Tree Position

R-P312/S116 > Z290 > L21/S145 > DF13 > DF21/S192 > FGC3213 > ZZ1 > S3058 > S424 > LSC > LSC1 > LSC1a > ZZ23 > ZZ43

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
NA12043
Manual
Edits
9468134-TTG-T 9630525-TTG-T 17×TG+
13242098-A-G 11086422-A-G +
17090827-T-C 14978947-T-C YY+
17622745-A-C 15510865-A-C YY10×C+
17632563-G-A 15520683-G-A YY+
18867331-A-T 16755451-A-T YY+
19486847-A-T 17374967-A-T Y+
21617562-T-G 19455676-T-G YY+
22167267-T-G 20005381-T-G YY+
22970334-C-T 20808448-C-T YY+
24782876-A-G 22636729-A-G BY23044 P3_b2 +
2804896-G-T 2936855-G-T YY+
6806479-T-C 6938438-T-C PH213 YY+
8690199-T-G 8822158-T-G YY+
9921715-C-T 10084106-C-T Y+
13265718-A-C 11110042-A-C +
16336897-G-T 14225017-G-T YY23×T+
13365549-C-G 11209873-C-G +
13433861-C-G 11278185-C-G +
13807861-G-A 11687155-G-A BY39917Z13524 +
14444804-A-G 12324077-A-G Y+
14926498-G-T 12814563-G-T YY+
15208874-G-A 13096960-G-A YY+
16768623-C-A 14656743-C-A YY+
17523888-A-T 15412008-A-T Y+
17641926-G-T 15530046-G-T Y+
19437427-A-G 17325547-A-G Y+
21328865-A-T 19166979-A-T YY+
21515911-A-G 19354025-A-G YY+
21515944-G-A 19354058-G-A Y43383 YY+
22868325-G-A 20706439-G-A YY+
16990274-G-A 14878394-G-A S19063 YY+
14772676-A-T 12660745-A-T YY21×T+
22970374-C-T 20808488-C-T YY+
3652822-A-G 3784781-A-G +
6403289-A-G 6535248-A-G A18684 +
13362393-A-G 11206717-A-G +
13386125-A-T 11230449-A-T +
13545860-C-G 11390184-C-G +
13640367-T-C 11484691-T-C +
13738359-C-T 11582683-C-T +
14386272-A-T 12265568-A-T CTS2604 Y+
14926502-A-T 12814567-A-T YY+
19128830-C-T 17016950-C-T S21832 YY+
22970326-A-T 20808440-A-T YY+
58823337-A-C 56767534-T-G +
2951878-T-A 3083837-T-A +
3178102-T-A 3310061-T-A +
5491186-C-T 5623145-C-T F9367 +
14696029-G-A 12584095-G-A YY+
6403276-A-T 6535235-A-T +
7263862-A-C 7395821-A-C YY+
8842918-C-A 8974877-C-A YY+
9075222-C-T 9237613-C-T Y+
9075227-G-T 9237618-G-T Y+
13281996-T-G 11126320-T-G +
13300109-C-G 11144433-C-G +
13346407-G-A 11190731-G-A +
13415010-A-G 11259334-A-G +
13529810-T-G 11374134-T-G +
13637217-C-T 11481541-C-T +
13889161-A-G 11768455-A-G Y+
14386294-C-A 12265590-C-A Y+
14532749-G-C 12420950-G-C Y+
22970331-G-T 20808445-G-T YY+
24003057-A-G 21856910-A-G Y+
5787814-A-C 5919773-A-C +
17794170-CTTT-C 15682290-CTTT-C +
17189374-AG-A 15077494-AG-A +
24408989-TG-T 22262842-TG-T +
28721517-AG-A 26575370-AG-A +
3812716-GC-G 3944675-GC-G +
4424373-G-GT 4556332-G-GT +
5608178-TAC-T 5740137-TAC-T 10×AC+
17533845-AG-A 15421965-AG-A +
19231317-TTC-T 17119437-TTC-T +
7148012-GC-G 7279971-GC-G +
7723973-T-TTTG 7855932-T-TTTG +
13936200-A-AAGAG 11815494-A-AAGAG +
16533469-CAT-C 14421589-CAT-C +
16641870-TAC-T 14529990-TAC-T +
3253847-AT-A 3385806-AT-A +
13529834-C-CA 11374158-C-CA +
5486695-AC-A 5618654-AC-A +
7165326-TC-T 7297285-TC-T +
7415616-TAAATA-T 7547575-TAAATA-T +
13819006-T-TGGAAA 11698300-T-TGGAAA +
