Run ID: SRR19303813
Sample name:
Date: 2025-02-11T18:21:13.119255
Number of reads: 1991908
Percentage reads mapped: 28.93
Median coverage: 55.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.8 | Euro-American (mainly T) | RD219 | 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 |
|---|---|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13705 | c.-147G>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
| rpoB | 760975 | p.Met390Thr | missense_variant | 1.0 | rifampicin | Uncertain significance |
| rpoC | 764611 | c.1242G>C | synonymous_variant | 0.27 | rifampicin | |
| rpoC | 764632 | c.1263T>C | synonymous_variant | 0.23 | rifampicin | Not assoc w R - Interim |
| rpoC | 764644 | c.1275G>C | synonymous_variant | 0.24 | rifampicin | Not assoc w R - Interim |
| rpoC | 764650 | c.1281G>T | synonymous_variant | 0.25 | rifampicin | Not assoc w R - Interim |
| rpoC | 764656 | c.1287C>G | synonymous_variant | 0.25 | rifampicin | |
| rpoC | 764662 | c.1293G>C | synonymous_variant | 0.24 | rifampicin | Not assoc w R - Interim |
| rpoC | 764668 | c.1299C>T | synonymous_variant | 0.24 | rifampicin | Not assoc w R - Interim |
| rpoC | 764671 | c.1302G>C | synonymous_variant | 0.24 | rifampicin | |
| rpoC | 764672 | p.Gln435Glu | missense_variant | 0.24 | rifampicin | |
| rpoC | 764677 | c.1308C>G | synonymous_variant | 0.24 | rifampicin | Not assoc w R - Interim |
| rpoC | 764686 | c.1317C>T | synonymous_variant | 0.23 | rifampicin | |
| rpoC | 764695 | c.1326T>C | synonymous_variant | 0.25 | rifampicin | |
| rpoC | 764701 | c.1332C>G | synonymous_variant | 0.25 | rifampicin | Not assoc w R - Interim |
| rpoC | 764705 | p.Leu446Lys | missense_variant | 0.23 | rifampicin | |
| rpoC | 764716 | c.1347G>C | synonymous_variant | 0.2 | rifampicin | Not assoc w R - Interim |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1129c | 1254598 | c.-65dupA | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1476336 | n.2679C>G | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>G | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>A | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
| linezolid | ||||||
| rrl | 1476359 | n.2702C>T | non_coding_transcript_exon_variant | 0.56 | capreomycin | |
| linezolid | ||||||
| rrl | 1476381 | n.2724G>A | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>C | non_coding_transcript_exon_variant | 0.61 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.56 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.56 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>C | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>G | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.47 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.45 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.44 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.37 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.25 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 1.0 | capreomycin | |
| ald | 3086767 | c.-53A>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.97 | ethionamide | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244990 | c.1758G>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| aftB | 4267715 | c.1122G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R |
