1k Genomes
1kG: HG02789MDKA Birth: Pakistan
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.
POS-REF-ALT (hg19) | POS-REF-ALT (hg38) | Blocks | Names | Region | McDonald BED | combBED | STR | 1kG HG02789 |
---|---|---|---|---|---|---|---|---|
13384620-C-T | 11228944-C-T | FGC13898 | FGC13898 | + | ||||
8455657-G-A | 8587616-G-A | PF5721 | PF5721 | Y | Y | + | ||
7862721-C-T | 7994680-C-T | FGC32369 Z31479 Y12929 | Y | Y | + | |||
22901129-A-T | 20739243-A-T | M3208 | Y | Y | + | |||
13880605-C-T | 11759899-C-T | FGC32392 Y12295 | Y | + | ||||
2661236-C-T | 2793195-C-T | Y12288 FGC7837 SK1172 | Y | Y | + | |||
2701380-A-C | 2833339-A-C | M3100 | Y | Y | + | |||
2707716-G-T | 2839675-G-T | M3101 | Y | Y | + | |||
2976942-T-A | 3108901-T-A | FGC7840 Z8015 | + | |||||
3132549-C-A | 3264508-C-A | + | ||||||
3544256-C-G | 3676215-C-G | FT568 | + | |||||
3778513-C-A | 3910472-C-A | FT318461 | + | |||||
4066788-A-G | 4198747-A-G | FGC55667 | + | |||||
4262001-T-G | 4393960-T-G | Y12913 | + | |||||
4404630-C-T | 4536589-C-T | FGC55681 | + | |||||
4491960-G-A | 4623919-G-A | FGC7839 Z8016 | + | |||||
4607414-G-A | 4739373-G-A | FT307288 | + | |||||
4644018-T-G | 4775977-T-G | FGC55684 | + | |||||
4724124-T-C | 4856083-T-C | FGC55659 | + | |||||
4874338-G-A | 5006297-G-A | Y12289 | + | |||||
4943744-A-G | 5075703-A-G | Z8017 FGC7835 | + | |||||
4948666-A-G | 5080625-A-G | FGC55664 | + | |||||
4999035-G-A | 5130994-G-A | FT1048 | + | |||||
5109061-T-G | 5241020-T-G | FGC55683 | + | |||||
5360974-T-A | 5492933-T-A | FGC55679 | + | |||||
5362126-T-C | 5494085-T-C | FGC55665 | + | |||||
5571466-A-G | 5703425-A-G | FGC55671 | + | |||||
5772750-A-T | 5904709-A-T | FGC55677 | + | |||||
6608678-C-T | 6740637-C-T | FGC55668 | + | |||||
6610792-T-C | 6742751-T-C | FGC55678 | + | |||||
6634249-C-T | 6766208-C-T | M3104 | Y | Y | + | |||
6752444-C-T | 6884403-C-T | FT8315 | Y | Y | + | |||
6848350-C-T | 6980309-C-T | M3105 | Y | Y | + | |||
6930974-C-T | 7062933-C-T | M3106 | Y | Y | + | |||
6934812-A-G | 7066771-A-G | Y12290 FGC32429 | Y | Y | + | |||
7034574-T-C | 7166533-T-C | FT327124 | Y | Y | + | |||
7049757-C-A | 7181716-C-A | M3107 | Y | Y | + | |||
7060651-C-T | 7192610-C-T | M3108 | Y | + | ||||
7078146-C-G | 7210105-C-G | M3109 | Y | Y | + | |||
7134340-T-C | 7266299-T-C | M3111 | Y | + | ||||
7158318-C-T | 7290277-C-T | M3642 | Y | Y | + | |||
7246792-C-T | 7378751-C-T | M3112 | Y | Y | + | |||
7264729-A-G | 7396688-A-G | M3113 | Y | Y | + | |||
7271477-C-G | 7403436-C-G | M3114 | Y | Y | + | |||
7322981-G-T | 7454940-G-T | M3115 | Y | Y | + | |||
7330625-G-A | 7462584-G-A | M3116 | Y | Y | + | |||
7552621-G-C | 7684580-G-C | M3117 | Y | Y | + | |||
7614629-A-C | 7746588-A-C | Y12914 FGC32385 | Y | Y | + | |||
7681636-C-G | 7813595-C-G | M3119 | Y | Y | + | |||
7762172-G-A | 7894131-G-A | Y | Y | + | ||||
7918570-C-T | 8050529-C-T | M3122 | Y | Y | + | |||
7938066-C-T | 8070025-C-T | M3123 | Y | Y | + | |||
7956864-G-T | 8088823-G-T | M3124 | Y | Y | + | |||
7975012-T-A | 8106971-T-A | Y | Y | + | ||||
8090420-A-T | 8222379-A-T | Y12291 FGC32377 | Y | Y | + | |||
