Run ID: SRR13861196
Sample name:
Date: 2024-04-16T03:25:01.909645
Number of reads: 824597
Percentage reads mapped: 20.64
Median coverage: 28.0
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 | 1425 | c.1426dupG | frameshift_variant | 1.0 | isoniazid | Uncertain significance |
| rpoB | 760728 | p.Tyr308Asn | missense_variant | 1.0 | rifampicin | |
| rpoC | 763928 | p.Glu187* | stop_gained | 1.0 | rifampicin | |
| rpoC | 766155 | p.Ala929Val | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 777185 | c.1296G>T | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| fbiC | 1302932 | p.Val1Gly | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1303151 | p.Gly74Asp | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1304895 | c.1965C>A | synonymous_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1305298 | p.Lys790Gln | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| Rv1258c | 1406311 | c.1030C>T | synonymous_variant | 0.96 | streptomycin | |
| isoniazid | ||||||
| pyrazinamide | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.52 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.61 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.61 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.61 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.61 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.66 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.66 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.65 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.65 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.65 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.66 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.65 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.66 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.68 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.67 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.68 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.64 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.64 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.64 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.64 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.31 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rpsA | 1834275 | p.Ile245Thr | missense_variant | 1.0 | pyrazinamide | |
| tlyA | 1917936 | c.-4C>A | upstream_gene_variant | 1.0 | capreomycin | |
| bacA | 2064894 | c.-166C>G | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| ndh | 2101676 | p.Ala456Val | missense_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| PPE35 | 2170823 | c.-212delT | upstream_gene_variant | 1.0 | pyrazinamide | |
| pncA | 2289356 | c.-115G>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| kasA | 2518234 | p.Glu40Asp | missense_variant | 1.0 | isoniazid | |
| Rv2752c | 3064837 | p.Leu452Trp | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv3083 | 3449643 | p.Asn380Lys | missense_variant | 1.0 | ethionamide | Uncertain significance |
| Rv3236c | 3611967 | p.Ser384Pro | missense_variant | 1.0 | pyrazinamide | |
| rpoA | 3877756 | p.Ile251Thr | missense_variant | 1.0 | rifampicin | |
| rpoA | 3878065 | p.Pro148Arg | missense_variant | 1.0 | rifampicin | |
| ddn | 3986977 | p.Pro45Arg | missense_variant | 1.0 | delamanid | |
| pretomanid | ||||||
| clpC1 | 4040538 | p.Leu56Arg | missense_variant | 1.0 | pyrazinamide | |
| glpK | 4138636 | p.Arg374Gly | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embA | 4245342 | p.Ser704Pro | missense_variant | 1.0 | ethambutol | |
| embB | 4248711 | c.2198_2199insT | frameshift_variant | 1.0 | ethambutol | |
| aftB | 4267498 | p.Glu447Lys | missense_variant | 1.0 | ethambutol | Uncertain significance |
| aftB | 4268559 | p.Leu93Gln | missense_variant | 1.0 | ethambutol | |
| whiB6 | 4338743 | c.-223_-222insC | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin |
