Run ID: ERR11466242
Sample name:
Date: 2024-04-15T01:22:04.901747
Number of reads: 4641164
Percentage reads mapped: 98.56
Median coverage: 129.0
Strain: lineage4.1.1.3
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.1 | Euro-American | None | 1.0 |
| lineage4.1.1.3 | Euro-American (X-type) | RD193 | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.1.1 | Euro-American (X-type) | 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 | 4982 | c.-258C>G | upstream_gene_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9323 | c.2022C>G | synonymous_variant | 0.12 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| mshA | 575566 | c.219G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| isoniazid | Not assoc w R - Interim | |||||
| Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.97 | ethionamide | Uncertain significance |
| rpoC | 765150 | p.Gly594Glu | missense_variant | 0.99 | rifampicin | Not assoc w R |
| rpoC | 766408 | c.3039C>G | synonymous_variant | 0.11 | rifampicin | |
| rpoC | 766411 | c.3042C>G | synonymous_variant | 0.11 | rifampicin | |
| rpoC | 766447 | c.3078T>C | synonymous_variant | 0.12 | rifampicin | |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rplC | 800219 | c.-590T>C | upstream_gene_variant | 0.98 | linezolid | |
| rplC | 800654 | c.-155T>C | upstream_gene_variant | 0.12 | linezolid | |
| rplC | 800703 | c.-106T>C | upstream_gene_variant | 0.13 | linezolid | |
| rplC | 800715 | c.-94A>C | upstream_gene_variant | 0.12 | linezolid | |
| rplC | 800720 | c.-89T>C | upstream_gene_variant | 0.12 | linezolid | |
| rplC | 800723 | c.-86C>G | upstream_gene_variant | 0.13 | linezolid | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.13 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474181 | n.524C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1474376 | n.719T>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
| linezolid | ||||||
| rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474823 | n.1166C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
| linezolid | ||||||
| rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475088 | n.1431A>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
| linezolid | ||||||
| rrl | 1475483 | n.1826C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475573 | n.1916G>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475599 | n.1942A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
| linezolid | Uncertain significance | |||||
| rrl | 1475761 | n.2104_2106delCGCinsGT | non_coding_transcript_exon_variant | 0.31 | capreomycin | |
| linezolid | ||||||
| rrl | 1475765 | n.2111delG | non_coding_transcript_exon_variant | 0.35 | capreomycin | |
| linezolid | ||||||
| rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.36 | capreomycin | |
| linezolid | ||||||
| rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.13 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476594 | n.2937C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476597 | n.2940G>A | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476603 | n.2946G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476608 | n.2951C>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| eis | 2715620 | c.-288C>T | upstream_gene_variant | 1.0 | amikacin | |
| kanamycin | ||||||
| Rv2477c | 2783914 | c.129T>C | synonymous_variant | 0.17 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783920 | c.123G>C | synonymous_variant | 0.17 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2783929 | c.114C>G | synonymous_variant | 0.16 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| fbiB | 3641298 | c.-237G>A | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
| embC | 4242803 | p.Val981Leu | missense_variant | 0.99 | ethambutol | Not assoc w R |
| embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin |
