Run ID: SRR13837926
Sample name:
Date: 2024-04-15T05:25:06.918008
Number of reads: 1469452
Percentage reads mapped: 95.02
Median coverage: 49.0
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 | rrs | n.277G>C | Mutation from literature | |
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 |
---|---|---|---|---|---|---|---|
rrs | 1472122 | n.277G>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5319 | p.Arg27Leu | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
mshA | 575032 | c.-316A>G | upstream_gene_variant | 0.98 | ethionamide | |
isoniazid | ||||||
rpoB | 760867 | p.Gly354Asp | missense_variant | 1.0 | rifampicin | |
rpoB | 762496 | c.2691delC | frameshift_variant | 1.0 | rifampicin | |
rpoC | 764793 | p.Met475Arg | missense_variant | 1.0 | rifampicin | |
rpoC | 766563 | p.Thr1065Ser | missense_variant | 1.0 | rifampicin | |
mmpL5 | 775976 | c.2505G>C | synonymous_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 776814 | p.Gln556Arg | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
rplC | 800623 | c.-186A>C | upstream_gene_variant | 1.0 | linezolid | |
rplC | 800769 | c.-40A>T | upstream_gene_variant | 1.0 | linezolid | |
Rv1129c | 1253289 | c.1246C>T | synonymous_variant | 1.0 | moxifloxacin | |
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
fbiC | 1302878 | c.-53C>G | upstream_gene_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fbiC | 1303535 | p.Ser202Leu | missense_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
Rv1258c | 1407569 | c.-229C>A | upstream_gene_variant | 0.98 | streptomycin | |
isoniazid | ||||||
pyrazinamide | ||||||
atpE | 1461256 | p.Met71Arg | missense_variant | 1.0 | bedaquiline | |
rrs | 1471638 | n.-208T>C | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1471836 | n.-10A>G | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
bacA | 2063043 | c.1686T>A | synonymous_variant | 0.98 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
katG | 2156157 | c.-46C>A | upstream_gene_variant | 1.0 | isoniazid | |
PPE35 | 2168627 | p.Ile662Met | missense_variant | 1.0 | pyrazinamide | |
Rv1979c | 2222100 | c.1065T>A | synonymous_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
pncA | 2289242 | c.-1T>C | upstream_gene_variant | 1.0 | pyrazinamide | |
Rv2477c | 2783664 | c.378delA | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
ribD | 2987205 | p.Ser123Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
ribD | 2987347 | p.Pro170Leu | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv2680 | 2995859 | c.-246C>A | upstream_gene_variant | 1.0 | capreomycin | |
Rv2681 | 2997492 | p.Val252Phe | missense_variant | 1.0 | capreomycin | |
Rv3083 | 3448903 | p.Asp134His | missense_variant | 1.0 | ethionamide | |
lpqB | 3624372 | p.Val180Ala | missense_variant | 1.0 | bedaquiline | |
rifampicin | Uncertain significance | |||||
mtrA | 3627051 | p.Asp100Val | missense_variant | 1.0 | bedaquiline | |
rifampicin | ||||||
clpC1 | 4039663 | p.Gly348Ser | missense_variant | 1.0 | pyrazinamide | |
embC | 4241256 | p.Arg465Thr | missense_variant | 1.0 | ethambutol | Uncertain significance |
embA | 4246449 | p.Val1073Phe | missense_variant | 1.0 | ethambutol | |
aftB | 4268192 | c.645G>C | synonymous_variant | 1.0 | ethambutol |