Run ID: SRR13861425
Sample name:
Date: 2024-10-05T10:19:30.534835
Number of reads: 797148
Percentage reads mapped: 19.95
Median coverage: 26.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
| 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 | fbiC | c.1301delC | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| fbiC | 1304229 | c.1301delC | frameshift_variant | 1.0 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 8880 | p.Lys527Gln | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| mmaA3 | 737817 | c.333A>G | synonymous_variant | 1.0 | isoniazid | |
| rpoB | 760972 | p.Arg389Leu | missense_variant | 0.95 | rifampicin | |
| rpoC | 765111 | p.Met581Lys | missense_variant | 1.0 | rifampicin | |
| rpoC | 765161 | p.Glu598Lys | missense_variant | 1.0 | rifampicin | |
| rpoC | 765540 | p.Ala724Val | missense_variant | 1.0 | rifampicin | |
| rpoC | 767068 | c.3699G>T | synonymous_variant | 1.0 | rifampicin | |
| mmpR5 | 778439 | c.-551C>A | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rplC | 801357 | p.His183Gln | missense_variant | 1.0 | linezolid | |
| rrs | 1472288 | n.444delT | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.27 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.27 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.26 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.26 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.29 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.26 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.27 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472973 | n.1128_1130delAATinsCG | non_coding_transcript_exon_variant | 0.27 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.29 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.28 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.26 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.25 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.25 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.24 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.25 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.22 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.24 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.54 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.66 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.67 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.68 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.72 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.71 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.74 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.76 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.76 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.74 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.73 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.72 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.71 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.35 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| tsnR | 1853872 | c.267G>T | synonymous_variant | 1.0 | linezolid | |
| tlyA | 1917989 | p.Ala17Gly | missense_variant | 1.0 | capreomycin | |
| bacA | 2063805 | c.924G>A | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| bacA | 2064585 | c.144C>A | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| ndh | 2102525 | p.Phe173Tyr | missense_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| ndh | 2102538 | c.504_505insT | frameshift_variant | 0.96 | isoniazid | Uncertain significance |
| delamanid | Uncertain significance | |||||
| ethionamide | Uncertain significance | |||||
| Rv1979c | 2222978 | p.Ile63Phe | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223052 | p.Glu38Val | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| pncA | 2289415 | c.-174C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| kasA | 2518057 | c.-58A>C | upstream_gene_variant | 1.0 | isoniazid | |
| kasA | 2518799 | p.Pro229Ser | missense_variant | 1.0 | isoniazid | |
| eis | 2714983 | p.Ala117Glu | missense_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| Rv2477c | 2784409 | c.-367T>A | upstream_gene_variant | 1.0 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2784611 | c.-569A>T | upstream_gene_variant | 1.0 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| fbiA | 3640404 | c.-139C>A | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiB | 3642056 | c.522C>G | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rpoA | 3877967 | p.Thr181Ser | missense_variant | 1.0 | rifampicin | Uncertain significance |
| rpoA | 3877972 | c.535delG | frameshift_variant | 1.0 | rifampicin | |
| clpC1 | 4039777 | c.927_928insG | frameshift_variant | 1.0 | pyrazinamide | |
| glpK | 4138934 | c.822A>C | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| embB | 4247545 | p.Ser344Arg | missense_variant | 1.0 | ethambutol | Uncertain significance |
| aftB | 4268812 | p.Ser9Pro | missense_variant | 1.0 | ethambutol |
