Run ID: SRR28393346
Sample name:
Date: 2024-10-05T05:26:12.957595
Number of reads: 8300263
Percentage reads mapped: 99.5
Median coverage: 245.0
Strain: lineage4.1.1.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 1.0 |
lineage4.1.1.1 | Euro-American (X-type) | RD183 | 0.98 |
lineage4 | Euro-American | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-770T>C | Assoc w R - Interim | Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Gly406Ala | Assoc w R | |
pyrazinamide | pncA | p.His71Pro | Assoc w R | |
streptomycin | gid | c.102delG | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-770T>C | Assoc w R - Interim | Alias fabG1_c.-8T>C |
clofazimine | ||||
para-aminosalicylic_acid | thyX | c.-16C>T | Mutation from literature | |
thyA | c.-3166_*2085del | Mutation from literature | ||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
inhA | 1673432 | c.-770T>C | upstream_gene_variant | 1.0 | ethionamide | Assoc w R - Interim | Alias fabG1_c.-8T>C |
isoniazid | Assoc w R - Interim | Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289030 | p.His71Pro | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 0.31 | para-aminosalicylic_acid | Mutation from literature | |
thyA | 3071594 | c.-3166_*2085del | transcript_ablation | 1.0 | para-aminosalicylic_acid | Mutation from literature | |
embB | 4247730 | p.Gly406Ala | missense_variant | 1.0 | ethambutol | Assoc w R | |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin | Assoc w R |
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 | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoC | 764822 | p.Asp485His | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
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 |
rplC | 800219 | c.-590T>C | upstream_gene_variant | 1.0 | linezolid | |
sigE | 1364205 | c.-208G>C | upstream_gene_variant | 1.0 | pyrazinamide | |
embR | 1416426 | p.Thr308Pro | missense_variant | 1.0 | ethambutol | Uncertain significance |
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 |
PPE35 | 2169996 | p.Ser206Asn | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
ahpC | 2726210 | c.18T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
thyX | 3067954 | c.-9G>A | upstream_gene_variant | 0.71 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3087713 | c.896_897dupCG | frameshift_variant | 0.66 | cycloserine | |
ald | 3087722 | c.905_906dupCC | frameshift_variant | 0.3 | cycloserine | |
fbiD | 3339550 | p.Gly145Arg | missense_variant | 1.0 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
fbiA | 3641447 | p.Thr302Met | missense_variant | 1.0 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Not assoc w R | |||||
rpoA | 3877553 | p.Glu319Lys | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoA | 3878601 | c.-95delG | upstream_gene_variant | 0.59 | rifampicin | Uncertain significance |
rpoA | 3878613 | c.-113_-107delCAACCCA | upstream_gene_variant | 0.37 | rifampicin | Uncertain significance |
panD | 4045235 | c.-954C>A | upstream_gene_variant | 1.0 | pyrazinamide | |
panD | 4045239 | c.-958C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
embC | 4240897 | c.1035C>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243218 | c.-15C>G | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326930 | p.Gly182Ser | missense_variant | 1.0 | ethionamide | 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 | 4338620 | c.-99G>T | upstream_gene_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin |