Run ID: ERR13290918
Sample name:
Date: 2025-02-11T20:37:47.987531
Number of reads: 6153630
Percentage reads mapped: 99.77
Median coverage: 192.0
Strain: lineage4.5
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.5 | Euro-American | RD122 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Asn | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Ile | Assoc w R | |
p.Gly406Asp | Assoc w R | |||
pyrazinamide | pncA | p.Ser59Pro | Assoc w R | |
streptomycin | gid | c.43delC | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.1235_1241delACGGTTT | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | thyA | c.-3521_*1627del | Mutation from literature | |
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Asn | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289067 | p.Ser59Pro | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
thyA | 3072052 | c.-3521_*1627del | transcript_ablation | 1.0 | para-aminosalicylic_acid | Mutation from literature | |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R | |
embB | 4247730 | p.Gly406Asp | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4326232 | c.1235_1241delACGGTTT | frameshift_variant | 1.0 | ethionamide | Assoc w R | |
gid | 4408159 | c.43delC | frameshift_variant | 1.0 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1505 | p.Arg502His | missense_variant | 0.94 | isoniazid | Uncertain significance |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7892 | c.591G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9788 | p.Asp829Glu | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
ccsA | 620029 | c.139C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
Rv0565c | 656962 | p.Gln170Pro | missense_variant | 1.0 | ethionamide | |
rpoC | 764363 | p.Gly332Ser | missense_variant | 1.0 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
fbiC | 1303032 | c.102A>G | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
tlyA | 1918600 | p.His221Tyr | missense_variant | 1.0 | capreomycin | |
PPE35 | 2170568 | p.Ile15Met | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2221722 | c.1443C>T | synonymous_variant | 1.0 | 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 | |||||
Rv2752c | 3064708 | c.1483delC | frameshift_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
thyX | 3067949 | c.-4C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
whiB7 | 3568842 | c.-163C>A | upstream_gene_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
rpoA | 3879070 | c.-563G>A | upstream_gene_variant | 1.0 | rifampicin | |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
embC | 4241500 | c.1638A>G | synonymous_variant | 1.0 | ethambutol | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.29 | ethambutol | |
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 | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin |