Run ID: SRR13837915
Sample name:
Date: 2024-04-14T13:00:45.869316
Number of reads: 1485856
Percentage reads mapped: 97.1
Median coverage: 51.0
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 | 1110 | c.1110T>G | synonymous_variant | 1.0 | isoniazid | |
| gyrB | 5760 | p.Trp174Leu | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrB | 6662 | p.Phe475Val | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | Uncertain significance | |||||
| rpoB | 760087 | p.Ser94Phe | missense_variant | 1.0 | rifampicin | |
| rpoC | 766854 | p.Leu1162Gln | missense_variant | 0.93 | rifampicin | |
| mmpL5 | 778416 | p.Pro22Leu | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rplC | 801126 | c.318C>T | synonymous_variant | 1.0 | linezolid | |
| Rv1129c | 1254196 | c.338delT | frameshift_variant | 1.0 | moxifloxacin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| sigE | 1364560 | p.His50Asn | missense_variant | 1.0 | pyrazinamide | |
| rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1473943 | n.286G>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1473945 | n.288T>A | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1473946 | n.289A>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1473986 | n.329T>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1473987 | n.330G>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1473995 | n.338G>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Not assoc w R |
| linezolid | Not assoc w R | |||||
| rrl | 1474009 | n.352A>G | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1474012 | n.355C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1475354 | n.1697A>T | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
| linezolid | Uncertain significance | |||||
| inhA | 1674867 | p.Trp222Cys | missense_variant | 0.95 | ethionamide | |
| isoniazid | ||||||
| katG | 2154601 | p.Gly504Val | missense_variant | 1.0 | isoniazid | |
| Rv1979c | 2222910 | c.255A>G | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| pepQ | 2859714 | c.705C>A | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| Rv2752c | 3066476 | c.-285C>T | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| ald | 3087172 | p.Glu118Ala | missense_variant | 1.0 | cycloserine | |
| ald | 3087905 | c.1086G>A | synonymous_variant | 1.0 | cycloserine | |
| Rv3236c | 3613280 | c.-164G>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv3236c | 3613355 | c.-239C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| lpqB | 3623494 | p.Ala473Pro | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| lpqB | 3624600 | p.Val104Gly | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| lpqB | 3624838 | p.Pro25Ser | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| alr | 3841499 | c.-79C>T | upstream_gene_variant | 1.0 | cycloserine | |
| rpoA | 3878156 | p.Val118Met | missense_variant | 0.98 | rifampicin | |
| clpC1 | 4039113 | p.Ala531Asp | missense_variant | 1.0 | pyrazinamide | |
| glpK | 4139244 | p.Ala171Gly | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embC | 4242095 | p.Ala745Pro | missense_variant | 1.0 | ethambutol | |
| embB | 4247621 | c.1108C>T | synonymous_variant | 1.0 | ethambutol | |
| ubiA | 4269585 | c.249G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| ubiA | 4269776 | p.Ala20Pro | missense_variant | 1.0 | ethambutol | |
| ethA | 4328211 | c.-739delG | upstream_gene_variant | 1.0 | ethionamide |
