Run ID: SRR13861198
Sample name:
Date: 2024-04-15T14:54:12.129536
Number of reads: 2261635
Percentage reads mapped: 56.6
Median coverage: 77.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 442 | p.Pro148Ala | missense_variant | 1.0 | isoniazid | |
| gyrB | 6667 | p.Gln476His | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7289 | c.-13_-12insT | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| rpoB | 760214 | p.Asn136Lys | missense_variant | 1.0 | rifampicin | |
| Rv1129c | 1253228 | p.Asp436Ala | missense_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv1129c | 1253885 | p.Lys217Arg | missense_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| fbiC | 1304005 | p.Pro359Ser | missense_variant | 1.0 | clofazimine | Uncertain significance |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| sigE | 1364782 | p.Val124Leu | missense_variant | 1.0 | pyrazinamide | |
| embR | 1417793 | c.-446C>T | upstream_gene_variant | 1.0 | ethambutol | |
| rrs | 1471943 | n.98T>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472075 | n.230A>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1473066 | n.1221A>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1473370 | n.1525T>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.21 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.28 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.28 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.32 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.32 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.35 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.35 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.35 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.35 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.35 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.36 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.35 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.33 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.32 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| fabG1 | 1673813 | p.Arg125Leu | missense_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| inhA | 1674784 | p.Arg195Gly | missense_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| bacA | 2064693 | p.Trp12Cys | missense_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| ndh | 2101793 | p.Trp417* | stop_gained | 1.0 | ethionamide | Uncertain significance |
| delamanid | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| PPE35 | 2169624 | p.Gly330Asp | missense_variant | 1.0 | pyrazinamide | |
| kasA | 2519223 | p.Thr370Ile | missense_variant | 0.99 | isoniazid | |
| ahpC | 2726213 | c.21C>T | synonymous_variant | 0.99 | isoniazid | |
| Rv2477c | 2783213 | p.Ala277Val | missense_variant | 1.0 | ethambutol | Uncertain significance |
| moxifloxacin | ||||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| Rv2477c | 2783662 | p.Glu127Asp | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | ||||||
| levofloxacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| Rv2477c | 2784275 | c.-234dupC | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| ribD | 2987016 | p.Gly60Arg | missense_variant | 0.99 | para-aminosalicylic_acid | |
| Rv2680 | 2996618 | p.Trp172Arg | missense_variant | 1.0 | capreomycin | |
| Rv2681 | 2997515 | c.777T>G | synonymous_variant | 1.0 | capreomycin | |
| Rv2681 | 2997779 | c.1041C>G | synonymous_variant | 1.0 | capreomycin | |
| Rv2752c | 3065644 | p.Thr183Ser | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv2752c | 3066590 | c.-399A>G | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| thyA | 3074595 | c.-124C>A | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| lpqB | 3624763 | p.Val50Leu | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| lpqB | 3625054 | c.-144C>G | upstream_gene_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| alr | 3841581 | c.-161T>A | upstream_gene_variant | 1.0 | cycloserine | |
| embC | 4242810 | p.Leu983Gln | missense_variant | 1.0 | ethambutol | |
| embB | 4246553 | p.Arg14Trp | missense_variant | 1.0 | ethambutol | |
| embB | 4248920 | p.Val803Met | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4249551 | p.Arg1013Leu | missense_variant | 1.0 | ethambutol | |
| ethA | 4326296 | p.Leu393Gln | missense_variant | 1.0 | ethionamide | |
| gid | 4408480 | c.-278G>C | upstream_gene_variant | 1.0 | streptomycin |
