Run ID: SRR13837808
Sample name:
Date: 2024-10-05T02:16:47.174166
Number of reads: 2938817
Percentage reads mapped: 96.02
Median coverage: 98.0
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 |
|---|---|---|---|---|---|---|
| gyrB | 5540 | p.Thr101Ser | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| nusG | 734249 | c.-5A>G | upstream_gene_variant | 0.99 | rifampicin | |
| nusG | 734917 | p.Phe222Leu | missense_variant | 1.0 | rifampicin | |
| mmaA3 | 737354 | p.Glu266Gln | missense_variant | 1.0 | isoniazid | |
| mmaA3 | 738216 | c.-68_-67insA | upstream_gene_variant | 1.0 | isoniazid | |
| rpoB | 760558 | c.753delC | frameshift_variant | 1.0 | rifampicin | |
| rpoB | 760611 | p.Leu269Val | missense_variant | 1.0 | rifampicin | |
| rpoB | 762490 | p.Val895Gly | missense_variant | 0.99 | rifampicin | |
| rpoC | 765707 | c.2340delA | frameshift_variant | 1.0 | rifampicin | |
| Rv1129c | 1253076 | c.1459T>G | stop_lost&splice_region_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.18 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| tsnR | 1854059 | p.Leu152Val | missense_variant | 1.0 | linezolid | |
| ndh | 2101690 | p.Glu451Asp | missense_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| PPE35 | 2168961 | p.Gly551Val | missense_variant | 1.0 | pyrazinamide | |
| PPE35 | 2170927 | c.-315A>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2222084 | p.Leu361Ile | missense_variant | 0.99 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2222431 | p.Met245Arg | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223625 | c.-461C>A | upstream_gene_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| ald | 3087020 | c.201C>T | synonymous_variant | 1.0 | cycloserine | |
| mtrB | 3625191 | p.Val475Leu | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3625358 | p.Asn419Thr | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3625682 | p.Leu311Gln | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| alr | 3841157 | c.264A>G | synonymous_variant | 1.0 | cycloserine | |
| rpoA | 3878047 | p.Ala154Asp | missense_variant | 1.0 | rifampicin | |
| embB | 4247452 | c.939C>T | synonymous_variant | 1.0 | ethambutol | |
| ethR | 4326799 | c.-750G>A | upstream_gene_variant | 1.0 | ethionamide |
