Run ID: ERR6197021
Sample name:
Date: 02-04-2023 01:49:29
Number of reads: 2482394
Percentage reads mapped: 94.98
Strain: lineage4.7;lineage4.3.4.2
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.45 |
lineage4.7 | Euro-American (mainly T) | T1;T5 | None | 0.49 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.48 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 0.49 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.34 | rifampicin |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 1.0 | streptomycin |
rrs | 1473247 | n.1402C>A | non_coding_transcript_exon_variant | 0.75 | kanamycin, capreomycin, aminoglycosides, amikacin |
rrs | 1473329 | n.1484G>T | non_coding_transcript_exon_variant | 0.81 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.51 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 0.59 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6140 | p.Val301Leu | missense_variant | 0.33 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.28 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.37 |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.14 |
rpoB | 763005 | p.Cys1067Val | missense_variant | 0.15 |
rpoC | 763028 | c.-342T>C | upstream_gene_variant | 0.11 |
rpoC | 763053 | c.-317T>C | upstream_gene_variant | 0.12 |
rpoC | 763070 | c.-300T>C | upstream_gene_variant | 0.1 |
rpoC | 763615 | c.246G>C | synonymous_variant | 0.16 |
rpoC | 763620 | p.Arg84Gln | missense_variant | 0.12 |
rpoC | 763622 | p.Ala85Ser | missense_variant | 0.16 |
rpoC | 763630 | c.261G>T | synonymous_variant | 0.12 |
rpoC | 763633 | c.264T>C | synonymous_variant | 0.12 |
rpoC | 763642 | c.273G>C | synonymous_variant | 0.17 |
rpoC | 763660 | c.291T>G | synonymous_variant | 0.13 |
rpoC | 763663 | c.294C>T | synonymous_variant | 0.13 |
rpoC | 763666 | c.297G>C | synonymous_variant | 0.14 |
rpoC | 763669 | c.300C>G | synonymous_variant | 0.15 |
rpoC | 763672 | c.303C>A | synonymous_variant | 0.14 |
rpoC | 763696 | c.327T>C | synonymous_variant | 0.14 |
rpoC | 763699 | c.330G>T | synonymous_variant | 0.14 |
rpoC | 763702 | c.333C>T | synonymous_variant | 0.12 |
rpoC | 763705 | c.336G>C | synonymous_variant | 0.12 |
rpoC | 763708 | c.339G>C | synonymous_variant | 0.13 |
rpoC | 763714 | c.345G>T | synonymous_variant | 0.12 |
rpoC | 763717 | c.348T>C | synonymous_variant | 0.15 |
rpoC | 763720 | c.351G>T | synonymous_variant | 0.12 |
rpoC | 763729 | c.360G>T | synonymous_variant | 0.12 |
rpoC | 763732 | c.363C>T | synonymous_variant | 0.14 |
rpoC | 764918 | p.Val517Leu | missense_variant | 0.5 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.51 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471923 | n.78T>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1471925 | n.80_81insGCAGCTTG | non_coding_transcript_exon_variant | 1.0 |
rrs | 1471928 | n.83T>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1471930 | n.88_89delGA | non_coding_transcript_exon_variant | 1.0 |
rrs | 1471934 | n.89A>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1471978 | n.133C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472549 | n.704G>A | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472558 | n.713G>A | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472569 | n.724G>A | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472573 | n.728C>T | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472574 | n.729T>A | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472581 | n.736A>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472584 | n.739A>T | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472647 | n.802C>T | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472655 | n.810G>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472660 | n.815T>C | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472973 | n.1128A>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.88 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.88 |
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.89 |
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.91 |
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.91 |
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473102 | n.1257C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473115 | n.1270G>T | non_coding_transcript_exon_variant | 0.82 |
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473132 | n.1287T>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473135 | n.1290C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.75 |
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.94 |
rrs | 1473270 | n.1425G>A | non_coding_transcript_exon_variant | 0.67 |
rrs | 1473276 | n.1431A>G | non_coding_transcript_exon_variant | 0.76 |
rrs | 1473292 | n.1447G>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473293 | n.1448G>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473301 | n.1456T>C | non_coding_transcript_exon_variant | 0.77 |
rrs | 1473305 | n.1460G>T | non_coding_transcript_exon_variant | 0.76 |
rrs | 1473316 | n.1471C>T | non_coding_transcript_exon_variant | 0.76 |
rrl | 1475775 | n.2118G>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475869 | n.2212C>A | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.86 |
rrl | 1475883 | n.2226A>T | non_coding_transcript_exon_variant | 0.86 |
rrl | 1475884 | n.2227A>G | non_coding_transcript_exon_variant | 0.57 |
rrl | 1475897 | n.2240T>C | non_coding_transcript_exon_variant | 0.57 |
rrl | 1475898 | n.2241A>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475899 | n.2242G>A | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475900 | n.2243A>G | non_coding_transcript_exon_variant | 0.57 |
rrl | 1475902 | n.2245T>C | non_coding_transcript_exon_variant | 0.57 |
rrl | 1475906 | n.2249C>T | non_coding_transcript_exon_variant | 0.57 |
rrl | 1475916 | n.2259C>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475975 | n.2318C>T | non_coding_transcript_exon_variant | 0.8 |
rrl | 1475977 | n.2320A>G | non_coding_transcript_exon_variant | 0.8 |
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.8 |
rrl | 1475997 | n.2340A>T | non_coding_transcript_exon_variant | 0.8 |
rrl | 1476160 | n.2503T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476164 | n.2507A>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476214 | n.2557G>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476215 | n.2558C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476245 | n.2588C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476250 | n.2593C>G | non_coding_transcript_exon_variant | 0.71 |
rrl | 1476252 | n.2595T>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476253 | n.2596A>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476256 | n.2599A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476257 | n.2600G>C | non_coding_transcript_exon_variant | 0.71 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476262 | n.2605G>A | non_coding_transcript_exon_variant | 0.73 |
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476298 | n.2641C>A | non_coding_transcript_exon_variant | 0.87 |
rrl | 1476299 | n.2642C>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476300 | n.2643G>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476301 | n.2644A>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476307 | n.2650A>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476308 | n.2651G>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476309 | n.2652G>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476337 | n.2680C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476535 | n.2878G>A | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476539 | n.2882A>G | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476573 | n.2916A>T | non_coding_transcript_exon_variant | 1.0 |
rpsA | 1833469 | c.-73G>T | upstream_gene_variant | 0.45 |
rpsA | 1834249 | c.708T>C | synonymous_variant | 0.1 |
rpsA | 1834261 | c.720A>G | synonymous_variant | 0.12 |
rpsA | 1834306 | c.765T>C | synonymous_variant | 0.11 |
rpsA | 1834312 | c.771G>A | synonymous_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289200 | c.42C>T | synonymous_variant | 0.51 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.54 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.51 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.54 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.48 |
fbiA | 3641119 | p.Ser193Pro | missense_variant | 0.47 |
alr | 3840719 | c.702A>G | synonymous_variant | 0.33 |
rpoA | 3878641 | c.-135delG | upstream_gene_variant | 0.15 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.47 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4249732 | c.3219C>G | synonymous_variant | 0.42 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407970 | p.Pro78Leu | missense_variant | 0.4 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.3 |