TB-Profiler result

Run: SRR1173861
Summary

Run ID: SRR1173861

Sample name:

Date: 2024-04-15T00:29:57.676570

Number of reads: 3923791

Percentage reads mapped: 99.41

Median coverage: 80.0

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 0.45
lineage4.1.1.3 Euro-American (X-type) RD193 0.42
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.59
lineage4.1.1 Euro-American (X-type) None 0.4
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>G Uncertain significance Mutation from literature
pyrazinamide pncA p.Arg154Gly Assoc w R
p.Ser59Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.878G>A Assoc w R - Interim
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine ald c.464delG Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.1192_1194dupGTG Mutation from literature
c.869dupA 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 0.59 streptomycin Assoc w R
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.37 streptomycin Assoc w R - Interim
inhA 1673425 c.-777C>T upstream_gene_variant 0.38 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288782 p.Arg154Gly missense_variant 0.44 pyrazinamide Assoc w R
pncA 2289067 p.Ser59Pro missense_variant 0.62 pyrazinamide Assoc w R
ald 3087278 c.464delG frameshift_variant 0.49 cycloserine Mutation from literature
embA 4243217 c.-16C>G upstream_gene_variant 0.38 ethambutol Uncertain significance Mutation from literature
ethA 4326279 c.1192_1194dupGTG conservative_inframe_insertion 0.32 ethionamide Mutation from literature
ethA 4326604 c.869dupA frameshift_variant 0.3 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 0.52 isoniazid Not assoc w R
gyrB 6815 p.Lys526Gln missense_variant 0.58 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.4 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.36 ethionamide Uncertain significance
rpoB 762285 p.Arg827Cys missense_variant 0.47 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.54 rifampicin Not assoc w R
rpoC 766485 p.Val1039Ala missense_variant 0.54 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
rpsL 781435 c.-125G>C upstream_gene_variant 0.39 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.36 linezolid
Rv1129c 1253535 p.Phe334Leu missense_variant 0.62 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.6 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.46 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 0.54 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2783181 p.Leu288Val missense_variant 0.61 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.28 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.4 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840764 c.657G>C synonymous_variant 0.6 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.4 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGA frameshift_variant&missense_variant 0.7 ethambutol
embB 4249408 c.2895G>A synonymous_variant 0.36 ethambutol Not assoc w R
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 0.41 capreomycin
amikacin
kanamycin
gid 4407798 c.405G>T synonymous_variant 0.28 streptomycin Not assoc w R