Run ID: SRR18511647
Sample name:
Date: 2024-10-03T22:41:37.813081
Number of reads: 4219790
Percentage reads mapped: 53.5
Median coverage: 130.0
Strain: lineage2.2.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage2 | East-Asian | RD105 | 1.0 |
| 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 | ||||
| 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 | 5034 | c.-206G>T | upstream_gene_variant | 0.97 | 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 | |||||
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | Not assoc w R - Interim | |||||
| clofazimine | Not assoc w R | |||||
| mshA | 575907 | p.Ala187Val | missense_variant | 1.0 | isoniazid | Not assoc w R |
| ethionamide | Not assoc w R | |||||
| ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| Rv0565c | 657142 | p.Arg110His | missense_variant | 1.0 | ethionamide | Uncertain significance |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 764371 | c.1002G>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
| rpoC | 764383 | c.1014C>G | synonymous_variant | 0.17 | rifampicin | |
| rpoC | 764387 | c.1018T>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoC | 764398 | c.1029G>C | synonymous_variant | 0.17 | rifampicin | |
| rpoC | 764405 | c.1036_1038delAGGinsCGC | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
| rpoC | 764428 | c.1059G>C | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
| rpoC | 764431 | c.1062G>C | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
| rpoC | 764434 | c.1065A>G | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
| rpoC | 764435 | c.1066_1068delAGGinsCGC | synonymous_variant | 0.18 | rifampicin | |
| rpoC | 764446 | p.Asp359Glu | missense_variant | 0.19 | rifampicin | |
| rpoC | 764450 | p.Gly361Arg | missense_variant | 0.18 | rifampicin | |
| rpoC | 764461 | p.Glu364Asp | missense_variant | 0.19 | rifampicin | |
| rpoC | 764470 | c.1101C>G | synonymous_variant | 0.17 | rifampicin | |
| rpoC | 764471 | p.Asn368Arg | missense_variant | 0.17 | rifampicin | |
| rpoC | 764479 | c.1110G>A | synonymous_variant | 0.16 | rifampicin | |
| rpoC | 764485 | c.1116G>C | synonymous_variant | 0.18 | rifampicin | |
| rpoC | 764498 | p.Ser377Ala | missense_variant | 0.15 | rifampicin | |
| rpoC | 764503 | c.1134G>T | synonymous_variant | 0.14 | rifampicin | |
| rpoC | 764521 | c.1152T>C | synonymous_variant | 0.1 | rifampicin | Not assoc w R - Interim |
| rpoC | 764605 | c.1236G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
| rpoC | 764611 | c.1242G>C | synonymous_variant | 0.14 | rifampicin | |
| rpoC | 764623 | c.1254C>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
| rpoC | 764632 | c.1263T>C | synonymous_variant | 0.1 | rifampicin | Not assoc w R - Interim |
| rpoC | 764641 | c.1272C>T | synonymous_variant | 0.11 | rifampicin | Not assoc w R - Interim |
| rpoC | 764650 | c.1281G>T | synonymous_variant | 0.1 | rifampicin | Not assoc w R - Interim |
| rpoC | 764664 | p.Val432Ala | missense_variant | 0.1 | rifampicin | |
| rpoC | 764668 | c.1299C>G | synonymous_variant | 0.1 | rifampicin | |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 | bedaquiline | Not assoc w R |
| clofazimine | Not assoc w R | |||||
| mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
| pyrazinamide | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1476336 | n.2679C>G | non_coding_transcript_exon_variant | 0.28 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>G | non_coding_transcript_exon_variant | 0.36 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>A | non_coding_transcript_exon_variant | 0.36 | capreomycin | |
| linezolid | ||||||
| rrl | 1476359 | n.2702C>T | non_coding_transcript_exon_variant | 0.38 | capreomycin | |
| linezolid | ||||||
| rrl | 1476368 | n.2711T>C | non_coding_transcript_exon_variant | 0.41 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.41 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>A | non_coding_transcript_exon_variant | 0.44 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>C | non_coding_transcript_exon_variant | 0.44 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.46 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.46 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.46 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.45 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.41 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.4 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.39 | 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 | 1476491 | n.2834T>C | non_coding_transcript_exon_variant | 0.27 | capreomycin | |
| linezolid | ||||||
| rrl | 1476501 | n.2844C>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.23 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rpsA | 1833820 | p.Lys93Asn | missense_variant | 0.97 | pyrazinamide | |
| 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 | 2153975 | p.Ala713Thr | missense_variant | 1.0 | isoniazid | |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | 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 | |||||
| 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 | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| mtrB | 3626562 | p.Pro18Ser | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| 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 |
| aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| 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 |
