Run ID: ERR1213874
Sample name:
Date: 2024-04-15T15:52:26.379022
Number of reads: 7628449
Percentage reads mapped: 99.06
Median coverage: 127.0
Strain: lineage2.2.1
Spoligotype:
Drug-resistance: MDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage2 | East-Asian | RD105 | 0.99 |
| lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 1.0 |
| lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
| isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| ethambutol | embB | p.Met306Val | Assoc w R | |
| pyrazinamide | pncA | c.-224_*330del | Assoc w R | |
| 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 |
|---|---|---|---|---|---|---|---|
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin | Assoc w R | |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| pncA | 2288350 | c.-224_*330del | transcript_ablation | 0.99 | pyrazinamide | Assoc w R | |
| embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R |
| 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 | |||||
| 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 | |||||
| Rv0010c | 13152 | p.Ala136Val | missense_variant | 1.0 | isoniazid | Uncertain significance |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| mshA | 575907 | p.Ala187Val | missense_variant | 1.0 | ethionamide | Not assoc w R |
| isoniazid | Not assoc w R | |||||
| ccsA | 620625 | p.Ile245Met | missense_variant | 0.98 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Uncertain significance | |||||
| Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.99 | ethionamide | Not assoc w R - Interim |
| Rv0565c | 657142 | p.Arg110His | missense_variant | 1.0 | ethionamide | Uncertain significance |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 0.98 | rifampicin | Not assoc w R |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.99 | streptomycin | Not assoc w R |
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
| isoniazid | Uncertain significance | |||||
| pyrazinamide | Uncertain significance | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1473632 | n.-26G>A | upstream_gene_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1473752 | n.95G>T | non_coding_transcript_exon_variant | 0.25 | capreomycin | |
| linezolid | ||||||
| rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1473815 | n.158T>C | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1473836 | n.179A>G | non_coding_transcript_exon_variant | 0.28 | capreomycin | |
| linezolid | Uncertain significance | |||||
| rrl | 1473876 | n.219G>A | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1473877 | n.220G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1473943 | n.286G>T | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1473944 | n.287G>T | non_coding_transcript_exon_variant | 0.25 | capreomycin | |
| linezolid | ||||||
| rrl | 1473995 | n.338G>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
| linezolid | ||||||
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Not assoc w R |
| linezolid | Not assoc w R | |||||
| rrl | 1474028 | n.371T>C | non_coding_transcript_exon_variant | 0.18 | capreomycin | |
| linezolid | ||||||
| rrl | 1474029 | n.372G>A | non_coding_transcript_exon_variant | 0.19 | capreomycin | |
| linezolid | ||||||
| rrl | 1474034 | n.377G>A | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
| linezolid | ||||||
| rrl | 1474040 | n.383G>A | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
| linezolid | ||||||
| rrl | 1474083 | n.426C>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1474111 | n.454T>C | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
| linezolid | ||||||
| rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474181 | n.524C>A | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
| linezolid | ||||||
| rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475202 | n.1545G>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475276 | n.1619T>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1475289 | n.1632G>A | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
| linezolid | ||||||
| rrl | 1475291 | n.1634A>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475297 | n.1640C>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
| linezolid | ||||||
| rrl | 1475315 | n.1658A>C | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
| linezolid | ||||||
| rrl | 1475446 | n.1789G>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
| linezolid | ||||||
| rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.98 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| katG | 2154724 | p.Arg463Leu | missense_variant | 0.99 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.99 | pyrazinamide | 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 | |||||
| Rv2752c | 3066632 | c.-441C>G | upstream_gene_variant | 0.99 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 0.99 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| mtrB | 3626562 | p.Pro18Ser | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| embC | 4240423 | c.561G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243460 | c.228C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4245966 | p.Phe912Leu | missense_variant | 1.0 | ethambutol | Uncertain significance |
| aftB | 4267647 | p.Asp397Gly | missense_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 | ||||||
| whiB6 | 4338957 | c.-436C>A | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
| gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 | streptomycin | Not assoc w R |
