Run ID: ERR2653235
Sample name:
Date: 2024-04-15T09:04:27.042614
Number of reads: 10880041
Percentage reads mapped: 98.41
Median coverage: 306.0
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 | 0.97 |
lineage4 | Euro-American | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | None | 0.99 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Asp354Ala | Assoc w R | |
pyrazinamide | pncA | p.Lys96Gln | Assoc w R | |
streptomycin | rrs | n.907A>C | Uncertain significance | Mutation from literature |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ald | c.464delG | Mutation from literature | |
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
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 | |
rrs | 1472752 | n.907A>C | non_coding_transcript_exon_variant | 0.15 | streptomycin | Uncertain significance | Mutation from literature |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288956 | p.Lys96Gln | missense_variant | 0.99 | pyrazinamide | Assoc w R | |
ald | 3087278 | c.464delG | frameshift_variant | 0.56 | cycloserine | Mutation from literature | |
embB | 4247574 | p.Asp354Ala | missense_variant | 0.99 | ethambutol | 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 | 7581 | p.Asp94Thr | missense_variant | 0.12 | levofloxacin | |
moxifloxacin | ||||||
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 | 0.99 | ethionamide | Uncertain significance |
rpoB | 762027 | p.Leu741Phe | missense_variant | 0.99 | rifampicin | |
rpoB | 762310 | p.His835Pro | missense_variant | 0.99 | rifampicin | Uncertain significance |
rpoB | 763123 | p.Ile1106Thr | missense_variant | 0.99 | rifampicin | Uncertain significance |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765730 | c.2361G>A | synonymous_variant | 0.99 | rifampicin | |
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 |
rpsL | 781767 | p.Glu70Lys | missense_variant | 1.0 | streptomycin | |
rplC | 800219 | c.-590T>C | upstream_gene_variant | 1.0 | linezolid | |
rplC | 801115 | p.Ala103Thr | missense_variant | 0.99 | linezolid | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1471868 | n.23T>G | non_coding_transcript_exon_variant | 0.89 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
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 | 2167931 | c.2682C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ahpC | 2726210 | c.18T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
Rv2752c | 3065692 | p.His167Arg | missense_variant | 1.0 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3641447 | p.Thr302Met | missense_variant | 0.99 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
rpoA | 3877553 | p.Glu319Lys | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoA | 3878559 | c.-53_-52insC | upstream_gene_variant | 0.12 | rifampicin | |
rpoA | 3878601 | c.-95delG | upstream_gene_variant | 0.38 | rifampicin | Uncertain significance |
rpoA | 3878613 | c.-113_-107delCAACCCA | upstream_gene_variant | 0.24 | rifampicin | Uncertain significance |
clpC1 | 4040925 | c.-228_-222delCGCGTTC | 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 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4327331 | p.Phe48Ser | missense_variant | 0.99 | ethionamide | 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 |