14196007-AG-A 12075301-AG-A +
16370646-TAC-T 14258766-TAC-T +
18423902-AG-A 16312022-AG-A P6_Gap +
21105513-T-TA 18943627-T-TA +
23241974-TGTA-T 21080088-TGTA-T +
28457769-AG-A 26311622-AG-A +
28818196-G-GGAATT 26672049-G-GGAATT +
24425343-G-GCATT 22279196-G-GCATT +
13686909-ACAC-A 11531233-ACAC-A +
28817653-GGAATGGAATGGAATGGAATGGAAT-G 26671506-GGAATGGAATGGAATGGAATGGAAT-G +
16365173-T-TAGAA 14253293-T-TAGAA +
13257286-TATA-T 11101610-TATA-T +
28595935-G-A 26449788-G-A Z15169 +
13139025-CCACT-C 10628511-CCACT-C +
28686404-C-A 26540257-C-A +
28758622-T-C 26612475-T-C Y+
24425340-C-CATGT 22279193-C-CATGT +
24425337-A-ATGCG 22279190-A-ATGCG +
24425341-A-ATGCG 22279194-A-ATGCG +
13819959-TGAATGGAATGGAATGGAATG-T 11699253-TGAATGGAATGGAATGGAATG-T 14×GAATG+
13811067-AGGAATGGAAT-A 11690361-AGGAATGGAAT-A 11×GGAAT+
13263065-GTA-G 11107389-GTA-G +
24447135-G-GAAAA 22300988-G-GAAAA +
28818206-G-GTAATT 26672059-G-GTAATT +
13194516-ATTCC-A 11038840-ATTCC-A +
15799177-CTCTTTCTTTCTT-C 13687297-CTCTTTCTTTCTT-C 13×TCTT+
13936201-A-AAAGG 11815495-A-AAAGG +
14255747-G-GT 12135041-G-GT +
7199198-TC-T 7331157-TC-T +
14881706-AAG-A 12769777-A-T +
5400487-TG-T 5532446-TG-T +
17662052-GTT-G 15550172-GTT-G +
13275929-A-AT 11120253-A-AT +
23315713-C-CTTT 21153827-C-CTTT 20×T+
28791280-ACGGAGTGGAG-A 26645133-ACGGAGTGGAG-A +
28792467-GGAGTGA-G 26646320-GGAGTGA-G +
5886194-TC-T 6018153-TC-T +
4794855-C-CTT 4926814-C-CTT 21×T+
13433830-A-AT 11278154-A-AT +
22011557-C-CAA 19849671-C-CAA 21×A+
2685664-TG-T 2817623-TG-T +
14418203-GTA-G 12297478-GTA-G 8×TA+
6093482-GT-G 6225441-GT-G +
6147466-G-T 6279425-G-T IR3_Dst +
5523893-A-T 5655852-A-T +
14637685-AGT-A 12525754-AGT-A 11×GT+
13738513-A-T 11582837-A-T +
13431841-G-T 11276165-G-T +
14953605-C-A 12841679-C-A YY14×A+
14834316-C-T 12722383-C-T YY+
3561528-T-A 3693487-T-A +
58849671-C-T 56741200-G-A +
28802524-C-G 26656377-C-G S835 +
28802525-G-A 26656378-G-A +
5395573-G-A 5527532-G-A +
19098201-G-A 16986321-G-A Y+
14532743-T-C 12420944-T-C Y+
13282007-T-TC 11126331-T-TC +
58852532-T-C 56738339-A-G +
58897945-C-G 56692926-G-C +
58893241-A-C 56697630-T-G +
22800096-A-G 20638210-A-G Y+
5344531-T-C 5476490-T-C +
13741497-G-C 11585821-G-C +
58878730-G-A 56712141-C-T +
13258031-A-C 11102355-A-C +
2987520-T-C 3119479-T-C +
13265949-T-A 11110273-T-A +
5408786-A-C 5540745-A-C +
13414378-G-T 11258702-G-T +
13738319-G-A 11582643-G-A +
13276363-T-C 11120687-T-C +
6006768-T-C 6138727-T-C +
22005442-A-C 19843556-A-C YY+
28802992-C-G 26656845-C-G BY30349 +
13570501-A-G 11414825-A-G +
23289139-A-G 21127253-A-G Y+
21637324-C-T 19475438-C-T PH4850 YY+
16224920-T-G 14113040-T-G YY+
21112410-T-TAC 18950524-T-TAC 17×AC+
28798972-G-A 26652825-G-A +
28791635-A-G 26645488-A-G Z27086 +
22443825-T-G 20281939-T-G PF1168 DYZ19 +
9971828-G-A 10134219-G-A A1078A1083 Y+
13386656-T-C 11230980-T-C PF514 +
