Run ID: SRR28393947
Sample name:
Date: 2024-05-22T08:23:16.225136
Number of reads: 13263650
Percentage reads mapped: 99.66
Median coverage: 415.0
Strain: lineage4
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Tyr337Phe | Mutation from literature | |
p.Tyr337Cys | Uncertain significance | Mutation from literature | ||
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | c.417dupG | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
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 | |
eis | c.-8C>A | Uncertain significance | Mutation from literature | |
cycloserine | ||||
ethionamide | ethA | c.754_755dupGC | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.82 | moxifloxacin | Assoc w R | High-level resistance |
levofloxacin | Assoc w R | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.17 | amikacin | Assoc w R | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
katG | 2155102 | p.Tyr337Phe | missense_variant | 0.35 | isoniazid | Mutation from literature | |
katG | 2155102 | p.Tyr337Cys | missense_variant | 0.65 | isoniazid | Uncertain significance | Mutation from literature |
pncA | 2288824 | c.417dupG | frameshift_variant | 1.0 | pyrazinamide | Assoc w R | |
eis | 2715340 | c.-8C>A | upstream_gene_variant | 0.85 | kanamycin | Uncertain significance | Mutation from literature |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4326718 | c.754_755dupGC | frameshift_variant | 0.14 | 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 | |||||
rpoB | 761889 | p.Val695Leu | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 | rifampicin | Uncertain significance |
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 | 801009 | c.201A>G | synonymous_variant | 1.0 | linezolid | 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 |
PPE35 | 2168776 | p.Pro613Thr | missense_variant | 0.83 | pyrazinamide | Uncertain significance |
Rv1979c | 2223214 | c.-50A>C | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2752c | 3065517 | c.675C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
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 | |||||
thyX | 3068021 | c.-76C>A | upstream_gene_variant | 0.83 | para-aminosalicylic_acid | |
Rv3083 | 3448439 | c.-64delA | upstream_gene_variant | 1.0 | ethionamide | |
rpoA | 3877947 | c.561C>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoA | 3878595 | c.-88C>T | upstream_gene_variant | 0.27 | rifampicin | |
rpoA | 3878635 | c.-128C>T | upstream_gene_variant | 0.23 | rifampicin | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269308 | p.Phe176Leu | missense_variant | 0.15 | ethambutol | Uncertain significance |
ethA | 4326800 | p.Leu225Pro | missense_variant | 0.87 | ethionamide | Uncertain significance |
ethA | 4328317 | c.-844C>T | upstream_gene_variant | 1.0 | ethionamide | |
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 |