8321328-T-C | 8453287-T-C | M3125 | Y | Y | + | |||
8362124-C-A | 8494083-C-A | Y12292 FGC32389 BY794 | Y | Y | + | |||
8371771-G-T | 8503730-G-T | M3128 | Y | Y | + | |||
8526343-C-T | 8658302-C-T | SK1170 | Y | Y | + | |||
8528374-G-C | 8660333-G-C | FT307661 | Y | Y | + | |||
8583848-C-T | 8715807-C-T | S7520 | Y | Y | + | |||
8625892-A-G | 8757851-A-G | M3129 | Y | Y | + | |||
8653573-C-G | 8785532-C-G | M3130 | Y | Y | + | |||
8709740-G-A | 8841699-G-A | FT307663 | Y | Y | + | |||
8868061-G-T | 9000020-G-T | M3132 S7541 | Y | + | ||||
9136262-T-C | 9298653-T-C | Y | + | |||||
9410456-G-A | 9572847-G-A | M3134 | Y | + | ||||
9417819-C-T | 9580210-C-T | Y12293 BY900 | Y | Y | + | |||
9456102-C-T | 9618493-C-T | M3135 | Y | Y | + | |||
9514850-G-A | 9677241-G-A | FGC55682 | + | |||||
9785430-T-A | 9947821-T-A | Y | 11×A | + | ||||
9884634-A-G | 10047025-A-G | M3136 | Y | Y | + | |||
9892172-T-C | 10054563-T-C | Y12918 BY928 | Y | Y | + | |||
9953619-C-T | 10116010-C-T | BY930 | Y | + | ||||
10028155-C-T | 10190546-C-T | FT80287 | Y | + | ||||
10033561-G-T | 10195952-G-T | BY4678 | FGC32428 | Y | + | |||
13253210-T-C | 11097534-T-C | + | ||||||
13366849-A-G | 11211173-A-G | + | ||||||
13456970-G-A | 11301294-G-A | Z35313 | + | |||||
13494181-A-T | 11338505-A-T | FT80276 | + | |||||
13495459-A-C | 11339783-A-C | FT80277 | + | |||||
13509986-G-T | 11354310-G-T | BY960 | + | |||||
13514450-T-A | 11358774-T-A | FT80279 | + | |||||
13540604-A-T | 11384928-A-T | FT80275 | + | |||||
13543778-G-C | 11388102-G-C | FGC80507 | + | |||||
13607046-T-C | 11451370-T-C | FGC55657 | + | |||||
13616971-C-T | 11461295-C-T | + | ||||||
13636078-T-C | 11480402-T-C | FGC55676 | + | |||||
13653765-G-A | 11498089-G-A | FGC32372 BY973 | + | |||||
13672927-T-C | 11517251-T-C | FGC32388 BY988 | + | |||||
13681109-T-G | 11525433-T-G | FGC32373 | + | |||||
13799778-C-G | 11679072-C-G | + | ||||||
13815032-C-T | 11694326-C-T | FT307714 | + | |||||
13823855-C-T | 11703149-C-T | S3577 | + | |||||
13849720-C-T | 11729014-C-T | Y12294 FGC32378 | + | |||||
13862455-G-T | 11741749-G-T | FT307735 | + | |||||
13950384-C-A | 11829678-C-A | M3138 | Y | + | ||||
14011700-A-G | 11890994-A-G | M3139 | Y | + | ||||
14060086-C-G | 11939380-C-G | M3140 | Y | Y | + | |||
14195507-C-T | 12074801-C-T | M3141 | Y | + | ||||
14238168-G-A | 12117462-G-A | M3142 | Y | Y | + | |||
14302515-A-G | 12181809-A-G | M3143 | Y | + | ||||
14374565-G-A | 12253861-G-A | Y12296 FGC32383 | Y | Y | + | |||
14418718-G-A | 12297993-G-A | Y12297 BY1090 | Y | Y | + | |||
14552166-A-C | 12440367-A-C | M3144 | Y | Y | + | |||
14656379-G-C | 12544444-G-C | Y12298 BY1109 | Y | Y | + | |||
14709383-C-T | 12597450-C-T | Y | Y | + | ||||
14745812-C-T | 12633881-C-T | FT307759 | Y | Y | + | |||
14894401-A-G | 12782467-A-G | M3145 | Y | Y | + | |||
14896655-A-G | 12784721-A-G | M3146 | Y | Y | + | |||
14936539-C-G | 12824604-C-G | M3147 | Y | Y | + | |||
14978796-T-A | 12866872-T-A | M3148 | Y | Y | + | |||
15008352-A-C | 12896437-A-C | M3149 | Y | Y | + | |||
15031385-A-G | 12919473-A-G | M283 | Y | Y | + | |||
15079273-C-T | 12967363-C-T | Y67704 | Y | Y | + | |||
15102439-C-T | 12990527-C-T | Y14599 | Y | + | ||||
15243482-C-T | 13131568-C-T | Y | + | |||||
15288689-T-C | 13176788-T-C | Y | + | |||||
15327403-G-A | 13215521-G-A | M3150 | Y | Y | + | |||
15357278-C-T | 13245397-C-T | Y12927 FGC32376 BY1172 | Y | Y | + | |||
15421572-A-G | 13309692-A-G | M3151 | Y | Y | + | |||
15426063-C-A | 13314183-C-A | Y | Y | + | ||||
15531854-A-G | 13419974-A-G | S7535 M3153 | Y | Y | + | |||
15552076-A-C | 13440196-A-C | M3154 | Y | Y | + | |||
15577988-A-G | 13466108-A-G | M3155 | Y | Y | + | |||
15614055-C-A | 13502175-C-A | FT307772 | Y | Y | + | |||
15623115-C-T | 13511235-C-T | S7524 | Y | Y | + | |||
15731802-G-C | 13619922-G-C | M3156 | Y | Y | + | |||
15748155-C-T | 13636275-C-T | M3157 | Y | Y | + | |||
15793624-C-T | 13681744-C-T | M3158 | Y | + | ||||
15841890-C-T | 13730010-C-T | M3159 | Y | Y | + | |||
15968360-G-A | 13856480-G-A | M3160 | Y | Y | + | |||
16064108-C-A | 13952228-C-A | M3161 | Y | + | ||||
16073132-G-A | 13961252-G-A | FT329859 | Y | + | ||||
16330843-G-A | 14218963-G-A | M3162 | Y | Y | + | |||
16430852-A-C | 14318972-A-C | FGC55669 | Y | Y | + | |||
16435550-A-G | 14323670-A-G | M3164 | Y | Y | + | |||
16561117-T-A | 14449237-T-A | M3165 | Y | Y | + | |||
16891681-C-T | 14779801-C-T | Y12299 FGC32384 | Y | Y | + | |||
16946687-A-G | 14834807-A-G | Y12300 SK1168 | Y | Y | + | |||
16972984-A-G | 14861104-A-G | M3167 | Y | + | ||||
17009992-A-C | 14898112-A-C | Y12923 SK1169 | Y | Y | + | |||
17074441-C-T | 14962561-C-T | M3170 | Y | Y | + | |||
17083744-T-C | 14971864-T-C | M3171 | Y | + | ||||
17260550-C-T | 15148670-C-T | M3172 | Y | + | ||||
17339157-G-A | 15227277-G-A | Y12924 FGC32379 | Y | Y | + | |||
17422688-C-T | 15310808-C-T | M3173 | Y | Y | + | |||
17771443-C-T | 15659563-C-T | M3175 | Y | Y | + | |||
17837686-G-A | 15725806-G-A | Y | + | |||||
17862980-G-T | 15751100-G-T | FT330600 | Y | Y | + | |||
18045777-T-C | 15933897-T-C | M3177 | Y | Y | + | |||
18111262-T-G | 15999382-T-G | M3178 | Y | Y | + | |||
18147236-G-A | 16035356-G-A | M3180 | Y | Y | + | |||
18386685-G-C | 16274805-G-C | FT307819 | P6_Gap | + | ||||
18406556-C-T | 16294676-C-T | Y12302 FGC32380 | P6_Gap | + | ||||
18550969-A-C | 16439089-A-C | Y12303 FGC2909 | Y | + | ||||
18610798-T-C | 16498918-T-C | FT330920 | Y | Y | + | |||
18750052-G-T | 16638172-G-T | FGC7834 Z8019 | Y | + | ||||
18943784-C-T | 16831904-C-T | M3182 | Y | Y | + | |||
18969005-C-T | 16857125-C-T | M3183 | Y | + | ||||
19084194-C-T | 16972314-C-T | FGC55680 | Y | + | ||||
19107202-A-T | 16995322-A-T | Y12304 FGC32381 BY1502 | Y | Y | + | |||
19141245-C-A | 17029365-C-A | M3184 | Y | Y | + | |||
19196316-T-C | 17084436-T-C | Y12917 FGC32371 BY1511 | Y | Y | + | |||
19297686-G-T | 17185806-G-T | FGC55662 | Y | + | ||||
19332228-C-G | 17220348-C-G | M3185 | Y | Y | + | |||
19505282-T-C | 17393402-T-C | Y12305 | Y | Y | + | |||
19506702-T-G | 17394822-T-G | FT331348 | Y | Y | + | |||
21143496-T-C | 18981610-T-C | Y12306 FGC32375 | Y | Y | + | |||
21157872-C-T | 18995986-C-T | Y12307 SK1171 | Y | + | ||||
21248555-T-C | 19086669-T-C | M3187 | Y | Y | + | |||
21290710-A-G | 19128824-A-G | M3188 | Y | Y | + | |||
21316307-T-G | 19154421-T-G | Y12308 FGC32387 BY1740 | Y | Y | + | |||
21328577-T-C | 19166691-T-C | Y12309 FGC32394 | Y | Y | + | |||
21404903-C-T | 19243017-C-T | M3190 | Y | Y | + | |||
21480778-G-A | 19318892-G-A | M3191 | Y | Y | + | |||
21483139-C-T | 19321253-C-T | M3192 | Y | Y | + | |||
21562717-T-A | 19400831-T-A | FTA6208 | Y | Y | + | |||
21606687-T-C | 19444801-T-C | M3194 | Y | Y | + | |||
21768826-A-C | 19606940-A-C | Y12310 FGC32390 | Y | Y | + | |||
21780912-A-G | 19619026-A-G | FT331728 | Y | Y | + | |||
21799648-C-T | 19637762-C-T | M3195 | Y | Y | + | |||
21820771-G-A | 19658885-G-A | FT331763 | Y | + | ||||
21839695-C-T | 19677809-C-T | FTA6221 | Y | + | ||||
21912838-G-A | 19750952-G-A | M3196 | Y | + | ||||
21950193-G-A | 19788307-G-A | M3197 | Y | Y | + | |||
21992731-T-C | 19830845-T-C | M3198 | Y | Y | + | |||
22015400-C-A | 19853514-C-A | M3199 | Y | + | ||||
22064715-C-T | 19902829-C-T | M3200 | Y | + | ||||
22107729-A-G | 19945843-A-G | M3201 | Y | Y | + | |||
22174429-G-A | 20012543-G-A | Y12928 BY1821 | Y | Y | + | |||
22298187-A-G | 20136301-A-G | FGC32386 | DYZ19 | + | ||||
22362204-A-C | 20200318-A-C | BY217695 | DYZ19 | + | ||||
22472600-C-T | 20310714-C-T | FGC32374 BY2044 | DYZ19 | + | ||||
22489092-T-G | 20327206-T-G | DYZ19 | + | |||||
22534094-G-C | 20372208-G-C | FTB18190 | Y | + | ||||
22553237-A-G | 20391351-A-G | M3203 | Y | Y | + | |||
22566533-T-C | 20404647-T-C | Y | Y | + | ||||
22766998-A-G | 20605112-A-G | Y12311 BY2086 | Y | Y | + | |||
22788846-G-A | 20626960-G-A | M3205 | Y | Y | + | |||
22883627-G-C | 20721741-G-C | M3207 | Y | + | ||||
23077854-A-G | 20915968-A-G | M3210 | Y | + | ||||
23187821-G-A | 21025935-G-A | Y12930 Z8020 FGC7836 | Y | + | ||||
23192445-T-C | 21030559-T-C | FGC55675 | Y | + | ||||
23243887-G-C | 21082001-G-C | S315 L72 | Y | Y | + | |||
23247088-A-G | 21085202-A-G | Y12312 BY2139 | Y | Y | + | |||
23262062-C-T | 21100176-C-T | M3212 | Y | Y | + | |||
23303011-G-C | 21141125-G-C | S7536 | Y | Y | + | |||
23316156-A-G | 21154270-A-G | Y12926 FGC32391 | Y | Y | + | |||
23364100-A-G | 21202214-A-G | Z8021 | Y | + | ||||
23405943-G-C | 21244057-G-C | M3215 | Y | Y | + | |||
23467992-C-G | 21306106-C-G | M3216 | Y | Y | + | |||
23480651-A-C | 21318765-A-C | Y12313 FGC32370 BY2159 | Y | Y | + | |||
23835130-G-A | 21673244-G-A | M3218 | Y | + | ||||
23860092-A-C | 21698206-A-C | M3219 | Y | + | ||||
23990820-G-T | 21844673-G-T | M3220 | Y | + | ||||
24505021-T-C | 22358874-T-C | Y12314 BY2282 | + | |||||
24553406-C-G | 22407259-C-G | P3_t2 | + | |||||
28599719-G-T | 26453572-G-T | FGC55658 | + | |||||
28666060-G-T | 26519913-G-T | M3221 | + | |||||
28686219-T-A | 26540072-T-A | FGC55660 | + | |||||
28686956-G-A | 26540809-G-A | M3222 | + | |||||
28736268-G-A | 26590121-G-A | FGC55663 | + | |||||
28744734-T-G | 26598587-T-G | M3223 | + | |||||
28771017-G-A | 26624870-G-A | S7538 | + | |||||
28790165-T-A | 26644018-T-A | + | ||||||
28805013-G-A | 26658866-G-A | + |
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.