TB-Profiler result

Run: SRR28393262
Summary

Run ID: SRR28393262

Sample name:

Date: 2024-10-04T17:18:56.052671

Number of reads: 5101392

Percentage reads mapped: 99.72

Median coverage: 132.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Gly Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid katG c.597dupC Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Lys48Thr Assoc w R - Interim
streptomycin gid c.258_259delCC Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761139 p.His445Gly missense_variant 1.0 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
katG 2155514 c.597dupC frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289099 p.Lys48Thr missense_variant 0.99 pyrazinamide Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 0.99 ethambutol Assoc w R
gid 4407943 c.258_259delCC frameshift_variant 0.98 streptomycin Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
dnaA 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8257 p.Lys319Thr missense_variant 0.93 levofloxacin
moxifloxacin Uncertain significance
gyrA 9692 c.2391G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13636 c.-78A>C upstream_gene_variant 0.99 isoniazid Uncertain significance
rpoB 761905 p.Pro700Leu missense_variant 0.99 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 0.98 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
Rv1129c 1254056 p.Asp160Ala missense_variant 0.99 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.9 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1833972 p.Leu144Pro missense_variant 1.0 pyrazinamide Uncertain significance
rpsA 1834815 p.His425Arg missense_variant 0.98 pyrazinamide Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726141 c.-52C>A upstream_gene_variant 0.98 isoniazid Uncertain significance
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
alr 3840764 c.657G>C synonymous_variant 0.99 cycloserine
glpK 4139183 c.572dupG frameshift_variant 0.97 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240973 p.Val371Ile missense_variant 1.0 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247552 p.Ser347Val missense_variant 1.0 ethambutol Uncertain significance
ethA 4326756 p.Trp240Arg missense_variant 0.99 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