Run ID: SRR13861596
Sample name:
Date: 2024-04-15T14:54:28.899983
Number of reads: 1428964
Percentage reads mapped: 28.61
Median coverage: 47.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 0.98 |
| lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | rrs | n.277G>C | Mutation from literature | |
| 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 |
|---|---|---|---|---|---|---|---|
| rrs | 1472122 | n.277G>C | non_coding_transcript_exon_variant | 0.86 | streptomycin | Mutation from literature |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5319 | p.Arg27Leu | missense_variant | 0.97 | levofloxacin | |
| moxifloxacin | ||||||
| mshA | 575032 | c.-316A>G | upstream_gene_variant | 0.98 | ethionamide | |
| isoniazid | ||||||
| rpoB | 760867 | p.Gly354Asp | missense_variant | 0.95 | rifampicin | |
| rpoB | 762496 | c.2691delC | frameshift_variant | 0.86 | rifampicin | |
| rpoC | 764434 | c.1065A>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoC | 764446 | c.1077T>C | synonymous_variant | 0.2 | rifampicin | |
| rpoC | 764793 | p.Met475Arg | missense_variant | 0.94 | rifampicin | |
| rpoC | 766483 | c.3114G>C | synonymous_variant | 0.18 | rifampicin | |
| rpoC | 766484 | c.3115_3117delGTAinsAC | frameshift_variant&missense_variant | 0.17 | rifampicin | |
| rpoC | 766492 | c.3123T>C | synonymous_variant | 0.18 | rifampicin | |
| rpoC | 766495 | c.3126C>T | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
| rpoC | 766563 | p.Thr1065Ser | missense_variant | 0.85 | rifampicin | |
| rpoC | 766933 | c.3564A>G | synonymous_variant | 0.14 | rifampicin | |
| rpoC | 766945 | c.3576A>G | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
| rpoC | 766963 | c.3594T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| rpoC | 766978 | c.3609C>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| rpoC | 766996 | c.3627C>T | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoC | 767009 | c.3640_3642delTCGinsAGC | synonymous_variant | 0.17 | rifampicin | |
| rpoC | 767014 | c.3645G>C | synonymous_variant | 0.17 | rifampicin | |
| rpoC | 767033 | c.3664_3666delTCGinsAGT | synonymous_variant | 0.17 | rifampicin | |
| rpoC | 767059 | c.3690T>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoC | 767062 | c.3693C>A | synonymous_variant | 0.19 | rifampicin | |
| rpoC | 767074 | c.3705T>C | synonymous_variant | 0.17 | rifampicin | |
| rpoC | 767098 | c.3729T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
| mmpL5 | 775976 | c.2505G>C | synonymous_variant | 0.95 | clofazimine | |
| bedaquiline | ||||||
| mmpL5 | 776814 | p.Gln556Arg | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rplC | 800623 | c.-186A>C | upstream_gene_variant | 0.91 | linezolid | |
| rplC | 800769 | c.-40A>T | upstream_gene_variant | 0.91 | linezolid | |
| Rv1129c | 1253289 | c.1246C>T | synonymous_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| fbiC | 1302878 | c.-53C>G | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1303535 | p.Ser202Leu | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| Rv1258c | 1407569 | c.-229C>A | upstream_gene_variant | 1.0 | streptomycin | |
| isoniazid | ||||||
| pyrazinamide | ||||||
| atpE | 1461256 | p.Met71Arg | missense_variant | 0.96 | bedaquiline | |
| rrs | 1471638 | n.-208T>C | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1471836 | n.-10A>G | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1473937 | n.280C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475333 | n.1676T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
| linezolid | ||||||
| rrl | 1475355 | n.1698C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475369 | n.1712G>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1475419 | n.1762C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.37 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.55 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.53 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.53 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.53 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.53 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.53 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.51 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.52 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.53 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.52 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.53 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.5 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| bacA | 2063043 | c.1686T>A | synonymous_variant | 0.98 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| katG | 2156157 | c.-46C>A | upstream_gene_variant | 1.0 | isoniazid | |
| PPE35 | 2168627 | p.Ile662Met | missense_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2222100 | c.1065T>A | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| pncA | 2289242 | c.-1T>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv2477c | 2783664 | c.378delA | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| Rv2477c | 2783794 | c.249G>A | synonymous_variant | 0.16 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783815 | c.228A>G | synonymous_variant | 0.16 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783833 | c.210G>C | synonymous_variant | 0.19 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783843 | p.Gly67Asp | missense_variant | 0.19 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783860 | p.Asp61Glu | missense_variant | 0.21 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783863 | c.180C>T | synonymous_variant | 0.17 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783883 | c.160T>C | synonymous_variant | 0.17 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783884 | c.159T>C | synonymous_variant | 0.17 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783887 | c.156C>G | synonymous_variant | 0.19 | ethambutol | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| streptomycin | Not assoc w R - Interim | |||||
| levofloxacin | Not assoc w R - Interim | |||||
| kanamycin | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R - Interim | |||||
| Rv2477c | 2783920 | c.123G>C | synonymous_variant | 0.2 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| ribD | 2987205 | p.Ser123Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ribD | 2987347 | p.Pro170Leu | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2680 | 2995859 | c.-246C>A | upstream_gene_variant | 1.0 | capreomycin | |
| Rv2681 | 2997492 | p.Val252Phe | missense_variant | 1.0 | capreomycin | |
| Rv3083 | 3448903 | p.Asp134His | missense_variant | 1.0 | ethionamide | |
| lpqB | 3624372 | p.Val180Ala | missense_variant | 0.95 | bedaquiline | |
| rifampicin | Uncertain significance | |||||
| mtrA | 3627051 | p.Asp100Val | missense_variant | 0.95 | bedaquiline | |
| rifampicin | ||||||
| rpoA | 3877656 | c.852T>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
| rpoA | 3877743 | c.765T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
| rpoA | 3877770 | c.738A>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| rpoA | 3877776 | c.732T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| rpoA | 3878376 | c.132G>C | synonymous_variant | 0.14 | rifampicin | |
| rpoA | 3878385 | c.123C>G | synonymous_variant | 0.14 | rifampicin | |
| rpoA | 3878391 | c.117T>C | synonymous_variant | 0.14 | rifampicin | |
| rpoA | 3878396 | c.112C>T | synonymous_variant | 0.14 | rifampicin | |
| clpC1 | 4039663 | p.Gly348Ser | missense_variant | 0.96 | pyrazinamide | |
| embC | 4241256 | p.Arg465Thr | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4246449 | p.Val1073Phe | missense_variant | 1.0 | ethambutol | |
| embB | 4248097 | c.1584C>G | synonymous_variant | 0.16 | ethambutol | |
| embB | 4248127 | c.1614G>C | synonymous_variant | 0.13 | ethambutol | |
| embB | 4248133 | c.1620C>G | synonymous_variant | 0.18 | ethambutol | |
| embB | 4248157 | c.1644A>G | synonymous_variant | 0.19 | ethambutol | Not assoc w R - Interim |
| aftB | 4268192 | c.645G>C | synonymous_variant | 1.0 | ethambutol |
