TB-Profiler result

Run: SRR10315576
Summary

Run ID: SRR10315576

Sample name:

Date: 2025-02-11T19:47:03.272429

Number of reads: 5739013

Percentage reads mapped: 99.07

Median coverage: 169.0

Strain: lineage4.1.1.3;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
lineage4.1 Euro-American None 0.23
lineage4.1.1.3 Euro-American (X-type) RD193 0.25
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.76
lineage4.1.1 Euro-American (X-type) None 0.23
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 embB p.Met306Val Assoc w R
pyrazinamide pncA p.Ser59Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1307delC Assoc w R
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 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.81 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.77 isoniazid Assoc w R High-level resistance
pncA 2289067 p.Ser59Pro missense_variant 0.81 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.75 ethambutol Assoc w R
ethA 4326166 c.1307delC frameshift_variant 0.79 ethionamide 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 0.82 isoniazid Not assoc w R
gyrB 6815 p.Lys526Gln missense_variant 0.78 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7234 c.1995C>T synonymous_variant 0.26 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.38 isoniazid
ethionamide
Rv0565c 657269 p.Ser68Pro missense_variant 0.19 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.23 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_variant 0.19 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
rplC 800219 c.-590T>C upstream_gene_variant 0.23 linezolid
Rv1129c 1253535 p.Phe334Leu missense_variant 0.72 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 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.21 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154769 p.Asp448Ala missense_variant 0.75 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2783181 p.Leu288Val missense_variant 0.79 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.25 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.21 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3641807 c.273C>G synonymous_variant 0.31 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
alr 3840764 c.657G>C synonymous_variant 0.79 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.31 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.17 ethambutol Not assoc w R
ethR 4327691 p.Asp48Gly missense_variant 0.27 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
whiB6 4338732 c.-211C>T upstream_gene_variant 0.27 kanamycin
capreomycin
amikacin