1k Genomes
1kG: NA12043MDKA Birth:

Tree Position
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.
Position | Blocks | Names | Region | McDonald BED | combBED | STR | 1kG NA12043 | Manual Edits |
---|---|---|---|---|---|---|---|---|
hg19:Y:28798972-G-A hg38:Y:26652825-G-A | FT462122 | + | ||||||
hg19:Y:28791635-A-G hg38:Y:26645488-A-G | Z27086 | + | ||||||
hg19:Y:22443825-T-G hg38:Y:20281939-T-G | PF1168 | DYZ19 | + | |||||
hg19:Y:9971828-G-A hg38:Y:10134219-G-A | A1079 | A1083 | Y | + | ||||
hg19:Y:13386656-T-C hg38:Y:11230980-T-C | PF514 | + | ||||||
hg19:Y:14696025-G-A hg38:Y:12584091-G-A | Y | Y | + | |||||
hg19:Y:16990254-G-A hg38:Y:14878374-G-A | Y | Y | + | |||||
hg19:Y:22268475-T-TCC hg38:Y:20106589-T-TCC | DYZ19 | + | ||||||
hg19:Y:58891779-T-C hg38:Y:56699092-A-G | + | |||||||
hg19:Y:13257061-C-T hg38:Y:11101385-C-T | + | |||||||
hg19:Y:4270959-AAGATAGATAGAT-A hg38:Y:4402918-AAGATAGATAGAT-A | 15×AGAT | + | ||||||
hg19:Y:4446664-T-G hg38:Y:4578623-T-G | + | |||||||
hg19:Y:6772618-C-A hg38:Y:6904577-C-A | FT299989 | Y | + | |||||
hg19:Y:8511050-A-G hg38:Y:8643009-A-G | Y | Y | + | |||||
hg19:Y:14503598-G-A hg38:Y:12391803-G-A | FT300955 | Y | Y | + | ||||
hg19:Y:15028612-C-A hg38:Y:12916700-C-A | PH1575 | Y | Y | + | ||||
hg19:Y:15426242-C-T hg38:Y:13314362-C-T | FT301165 | Y | Y | + | ||||
hg19:Y:15555006-G-T hg38:Y:13443126-G-T | BY2940 | PH1752 YP6449 | Y | Y | + | |||
hg19:Y:15778378-G-GT hg38:Y:13666498-G-GT | Y315 | 9×T | + | |||||
hg19:Y:17832878-C-T hg38:Y:15720998-C-T | FT301745 | Y | Y | + | ||||
hg19:Y:18741627-C-G hg38:Y:16629747-C-G | PH3966 | Y | Y | + | ||||
hg19:Y:18870808-C-CT hg38:Y:16758928-C-CT | 9×T | + | ||||||
hg19:Y:19130731-C-T hg38:Y:17018851-C-T | Y | Y | + | |||||
hg19:Y:19228904-A-T hg38:Y:17117024-A-T | FGC29169 | Y | Y | + | ||||
hg19:Y:19270817-C-T hg38:Y:17158937-C-T | Y | Y | + | |||||
hg19:Y:21396964-C-T hg38:Y:19235078-C-T | BY132589 | Y | Y | + | ||||
hg19:Y:21637324-C-T hg38:Y:19475438-C-T | PH4850 | Y | Y | + | ||||
hg19:Y:22800096-A-G hg38:Y:20638210-A-G | FT302718 | Y | + | |||||
hg19:Y:23289139-A-G hg38:Y:21127253-A-G | FT302857 | Y | + | |||||
hg19:Y:13431841-G-T hg38:Y:11276165-G-T | + | |||||||
hg19:Y:14953605-C-A hg38:Y:12841679-C-A | Y | Y | 14×A | + | ||||
hg19:Y:14834316-C-T hg38:Y:12722383-C-T | BY97875 | Y | Y | + | ||||
hg19:Y:3561528-T-A hg38:Y:3693487-T-A | + | |||||||
hg19:Y:28802524-C-G hg38:Y:26656377-C-G | S835 | + | ||||||
hg19:Y:28802525-G-A hg38:Y:26656378-G-A | + | |||||||
hg19:Y:19098201-G-A hg38:Y:16986321-G-A | Y | + | ||||||
hg19:Y:13282007-T-TC hg38:Y:11126331-T-TC | + | |||||||
hg19:Y:58852532-T-C hg38:Y:56738339-A-G | + | |||||||
hg19:Y:58897945-C-G hg38:Y:56692926-G-C | + | |||||||
hg19:Y:13738513-A-T hg38:Y:11582837-A-T | DYZ17 | + | ||||||
hg19:Y:58893241-A-C hg38:Y:56697630-T-G | + | |||||||
hg19:Y:13741497-G-C hg38:Y:11585821-G-C | DYZ17 | + | ||||||
hg19:Y:58878730-G-A hg38:Y:56712141-C-T | + | |||||||
hg19:Y:13258031-A-C hg38:Y:11102355-A-C | + | |||||||
hg19:Y:2987520-T-C hg38:Y:3119479-T-C | + | |||||||
hg19:Y:22005442-A-C hg38:Y:19843556-A-C | Y | Y | + | |||||
hg19:Y:28802992-C-G hg38:Y:26656845-C-G | BY30349 | + | ||||||
hg19:Y:16224920-T-G hg38:Y:14113040-T-G | Y | Y | + | |||||
hg19:Y:19472669-A-C hg38:Y:17360789-A-C | Y | Y | + | |||||
hg19:Y:5179928-T-G hg38:Y:5311887-T-G | + | |||||||
hg19:Y:13508902-A-G hg38:Y:11353226-A-G | + | |||||||
hg19:Y:22902573-T-G hg38:Y:20740687-T-G | Y | Y | + | |||||
hg19:Y:4537608-A-T hg38:Y:4669567-A-T | + | |||||||
hg19:Y:5972099-T-G hg38:Y:6104058-T-G | + | |||||||
hg19:Y:23831252-C-T hg38:Y:21669366-C-T | Y | 26×T | + | |||||
hg19:Y:4537610-C-T hg38:Y:4669569-C-T | + | |||||||
hg19:Y:9645653-C-T hg38:Y:9808044-C-T | IR3_Prx | 20×T | + | |||||
hg19:Y:58863277-A-C hg38:Y:56727594-T-G | + | |||||||
hg19:Y:3568672-T-C hg38:Y:3700631-T-C | + | |||||||
hg19:Y:3653017-T-C hg38:Y:3784976-T-C | + | |||||||
hg19:Y:4161724-A-C hg38:Y:4293683-A-C | + | |||||||
hg19:Y:9231660-G-A hg38:Y:9394051-G-A | Y | + | ||||||
hg19:Y:13508957-T-C hg38:Y:11353281-T-C | + | |||||||
hg19:Y:21515909-T-G hg38:Y:19354023-T-G | M12057 | Y | Y | + | ||||
hg19:Y:21993007-A-T hg38:Y:19831121-A-T | Y | Y | + | |||||
hg19:Y:28791631-G-A hg38:Y:26645484-G-A | Z27085 | + | ||||||
hg19:Y:28799002-G-A hg38:Y:26652855-G-A | + | |||||||
hg19:Y:6405526-G-A hg38:Y:6537485-G-A | FT110754 | + | ||||||
hg19:Y:6695889-A-C hg38:Y:6827848-A-C | Y | Y | + | |||||
hg19:Y:7758719-G-T hg38:Y:7890678-G-T | Y | + | ||||||
hg19:Y:13392342-G-A hg38:Y:11236666-G-A | + | |||||||
hg19:Y:13507437-G-C hg38:Y:11351761-G-C | F10876 | + | ||||||
hg19:Y:14698451-T-C hg38:Y:12586517-T-C | Y | Y | + | |||||
hg19:Y:22537275-C-A hg38:Y:20375389-C-A | Y | 15×A | + | |||||
hg19:Y:22974074-T-A hg38:Y:20812188-T-A | Y | Y | + | |||||
hg19:Y:28315872-T-G hg38:Y:26169725-T-G | P1_b4 | + | ||||||
hg19:Y:28596688-A-C hg38:Y:26450541-A-C | + | |||||||
hg19:Y:3084439-A-G hg38:Y:3216398-A-G | + | |||||||
hg19:Y:3205886-C-A hg38:Y:3337845-C-A | + | |||||||
hg19:Y:4778043-T-G hg38:Y:4910002-T-G | + | |||||||
hg19:Y:5523890-G-T hg38:Y:5655849-G-T | + | |||||||
hg19:Y:5523893-A-T hg38:Y:5655852-A-T | + | |||||||
hg19:Y:5787814-A-C hg38:Y:5919773-A-C | + | |||||||
hg19:Y:6147466-G-T hg38:Y:6279425-G-T | IR3_Dst | + | ||||||
hg19:Y:13362393-A-G hg38:Y:11206717-A-G | + | |||||||
hg19:Y:13386125-A-T hg38:Y:11230449-A-T | + | |||||||
hg19:Y:13640367-T-C hg38:Y:11484691-T-C | + | |||||||
hg19:Y:13738359-C-T hg38:Y:11582683-C-T | DYZ17 | + | ||||||
hg19:Y:14386272-A-T hg38:Y:12265568-A-T | CTS2604 | Y | + | |||||
hg19:Y:14926502-A-T hg38:Y:12814567-A-T | Y | Y | + | |||||
hg19:Y:19128830-C-T hg38:Y:17016950-C-T | S21832 | Y | Y | + | ||||
hg19:Y:22970326-A-T hg38:Y:20808440-A-T | Y | Y | + | |||||
hg19:Y:58823337-A-C hg38:Y:56767534-T-G | + | |||||||
hg19:Y:3178102-T-A hg38:Y:3310061-T-A | + | |||||||
hg19:Y:3652822-A-G hg38:Y:3784781-A-G | + | |||||||
hg19:Y:7263862-A-C hg38:Y:7395821-A-C | Y | Y | + | |||||
hg19:Y:8842918-C-A hg38:Y:8974877-C-A | Y | Y | + | |||||
hg19:Y:9075222-C-T hg38:Y:9237613-C-T | Y | + | ||||||
hg19:Y:9075227-G-T hg38:Y:9237618-G-T | Y | + | ||||||
hg19:Y:13281996-T-G hg38:Y:11126320-T-G | + | |||||||
hg19:Y:13300109-C-G hg38:Y:11144433-C-G | + | |||||||
hg19:Y:13346407-G-A hg38:Y:11190731-G-A | + | |||||||
hg19:Y:13415010-A-G hg38:Y:11259334-A-G | + | |||||||
hg19:Y:13529810-T-G hg38:Y:11374134-T-G | + | |||||||
hg19:Y:13889161-A-G hg38:Y:11768455-A-G | Y | + | ||||||
hg19:Y:14386294-C-A hg38:Y:12265590-C-A | Y | + | ||||||
hg19:Y:14532749-G-C hg38:Y:12420950-G-C | Y | + | ||||||
hg19:Y:14696029-G-A hg38:Y:12584095-G-A | Y | Y | + | |||||
hg19:Y:14772676-A-T hg38:Y:12660745-A-T | FT311941 | Y | Y | 21×T | + | |||
hg19:Y:16336897-G-T hg38:Y:14225017-G-T | FTB17625 | Y | Y | 23×T | + | |||
hg19:Y:16990274-G-A hg38:Y:14878394-G-A | S19063 | Y | Y | + | ||||
hg19:Y:17090827-T-C hg38:Y:14978947-T-C | Y | Y | + | |||||
hg19:Y:17632563-G-A hg38:Y:15520683-G-A | Y | Y | + | |||||
hg19:Y:18867331-A-T hg38:Y:16755451-A-T | Y | Y | + | |||||
hg19:Y:19486847-A-T hg38:Y:17374967-A-T | Y | + | ||||||
hg19:Y:21617562-T-G hg38:Y:19455676-T-G | Y | Y | + | |||||
hg19:Y:22167267-T-G hg38:Y:20005381-T-G | Y | Y | + | |||||
hg19:Y:22970334-C-T hg38:Y:20808448-C-T | Y | Y | + | |||||
hg19:Y:24782876-A-G hg38:Y:22636729-A-G | BY23044 | P3_b2 | + | |||||
hg19:Y:2804896-G-T hg38:Y:2936855-G-T | Y | Y | + | |||||
hg19:Y:6806479-T-C hg38:Y:6938438-T-C | PH213 | Y | Y | + | ||||
hg19:Y:8690199-T-G hg38:Y:8822158-T-G | Y | Y | + | |||||
hg19:Y:9921715-C-T hg38:Y:10084106-C-T | FTB67730 | Y | + | |||||
hg19:Y:13242098-A-G hg38:Y:11086422-A-G | + | |||||||
hg19:Y:13265718-A-C hg38:Y:11110042-A-C | + | |||||||
hg19:Y:13365549-C-G hg38:Y:11209873-C-G | + | |||||||
hg19:Y:13433861-C-G hg38:Y:11278185-C-G | + | |||||||
hg19:Y:13807861-G-A hg38:Y:11687155-G-A | BY39917 | Z13524 | DYZ17 | + | ||||
hg19:Y:14444804-A-G hg38:Y:12324077-A-G | FT300929 | Y | + | |||||
hg19:Y:14926498-G-T hg38:Y:12814563-G-T | Y | Y | + | |||||
hg19:Y:15208874-G-A hg38:Y:13096960-G-A | Y | Y | + | |||||
hg19:Y:16768623-C-A hg38:Y:14656743-C-A | Y | Y | + | |||||
hg19:Y:17523888-A-T hg38:Y:15412008-A-T | Y | + | ||||||
hg19:Y:17641926-G-T hg38:Y:15530046-G-T | Y | + | ||||||
hg19:Y:19437427-A-G hg38:Y:17325547-A-G | Y | + | ||||||
hg19:Y:21328865-A-T hg38:Y:19166979-A-T | Y | Y | + | |||||
hg19:Y:21515911-A-G hg38:Y:19354025-A-G | Y | Y | + | |||||
hg19:Y:21515944-G-A hg38:Y:19354058-G-A | Y43383 | Y | Y | + | ||||
hg19:Y:22868325-G-A hg38:Y:20706439-G-A | Y | Y | + | |||||
hg19:Y:22970331-G-T hg38:Y:20808445-G-T | Y | Y | + | |||||
hg19:Y:22970374-C-T hg38:Y:20808488-C-T | Y | Y | + | |||||
hg19:Y:24003057-A-G hg38:Y:21856910-A-G | FT332719 | Y | + | |||||
hg19:Y:28595935-G-A hg38:Y:26449788-G-A | Z15169 | + | ||||||
hg19:Y:28686404-C-A hg38:Y:26540257-C-A | + | |||||||
hg19:Y:28758622-T-C hg38:Y:26612475-T-C | FT303155 | Y | + | |||||
hg19:Y:24425340-C-CATGT hg38:Y:22279193-C-CATGT | + | |||||||
hg19:Y:24425337-A-ATGCG hg38:Y:22279190-A-ATGCG | + | |||||||
hg19:Y:24425341-A-ATGCG hg38:Y:22279194-A-ATGCG | + | |||||||
hg19:Y:13811067-AGGAATGGAAT-A hg38:Y:11690361-AGGAATGGAAT-A | DYZ17 | 11×GGAAT | + | |||||
hg19:Y:13263065-GTA-G hg38:Y:11107389-GTA-G | + | |||||||
hg19:Y:24447135-G-GAAAA hg38:Y:22300988-G-GAAAA | + | |||||||
hg19:Y:28818206-G-GTAATT hg38:Y:26672059-G-GTAATT | + | |||||||
hg19:Y:13194516-ATTCC-A hg38:Y:11038840-ATTCC-A | + | |||||||
hg19:Y:13936201-A-AAAGG hg38:Y:11815495-A-AAAGG | + | |||||||
hg19:Y:13139025-CCACT-C hg38:Y:10628511-CCACT-C | + | |||||||
hg19:Y:14255747-G-GT hg38:Y:12135041-G-GT | + | |||||||
hg19:Y:14881706-AAG-A hg38:Y:12769777-A-T | Y | Y | + | |||||
hg19:Y:5400487-TG-T hg38:Y:5532446-TG-T | + | |||||||
hg19:Y:17662052-GTT-G hg38:Y:15550172-GTT-G | + | |||||||
hg19:Y:23315713-C-CTTT hg38:Y:21153827-C-CTTT | 20×T | + | ||||||
hg19:Y:28791280-ACGGAGTGGAG-A hg38:Y:26645133-ACGGAGTGGAG-A | + | |||||||
hg19:Y:28792467-GGAGTGA-G hg38:Y:26646320-GGAGTGA-G | + | |||||||
hg19:Y:5886194-TC-T hg38:Y:6018153-TC-T | + | |||||||
hg19:Y:4794855-C-CTT hg38:Y:4926814-C-CTT | 21×T | + | ||||||
hg19:Y:13433830-A-AT hg38:Y:11278154-A-AT | + | |||||||
hg19:Y:2685664-TG-T hg38:Y:2817623-TG-T | + | |||||||
hg19:Y:6093482-GT-G hg38:Y:6225441-GT-G | + | |||||||
hg19:Y:7199198-TC-T hg38:Y:7331157-TC-T | + | |||||||
hg19:Y:16365173-T-TAGAA hg38:Y:14253293-T-TAGAA | + | |||||||
hg19:Y:17189374-AG-A hg38:Y:15077494-AG-A | + | |||||||
hg19:Y:24408989-TG-T hg38:Y:22262842-TG-T | + | |||||||
hg19:Y:28721517-AG-A hg38:Y:26575370-AG-A | + | |||||||
hg19:Y:3812716-GC-G hg38:Y:3944675-GC-G | + | |||||||
hg19:Y:4424373-G-GT hg38:Y:4556332-G-GT | + | |||||||
hg19:Y:19231317-TTC-T hg38:Y:17119437-TTC-T | + | |||||||
hg19:Y:7148012-GC-G hg38:Y:7279971-GC-G | + | |||||||
hg19:Y:7723973-T-TTTG hg38:Y:7855932-T-TTTG | + | |||||||
hg19:Y:13936200-A-AAGAG hg38:Y:11815494-A-AAGAG | + | |||||||
hg19:Y:16641870-TAC-T hg38:Y:14529990-TAC-T | + | |||||||
hg19:Y:17794170-CTTT-C hg38:Y:15682290-CTTT-C | + | |||||||
hg19:Y:3253847-AT-A hg38:Y:3385806-AT-A | + | |||||||
hg19:Y:5486695-AC-A hg38:Y:5618654-AC-A | + | |||||||
hg19:Y:7165326-TC-T hg38:Y:7297285-TC-T | + | |||||||
hg19:Y:7415616-TAAATA-T hg38:Y:7547575-TAAATA-T | + | |||||||
hg19:Y:13819006-T-TGGAAA hg38:Y:11698300-T-TGGAAA | DYZ17 | + | ||||||
hg19:Y:14196007-AG-A hg38:Y:12075301-AG-A | + | |||||||
hg19:Y:16370646-TAC-T hg38:Y:14258766-TAC-T | + | |||||||
hg19:Y:18423902-AG-A hg38:Y:16312022-AG-A | P6_Gap | + | ||||||
hg19:Y:21105513-T-TA hg38:Y:18943627-T-TA | + | |||||||
hg19:Y:23241974-TGTA-T hg38:Y:21080088-TGTA-T | + | |||||||
hg19:Y:28457769-AG-A hg38:Y:26311622-AG-A | + | |||||||
hg19:Y:28818196-G-GGAATT hg38:Y:26672049-G-GGAATT | + | |||||||
hg19:Y:24425343-G-GCATT hg38:Y:22279196-G-GCATT | + | |||||||
hg19:Y:13686909-ACAC-A hg38:Y:11531233-ACAC-A | DYZ17 | + | ||||||
hg19:Y:28817653-GGAATGGAATGGAATGGAATGGAAT-G hg38:Y:26671506-GGAATGGAATGGAATGGAATGGAAT-G | + | |||||||
hg19:Y:27146041-C-T hg38:Y:24999894-C-T | ZZ43_3 | P1_g3 | * | |||||
hg19:Y:26816357-G-A hg38:Y:24670210-G-A | ZZ43_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 |
---|---|---|---|
Manual | 16242632-T-TTCTATCTATCTA | 14130752-T-TTCTATCTATCTA | 3 reads cover this region and are positive. |
Manual | 22425174-A-G | 20263288-A-G | 4A 2G |
Manual | 22425290-C-T | 20263404-C-T | 5C 4T |
Manual | 14418140-GTATATATATATGTATATATATA-G | 12297437-G-. | Just one read covers the deletion, but it does look to be there. |
Manual | 9376352-G-A | 9538743-G-A | Checked BAM File. 4 A reads. |
Manual | 14211141-T-C | 12090435-T-C | Checked BAM File. Just one read and it is a C. |
Manual | 14611351-AG-A | 12499557-AG-A | Just one read, but it shows the deletion. |
Manual | 15683936-T-C | 13572056-T-C | Checked BAM File. 2 C reads. |
Manual | 16680097-GT-G | 14568217-GT-G | Checked BAM File. 6 reads all show the deletion. |
Manual | 19953026-T-A | 17841146-T-A | Checked BAM File. Just 3 reads, 1 A and 2 T. |
Manual | 22260454-G-A | 20098568-G-A | 4 reads, 2 A and 2 G. |
Manual | 22285004-C-T | 20123118-C-T | Some reads clearly belong elsewhere. Of the reads which fit here, 1 is C, 2 are T. |
Manual | 24899333-C-T | 22753186-C-T | Checked BAM file. 2 C reads, 2 T reads. |
Manual | 24939079-C-T | 22792932-C-T | 3C, 3T. |
Manual | 25892897-A-G | 23746750-A-G | Checked BAM File. A total of 4 reads, 3 G and 1 A. |
Manual | 26121103-C-T | 23974956-C-T | 1C, 2T. |
Manual | 13840815-C-CGAATG | 11720109-C-CGAATG | There 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. |
Manual | 4847052-T-G | 4979011-T-G | 3G |
Manual | 27146041-C-T | 24999894-C-T | 3C 1T |
Manual | 26816357-G-A | 24670210-G-A | 2G 2A |