5308801-G-T 5440760-G-T +
14696025-G-A 12584091-G-A YY+
16990254-G-A 14878374-G-A YY+
22268475-T-TCC 20106589-T-TCC DYZ19 +
58891779-T-C 56699092-A-G +
13257061-C-T 11101385-C-T +
4270959-AAGATAGATAGAT-A 4402918-AAGATAGATAGAT-A 15×AGAT+
4446664-T-G 4578623-T-G +
6772618-C-A 6904577-C-A Y+
21396964-C-T 19235078-C-T YY+
7534643-C-A 7666602-C-A YY17×A+
8511050-A-G 8643009-A-G YY+
14191088-C-CT 12070382-C-CT 11×T+
14503598-G-A 12391803-G-A YY+
15028612-C-A 12916700-C-A PH1575 YY+
15426242-C-T 13314362-C-T YY+
15555006-G-T 13443126-G-T PH1752 YP6449 YY+
15778378-G-GT 13666498-G-GT Y315 9×T+
17832878-C-T 15720998-C-T YY+
18741627-C-G 16629747-C-G PH3966 YY+
18870808-C-CT 16758928-C-CT 9×T+
19130731-C-T 17018851-C-T YY+
19228904-A-T 17117024-A-T FGC29169 YY+
19270817-C-T 17158937-C-T YY+
5999580-G-A 6131539-G-A +
14443801-T-A 12323074-T-A CTS2719 Y+
5523890-G-T 5655849-G-T +
13392342-G-A 11236666-G-A +
21515909-T-G 19354023-T-G M12057 YY+
21993007-A-T 19831121-A-T YY+
28791530-T-A 26645383-T-A +
28791631-G-A 26645484-G-A Z27085 +
28799002-G-A 26652855-G-A +
4340996-G-A 4472955-G-A +
6403278-C-G 6535237-C-G +
6405526-G-A 6537485-G-A +
6695889-A-C 6827848-A-C YY+
7758719-G-T 7890678-G-T Y+
13265722-C-G 11110046-C-G +
13275010-A-C 11119334-A-C +
13295813-G-T 11140137-G-T +
13507437-G-C 11351761-G-C F10876 +
13909348-G-A 11788642-G-A YY+
13508016-T-A 11352340-T-A +
13545867-C-T 11390191-C-T +
13637205-C-T 11481529-C-T +
14698451-T-C 12586517-T-C YY+
19339982-C-T 17228102-C-T YY+
20209001-T-C 18047115-T-C A13707 P5_Dst +
22537275-C-A 20375389-C-A Y15×A+
22974074-T-A 20812188-T-A YY+
28315872-T-G 26169725-T-G P1_b4 +
28596688-A-C 26450541-A-C +
58858927-C-T 56731944-G-A +
3084439-A-G 3216398-A-G +
3205886-C-A 3337845-C-A +
4778043-T-G 4910002-T-G +
13909371-T-C 11788665-T-C YY+
13637141-C-T 11481465-C-T +
19472669-A-C 17360789-A-C YY+
13508957-T-C 11353281-T-C +
58967702-T-A 56821555-T-A +
59000349-A-T 56854202-A-T +
14443806-G-A 12323079-G-A CTS2720 Y+
59002526-T-G 56856379-T-G +
5179928-T-G 5311887-T-G +
13508902-A-G 11353226-A-G +
13909325-T-G 11788619-T-G YY+
14533050-A-C 12421251-A-C Y+
22902573-T-G 20740687-T-G YY+
28454551-A-G 26308404-A-G P1_gr2 +
3194113-T-G 3326072-T-G +
4537608-A-T 4669567-A-T +
5972099-T-G 6104058-T-G +
6405591-T-G 6537550-T-G +
13503131-A-C 11347455-A-C +
13507935-C-A 11352259-C-A +
58863277-A-C 56727594-T-G +
13273993-C-A 11118317-C-A +
9231660-G-A 9394051-G-A Y+
4161724-A-C 4293683-A-C +
3653017-T-C 3784976-T-C +
3568672-T-C 3700631-T-C +
14443816-T-A 12323089-T-A CTS2721 Y+
13519437-A-C 11363761-A-C +
13273994-C-T 11118318-C-T +
9654288-A-G 9816679-A-G IR3_Prx +
9645653-C-T 9808044-C-T IR3_Prx 20×T+
4537610-C-T 4669569-C-T +
23831252-C-T 21669366-C-T Y26×T+
13640445-G-T 11484769-G-T +
27146041-C-T 24999894-C-T ZZ43ZZ43_3 P1_g3 *
26816357-G-A 24670210-G-A ZZ43ZZ43_2 P1_g2 *

