Run ID: SRR7645924
Sample name:
Date: 04-04-2023 19:58:46
Number of reads: 1588561
Percentage reads mapped: 94.65
Strain: lineage4.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.2 | Euro-American | H;T;LAM | None | 1.0 |
lineage4.2.1 | Euro-American (TUR) | H3;H4 | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7510 | p.His70Arg | missense_variant | 0.55 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761089 | p.Ser428Thr | missense_variant | 0.1 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.94 | rifampicin |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.97 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.72 | kanamycin, capreomycin, aminoglycosides, amikacin |
rrs | 1473247 | n.1402C>A | non_coding_transcript_exon_variant | 0.19 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 1.0 | kanamycin |
ald | 3086947 | c.130dupG | frameshift_variant | 0.36 | cycloserine |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 1.0 | ethambutol |
embB | 4247402 | p.Ser297Ala | missense_variant | 0.88 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7581 | p.Asp94Ser | missense_variant | 0.5 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491247 | c.465C>T | synonymous_variant | 0.97 |
ccsA | 619969 | p.Val27Ile | missense_variant | 1.0 |
rpoC | 763621 | c.252C>T | synonymous_variant | 0.12 |
rpoC | 763633 | c.264T>C | synonymous_variant | 0.12 |
rpoC | 763636 | c.267T>C | synonymous_variant | 0.12 |
rpoC | 763642 | c.273G>C | synonymous_variant | 0.12 |
rpoC | 763648 | c.279C>G | synonymous_variant | 0.13 |
rpoC | 763652 | p.Ile95Leu | missense_variant | 0.12 |
rpoC | 763660 | c.291T>C | synonymous_variant | 0.12 |
rpoC | 763666 | c.297G>T | synonymous_variant | 0.13 |
rpoC | 763669 | c.300C>G | synonymous_variant | 0.12 |
rpoC | 763672 | c.303C>G | synonymous_variant | 0.12 |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.93 |
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 | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472558 | n.713G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472569 | n.724G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472584 | n.739A>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472607 | n.762G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472790 | n.945T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472952 | n.1107T>C | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472955 | n.1110C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472973 | n.1128A>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.1 |
rrs | 1473164 | n.1319C>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473276 | n.1431A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474218 | n.561T>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474228 | n.571T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474830 | n.1173A>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474831 | n.1174A>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474864 | n.1207C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474904 | n.1247G>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1474905 | n.1248T>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1474932 | n.1275C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475699 | n.2042C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1475722 | n.2065G>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475753 | n.2096C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475869 | n.2212C>A | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1475883 | n.2226A>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475884 | n.2227A>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475898 | n.2241A>G | non_coding_transcript_exon_variant | 0.24 |
rrl | 1475899 | n.2242G>A | non_coding_transcript_exon_variant | 0.24 |
rrl | 1475916 | n.2259C>G | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475952 | n.2295A>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475963 | n.2306G>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475970 | n.2313C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475975 | n.2318C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475977 | n.2320A>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475978 | n.2321C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475997 | n.2340A>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476001 | n.2344T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476164 | n.2507A>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476165 | n.2508T>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476337 | n.2680C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476429 | n.2772A>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.16 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612316 | c.801T>A | synonymous_variant | 0.11 |
rpoA | 3878569 | c.-62C>T | upstream_gene_variant | 0.2 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4249594 | c.3081G>A | synonymous_variant | 1.0 |
ethA | 4326632 | p.His281Pro | missense_variant | 1.0 |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |