-A 4082954-G-A Z7378 +
4200039-T-A 4331998-T-A +
4200043-G-A 4332002-G-A +
4345751-C-A 4477710-C-A +
4502530-A-G 4634489-A-G F9063 +
4574082-C-T 4706041-C-T FT308213 +
4614006-A-C 4745965-A-C +
4630150-G-GTT 4762109-G-GTT +
4917601-C-T 5049560-C-T 16×T+
5287279-T-C 5419238-T-C FT323414 +
5462523-CCA-C 5594482-CCA-C +
5786630-T-A 5918589-T-A +
5786634-C-A 5918593-C-A +
5872838-A-C 6004797-A-C FTB70496 +
6019246-C-T 6151205-C-T +
6094931-G-T 6226890-G-T +
6346123-TAG-T 6478082-TAG-T +
6385618-G-A 6517577-G-A FT326387 +
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+
7160192-T-G 7292151-T-G YY+
7451294-C-CTTT 7583253-C-CTTT IR1_L 29×T+
7508384-T-TTCCA 7640343-T-TTCCA +
7608434-T-TCC 7740393-T-TCC +
7965574-T-A 8097533-T-A FT390240 Y+
8119690-T-G 8251649-T-G Z31279 YY+
8398857-AG-A 8530816-AG-A +
8555575-G-GTTTTTT 8687534-G-GTTTTTT +
8791639-T-A 8923598-T-A YY+
8826678-C-CAAAAA 8958637-C-CAAAAA 29×A+
9063235-A-C 9225626-A-C Z12147 Y+
9429477-TAATA-T 9591868-TAATA-T +
13140854-T-C 10630340-T-C +
13223577-A-G 11067901-A-G +
13241208-A-G 11085532-A-G +
13241224-G-A 11085548-G-A +
13241296-T-C 11085620-T-C +
13267775-C-CTCT 11112099-C-CTCT +
13269591-AAAC-A 11113915-AAAC-A +
13269592-AAC-A 11113916-AAC-A +
13269593-AC-A 11113917-AC-A +
13311960-G-C 11156284-G-C +
13362100-C-T 11206424-C-T +
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 +
13530217-A-C 11374541-A-C +
13621660-A-C 11465984-A-C +
13686909-ACACG-A 11531233-ACACG-A DYZ17 +
13686910-CACGAA-C 11531234-CACGAA-C DYZ17 +
13840860-G-GGAATA 11720154-G-GGAATA DYZ17 +
13888392-A-C 11767686-A-C YY+
13908362-A-G 11787656-A-G FGC81672 YY+
13930608-C-T 11809902-C-T S3829 Y+
13998090-TG-T 11877384-TG-T +
14061383-TG-T 11940677-TG-T +
14198069-C-CAT 12077363-C-CAT +
14233385-T-C 12112679-T-C YY+
14253770-T-G 12133064-T-G YY+
14406357-C-CG 12285654-C-CG +
14493173-A-C 12381370-A-C Y+
14825074-A-C 12713141-A-C YY+
15083558-A-C 12971648-A-C Y+
15124832-T-A 13012919-T-A S3824 YY+
15209565-C-A 13097651-C-A YY+
15209597-G-T 13097683-G-T M12329 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+
16003268-A-C 13891388-A-C Y+
16003275-G-A 13891395-G-A Y+
16059286-A-C 13947406-A-C Y+
16305989-C-T 14194109-C-T YY+
16345137-C-CCTCTTCTTT 14233257-C-CCTCTTCTTT +
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+
17998317-T-C 15886437-T-C P7_Gap Y+
18165126-C-A 16053246-C-A YY13×A+
18354219-A-AAAGG 16242339-A-AAAGG P6_Prx +
18966122-T-C 16854242-T-C YY+
19319878-ATATC-A 17207998-ATATC-A +
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 BY13277 P5_Dst 18×GA+
21084436-TA-T 18922550-TA-T +
21262846-C-T 19100960-C-T FGC33086 YY+
21273500-A-C 19111614-A-C Z5675 Y+
21273503-G-A 19111617-G-A Z5676 Y+
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 +
22237305-A-G 20075419-A-G DYZ19 +
22237307-A-G 20075421-A-G DYZ19 +
22261418-G-A 20099532-G-A DYZ19 +
22263224-T-A 20101338-T-A DYZ19 +
22297173-C-A 20135287-C-A DYZ19 +
22297317-C-T 20135431-C-T DYZ19 +
22297320-C-A 20135434-C-A DYZ19 +
22297546-C-T 20135660-C-T DYZ19 +
22297589-G-A 20135703-G-A DYZ19 +
22665237-T-G 20503351-T-G S3813 YY+
22684225-A-C 20522339-A-C YY+
22876958-G-A 20715072-G-A Y+
23773311-C-T 21611425-C-T FT219789 Y+
23807603-G-A 21645717-G-A Y+
26834299-C-T 24688152-C-T P1_g2 +
28598170-A-C 26452023-A-C +
28726933-G-T 26580786-G-T +
28814566-A-T 26668419-A-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. '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:

Manual7596723-T-C7728682-T-C4 reads all C.
Manual8868975-G-T9000934-G-T2 reads, both G.
Manual16647788-T-C14535908-T-CNo data in BAM file at this position.
Manual2817077-A-G2949036-A-GChecked BAM file. 3 reads all with G.
Manual9803918-T-C9966309-T-C6 reads with C.
Manual16652611-G-A14540731-G-A3 reads with A.
Manual5676205-A-G5808164-A-G3 reads with G, 1 read with A.