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
Manual24899333-C-T22753186-C-TChecked BAM file. 2 C reads, 2 T reads.
Manual15683936-T-C13572056-T-CChecked BAM File. 2 C reads.
Manual9376352-G-A9538743-G-AChecked BAM File. 4 A reads.
Manual16680097-GT-G14568217-GT-GChecked BAM File. 6 reads all show the deletion.
Manual14211141-T-C12090435-T-CChecked BAM File. Just one read and it is a C.
Manual25892897-A-G23746750-A-GChecked BAM File. A total of 4 reads, 3 G and 1 A.
Manual19953026-T-A17841146-T-AChecked BAM File. Just 3 reads, 1 A and 2 T.
Manual22260454-G-A20098568-G-A4 reads, 2 A and 2 G.
Manual13840815-C-CGAATG11720109-C-CGAATGThere are 9 repeats of GAATG starting at this position in the reference sequence. There are two reads long enough to contain the full sequence in the BAM file and both have the insertion.
Manual22285004-C-T20123118-C-TSome reads clearly belong elsewhere. Of the reads which fit here, 1 is C, 2 are T.
Manual24939079-C-T22792932-C-T3C, 3T.
Manual26121103-C-T23974956-C-T1C, 2T.
Manual14611351-AG-A12499557-AG-AJust one read, but it shows the deletion.
Manual22425174-A-G20263288-A-G4A 2G
Manual22425290-C-T20263404-C-T5C 4T
Manual27146041-C-T24999894-C-T3C 1T
Manual26816357-G-A24670210-G-A2G 2A
Manual4847052-T-G4979011-T-G3G
Manual16242632-T-TTCTATCTATCTA14130752-T-TTCTATCTATCTA3 reads cover this region and are positive.
Manual14418140-GTATATATATATGTATATATATA-G12297437-G-.Just one read covers the deletion, but it does look to be there.

Uncertain Mutations

NGS tests don't always cover all of the Y chromosome and, even when they do, the results can be inconclusive. The following mutations don't have clear results and have been assumed to be positive or negative. For those mutations that are assumed to be positive, the assumed SNP/INDEL will likely be found on the tree in some upstream block. It is unclear if it should be placed upstream of your results or parallel to them. The situation is reversed for mutations assumed negative. Those SNPs/INDELs will likely be found on a parallel branch on the tree, and it is unclear if they should be positioned upstream. As more results come in, the ambiguity may resolve itself, or it may be necessary to consult the BAM file for your test (available from FamilyTreeDNA or FullGenomes Corp) or by direct SNP testing (Sanger Sequencing - YSEQ or FamilyTreeDNA).

SNPs/INDELs:

BlockRegionPOS-REF-ALT (hg19)POS-REF-ALT (hg38)NamesNotes
52P5_Prx 20052811-T-C 17940931-T-C BY3360 Uncertain, but assumed positive.

*Mutations whose exact position can not be determined precisely from NGS tests, such as those in palindromes, are shown with a pink background.




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