Run ID: SRR15368784
Sample name:
Date: 2024-04-16T03:28:19.969392
Number of reads: 5621123
Percentage reads mapped: 49.59
Median coverage: 101.0
Strain: lineage2.2.1.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage2 | East-Asian | RD105 | 1.0 |
| lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.99 |
| lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
| lineage2.2.1.1 | East-Asian (Beijing) | RD105;RD207;RD181;RD150 | 0.99 |
| 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 | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7781 | c.480G>C | synonymous_variant | 0.9 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| 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 | 0.99 | ethionamide | Not assoc w R |
| isoniazid | Not assoc w R | |||||
| ccsA | 620625 | p.Ile245Met | missense_variant | 0.99 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Uncertain significance | |||||
| Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| Rv0565c | 657142 | p.Arg110His | missense_variant | 0.99 | ethionamide | Uncertain significance |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | 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 | |||||
| mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.97 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R | |||||
| mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1129c | 1254265 | p.Asp90Glu | missense_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| 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 | |||||
| embR | 1417777 | c.-430A>C | upstream_gene_variant | 1.0 | ethambutol | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472127 | n.282C>T | non_coding_transcript_exon_variant | 0.13 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472128 | n.283G>C | non_coding_transcript_exon_variant | 0.13 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472129 | n.284G>A | non_coding_transcript_exon_variant | 0.13 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472135 | n.290C>T | non_coding_transcript_exon_variant | 0.13 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.13 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.13 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 0.13 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472153 | n.308G>A | non_coding_transcript_exon_variant | 0.13 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.12 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrl | 1476336 | n.2679C>G | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>G | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>A | non_coding_transcript_exon_variant | 0.25 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476368 | n.2711T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.36 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476384 | n.2727G>C | non_coding_transcript_exon_variant | 0.34 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.38 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.37 | capreomycin | |
| linezolid | ||||||
| rrl | 1476428 | n.2771C>A | non_coding_transcript_exon_variant | 0.25 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>C | non_coding_transcript_exon_variant | 0.26 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>G | non_coding_transcript_exon_variant | 0.27 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.34 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.34 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.34 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.21 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| 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 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.98 | 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 | |||||
| kasA | 2518871 | p.His253Tyr | missense_variant | 0.97 | isoniazid | |
| eis | 2714846 | p.Val163Ile | missense_variant | 0.98 | amikacin | Not assoc w R |
| kanamycin | Not assoc w R | |||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.98 | pyrazinamide | Not assoc w R - Interim |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | 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 | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243460 | c.228C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
| embB | 4248115 | c.1602C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338471 | c.51G>A | synonymous_variant | 0.98 | capreomycin | Not assoc w R - Interim |
| amikacin | ||||||
| kanamycin | Not assoc w R - Interim | |||||
| 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 | ||||||
| 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 |
