Run ID: SRR13861221
Sample name:
Date: 2024-10-05T03:36:37.515453
Number of reads: 4203982
Percentage reads mapped: 70.13
Median coverage: 142.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.9 | Euro-American (H37Rv-like) | 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 |
|---|---|---|---|---|---|---|
| dnaA | 1209 | c.1209C>T | synonymous_variant | 0.14 | isoniazid | Not assoc w R - Interim |
| dnaA | 1230 | c.1230A>G | synonymous_variant | 0.15 | isoniazid | |
| dnaA | 1427 | p.Ala476Gly | missense_variant | 0.93 | isoniazid | |
| gyrA | 7346 | p.Ile15Met | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8335 | p.Met345Arg | missense_variant | 0.94 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9639 | p.Gly780Arg | missense_variant | 0.95 | levofloxacin | |
| moxifloxacin | ||||||
| fgd1 | 491505 | c.723G>A | synonymous_variant | 0.96 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| mshA | 576310 | p.Ile321Met | missense_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| Rv0565c | 657451 | p.Ala7Val | missense_variant | 1.0 | ethionamide | |
| mmpL5 | 775981 | p.Leu834Val | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| mmpL5 | 776732 | c.1749C>T | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| mmpL5 | 777942 | p.Pro180Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| rplC | 800343 | c.-466G>C | upstream_gene_variant | 1.0 | linezolid | |
| rplC | 800618 | c.-191T>C | upstream_gene_variant | 0.15 | linezolid | |
| fbiC | 1303422 | c.492A>G | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv1258c | 1406592 | p.Tyr250Cys | missense_variant | 0.99 | streptomycin | |
| pyrazinamide | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| embR | 1416737 | p.Arg204Gln | missense_variant | 1.0 | ethambutol | |
| rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472970 | n.1125C>G | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | ||||||
| amikacin | Uncertain significance | |||||
| rrs | 1472977 | n.1132G>C | non_coding_transcript_exon_variant | 0.16 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | ||||||
| amikacin | Uncertain significance | |||||
| rrs | 1472978 | n.1133T>C | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475277 | n.1620G>C | non_coding_transcript_exon_variant | 0.92 | capreomycin | |
| linezolid | ||||||
| rrl | 1475638 | n.1981C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
| linezolid | ||||||
| rrl | 1475659 | n.2002G>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
| linezolid | ||||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rpsA | 1834091 | p.Val184Met | missense_variant | 0.93 | pyrazinamide | |
| tlyA | 1918473 | c.534T>A | synonymous_variant | 0.98 | capreomycin | |
| Rv1979c | 2221849 | p.Leu439Gln | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2222231 | p.Met312Leu | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2222710 | p.Asn152Ile | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223809 | c.-646_-645insT | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| eis | 2714723 | p.Cys204Gly | missense_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| folC | 2746975 | p.Asp208Glu | missense_variant | 0.97 | para-aminosalicylic_acid | |
| Rv2477c | 2782420 | c.1623T>A | synonymous_variant | 1.0 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783068 | p.Asp325Glu | missense_variant | 0.13 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783203 | c.840C>T | synonymous_variant | 0.15 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783221 | c.822G>T | synonymous_variant | 0.15 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783224 | c.819C>G | synonymous_variant | 0.15 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783719 | c.324A>G | synonymous_variant | 0.14 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783815 | c.228A>G | synonymous_variant | 0.15 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783833 | c.210G>C | synonymous_variant | 0.15 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783843 | p.Gly67Asp | missense_variant | 0.15 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783860 | p.Asp61Glu | missense_variant | 0.15 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783863 | c.180C>T | synonymous_variant | 0.14 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783883 | c.160T>C | synonymous_variant | 0.16 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783884 | c.159T>C | synonymous_variant | 0.16 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783887 | c.156C>G | synonymous_variant | 0.17 | kanamycin | Not assoc w R - Interim |
| levofloxacin | Not assoc w R - Interim | |||||
| moxifloxacin | Not assoc w R - Interim | |||||
| streptomycin | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R - Interim | |||||
| ethambutol | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R - Interim | |||||
| Rv2477c | 2783920 | c.123G>C | synonymous_variant | 0.17 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2783953 | c.90G>A | synonymous_variant | 0.13 | kanamycin | Not assoc w R - Interim |
| levofloxacin | Not assoc w R - Interim | |||||
| moxifloxacin | Not assoc w R - Interim | |||||
| streptomycin | ||||||
| rifampicin | Not assoc w R - Interim | |||||
| ethambutol | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R - Interim | |||||
| Rv2477c | 2784310 | c.-268T>A | upstream_gene_variant | 0.98 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| pepQ | 2860233 | c.186T>G | synonymous_variant | 0.99 | bedaquiline | |
| clofazimine | ||||||
| thyA | 3073781 | p.Leu231Ile | missense_variant | 0.99 | para-aminosalicylic_acid | |
| Rv3083 | 3448420 | c.-84_-83insT | upstream_gene_variant | 1.0 | ethionamide | |
| whiB7 | 3568689 | c.-11delT | upstream_gene_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| mtrB | 3625750 | c.864G>A | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| bedaquiline | ||||||
| mtrB | 3625755 | p.Ala287Thr | missense_variant | 0.15 | rifampicin | Uncertain significance |
| bedaquiline | ||||||
| mtrB | 3625762 | c.852A>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| bedaquiline | ||||||
| mtrB | 3625765 | c.849C>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| bedaquiline | ||||||
| mtrB | 3625797 | p.Val273Met | missense_variant | 0.14 | rifampicin | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| mtrB | 3625806 | c.808A>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| bedaquiline | ||||||
| clpC1 | 4038748 | p.Arg653Cys | missense_variant | 0.12 | pyrazinamide | |
| clpC1 | 4039103 | c.1602T>C | synonymous_variant | 0.14 | pyrazinamide | |
| clpC1 | 4039106 | c.1599G>C | synonymous_variant | 0.15 | pyrazinamide | |
| clpC1 | 4039112 | c.1593C>G | synonymous_variant | 0.14 | pyrazinamide | |
| clpC1 | 4039898 | c.807C>G | synonymous_variant | 0.15 | pyrazinamide | |
| clpC1 | 4039904 | c.801A>G | synonymous_variant | 0.15 | pyrazinamide | |
| clpC1 | 4039928 | c.775_777delAGCinsTCG | synonymous_variant | 0.16 | pyrazinamide | |
| clpC1 | 4039931 | c.774T>C | synonymous_variant | 0.17 | pyrazinamide | |
| clpC1 | 4039946 | c.759A>T | synonymous_variant | 0.19 | pyrazinamide | |
| clpC1 | 4039952 | c.753T>C | synonymous_variant | 0.18 | pyrazinamide | |
| clpC1 | 4039958 | c.747G>C | synonymous_variant | 0.18 | pyrazinamide | |
| clpC1 | 4039979 | c.726C>G | synonymous_variant | 0.16 | pyrazinamide | |
| clpC1 | 4039996 | p.Glu237Gln | missense_variant | 0.14 | pyrazinamide | |
| clpC1 | 4040021 | c.684A>C | synonymous_variant | 0.14 | pyrazinamide | Not assoc w R - Interim |
| embC | 4240494 | p.Gly211Ala | missense_variant | 0.98 | ethambutol | Uncertain significance |
| embC | 4241732 | p.Ala624Pro | missense_variant | 0.95 | ethambutol | |
| embA | 4245672 | p.Gly814Arg | missense_variant | 0.94 | ethambutol | |
| embB | 4247458 | p.Tyr315* | stop_gained | 0.93 | ethambutol | |
| aftB | 4268265 | p.Leu191Gln | missense_variant | 1.0 | ethambutol |
