TB-Profiler result

Run: SRR18002879
Summary

Run ID: SRR18002879

Sample name:

Date: 2024-04-16T01:05:49.715640

Number of reads: 4124895

Percentage reads mapped: 88.89

Median coverage: 111.0

Strain: lineage4.4.2

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.94
lineage4.4 Euro-American None 0.92
lineage4.4.2 Euro-American None 0.92
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
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 embA c.-16C>T Uncertain significance Mutation from literature
embB p.Gln497Arg Assoc w R
pyrazinamide pncA p.Thr168Pro Assoc w R - Interim
streptomycin
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 761155 p.Ser450Leu missense_variant 0.97 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R High-level resistance
pncA 2288740 p.Thr168Pro missense_variant 0.93 pyrazinamide Assoc w R - Interim
embA 4243217 c.-16C>T upstream_gene_variant 0.87 ethambutol Uncertain significance Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 0.96 ethambutol 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
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
mshA 575254 c.-94C>T upstream_gene_variant 0.93 ethionamide
isoniazid
rpoB 763031 c.3225T>C synonymous_variant 0.16 rifampicin Not assoc w R
rpoC 764724 p.Phe452Cys missense_variant 0.95 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
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 2155854 c.258C>A synonymous_variant 0.92 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3066099 p.Met31Ile missense_variant 0.91 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.86 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626395 c.219G>A synonymous_variant 0.97 bedaquiline
rifampicin
embC 4238963 c.-900C>T upstream_gene_variant 0.94 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.95 ethambutol Not assoc w R
embB 4246548 p.Pro12Gln missense_variant 0.18 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.17 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.2 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.25 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.21 ethambutol Not assoc w R - Interim
embB 4247249 p.Gly246Arg missense_variant 0.95 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.12 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.92 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.95 ethambutol Not assoc w R
ethA 4327058 p.Gly139Val 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 0.98 capreomycin
amikacin
kanamycin
whiB6 4338793 c.-272C>A upstream_gene_variant 0.94 capreomycin
amikacin
kanamycin
gid 4407712 p.Gly164Ala missense_variant 0.94 streptomycin