Run ID: SRR28498635
Sample name:
Date: 2024-10-04T01:17:22.413647
Number of reads: 3380952
Percentage reads mapped: 99.59
Median coverage: 91.0
Strain: lineage4.3.4.1;lineage4.8
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.24 |
lineage4.3.4.1 | Euro-American (LAM) | RD174 | 0.21 |
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.78 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 0.23 |
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 |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.17 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.19 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13310 | c.249T>C | synonymous_variant | 0.77 | isoniazid | Not assoc w R - Interim |
fgd1 | 491424 | c.650_655delCCGCTG | disruptive_inframe_deletion | 0.72 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
mshA | 575915 | p.Asp190Asn | missense_variant | 0.82 | isoniazid | Uncertain significance |
ethionamide | Uncertain significance | |||||
rpoC | 763783 | c.414G>A | synonymous_variant | 0.28 | rifampicin | Not assoc w R - Interim |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.26 | rifampicin | Not assoc w R |
rpoC | 765325 | c.1956C>T | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 778965 | c.-485G>T | upstream_gene_variant | 0.8 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
sigE | 1364434 | p.Arg8Trp | missense_variant | 0.22 | pyrazinamide | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.78 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.18 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2168147 | p.Pro822Ser | missense_variant | 0.23 | pyrazinamide | Not assoc w R |
Rv1979c | 2223123 | c.42G>A | synonymous_variant | 0.22 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R - Interim | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
folC | 2746540 | c.1059G>A | synonymous_variant | 0.26 | para-aminosalicylic_acid | |
Rv2477c | 2784541 | c.-499G>A | upstream_gene_variant | 0.76 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.68 | capreomycin | |
Rv2681 | 2996821 | p.Gly28Ala | missense_variant | 0.25 | capreomycin | Uncertain significance |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.27 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.21 | cycloserine | |
Rv3083 | 3448322 | c.-182G>A | upstream_gene_variant | 0.77 | ethionamide | |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.28 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.17 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
alr | 3840710 | c.711A>G | synonymous_variant | 0.21 | cycloserine | |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.18 | pyrazinamide | Not assoc w R |
embC | 4240373 | c.511C>T | synonymous_variant | 0.84 | ethambutol | Not assoc w R - Interim |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4246904 | p.Val131Met | missense_variant | 0.79 | ethambutol | Uncertain significance |
whiB6 | 4338550 | c.-29A>T | upstream_gene_variant | 0.22 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 0.27 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
whiB6 | 4338735 | c.-214C>G | upstream_gene_variant | 0.27 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4408156 | p.Leu16Arg | missense_variant | 0.2 | streptomycin | Not assoc w R |