Run ID: SRR28393746
Sample name:
Date: 2024-05-22T11:17:29.532214
Number of reads: 4278897
Percentage reads mapped: 99.43
Median coverage: 98.0
Strain: lineage4.1.1.3
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 1.0 |
lineage4.1.1.3 | Euro-American (X-type) | RD193 | 1.0 |
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.Ser450Trp | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | pncA | p.Pro54Leu | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1401A>G | Assoc w R | |
capreomycin | rrs | n.1401A>G | Assoc w R | |
kanamycin | rrs | n.1401A>G | Assoc w R | |
cycloserine | ||||
ethionamide | ethA | p.Trp391* | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | thyX | c.-16C>T | Mutation from literature | |
thyA | c.-2233_*5248del | Mutation from literature | ||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Trp | missense_variant | 1.0 | rifampicin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Assoc w R | |
amikacin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289081 | p.Pro54Leu | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | Mutation from literature | |
thyA | 3068431 | c.-2233_*5248del | transcript_ablation | 0.98 | para-aminosalicylic_acid | Mutation from literature | |
ethA | 4326302 | p.Trp391* | stop_gained | 0.99 | ethionamide | 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 | 0.99 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.99 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
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 | |
fbiC | 1302954 | c.24G>A | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
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 |
katG | 2154678 | c.1434G>C | synonymous_variant | 0.99 | isoniazid | Not assoc w R - Interim |
PPE35 | 2169405 | p.Asn403Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2288839 | p.Thr135Ala | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
ahpC | 2726409 | p.Asp73His | missense_variant | 1.0 | isoniazid | Uncertain significance |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3087788 | c.970dupC | frameshift_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | 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 | 4243217 | c.-16C>A | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance |
embA | 4244833 | p.Val534Gly | missense_variant | 1.0 | ethambutol | Uncertain significance |
embA | 4244835 | p.Leu535Val | missense_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249678 | c.3165C>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
whiB6 | 4336763 | c.86_*1407del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4408144 | p.Arg20Pro | missense_variant | 1.0 | streptomycin | Uncertain significance |