Run ID: SRR13837521
Sample name:
Date: 2024-10-03T20:34:29.886695
Number of reads: 595077
Percentage reads mapped: 97.22
Median coverage: 20.0
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 | ddn | c.4_5insA | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
ddn | 3986847 | c.4_5insA | 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 |
---|---|---|---|---|---|---|
fgd1 | 490804 | p.Tyr8Asn | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
fgd1 | 490893 | c.111C>T | synonymous_variant | 0.93 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
mshA | 575498 | p.Ala51Pro | missense_variant | 1.0 | isoniazid | |
ethionamide | ||||||
Rv0565c | 656747 | p.Val242Ile | missense_variant | 1.0 | ethionamide | |
Rv0565c | 656828 | p.Tyr215His | missense_variant | 1.0 | ethionamide | |
rpoC | 763663 | c.294C>A | synonymous_variant | 1.0 | rifampicin | |
rpoC | 763955 | p.Lys196Gln | missense_variant | 0.97 | rifampicin | |
rpoC | 765682 | p.Asn771Lys | missense_variant | 0.94 | rifampicin | |
rpoC | 766342 | c.2973C>A | synonymous_variant | 1.0 | rifampicin | |
rpsL | 781579 | p.Leu7Arg | missense_variant | 1.0 | streptomycin | |
Rv1129c | 1254119 | p.Ser139Phe | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
embR | 1416509 | p.Arg280Pro | missense_variant | 1.0 | ethambutol | |
rrl | 1474164 | n.507C>A | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
inhA | 1674315 | c.114C>G | synonymous_variant | 1.0 | isoniazid | |
ethionamide | ||||||
katG | 2154959 | c.1153C>A | synonymous_variant | 1.0 | isoniazid | |
PPE35 | 2170236 | c.376_377insG | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
pncA | 2290061 | c.-820C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
folC | 2747798 | c.-200A>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
pepQ | 2860252 | p.Thr56Ser | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv2680 | 2996652 | p.Val183Ala | missense_variant | 1.0 | capreomycin | |
Rv2752c | 3065651 | p.Arg181Gly | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
Rv3083 | 3448855 | p.Val118Ile | missense_variant | 1.0 | ethionamide | |
whiB7 | 3569074 | c.-395A>G | upstream_gene_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
mtrB | 3626557 | p.Met19Ile | missense_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
mtrB | 3626629 | c.-17_-16insT | upstream_gene_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
rpoA | 3877765 | p.Ala248Gly | missense_variant | 1.0 | rifampicin | |
panD | 4044948 | c.-667A>G | upstream_gene_variant | 1.0 | pyrazinamide | |
embB | 4247059 | c.546C>G | synonymous_variant | 1.0 | ethambutol | |
embB | 4247144 | p.Ser211Pro | missense_variant | 1.0 | ethambutol | |
ubiA | 4269553 | p.Ala94Gly | missense_variant | 1.0 | ethambutol | |
gid | 4408259 | c.-57G>C | upstream_gene_variant | 1.0 | streptomycin |