TB-Profiler result

Run: ERR4822359
Summary

Run ID: ERR4822359

Sample name:

Date: 2024-04-16T00:06:37.032807

Number of reads: 2955815

Percentage reads mapped: 99.76

Median coverage: 94.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Pre-XDR-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
lineage4.9 Euro-American (H37Rv-like) None 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.Asp435Val Assoc w R
isoniazid katG p.Ser315Arg Assoc w R High-level resistance
ahpC c.-57C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
p.Asp354Ala Assoc w R
pyrazinamide pncA c.414_*1278del Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Ser91Pro Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>T Assoc w R - Interim
capreomycin rrs n.1402C>T Assoc w R
kanamycin rrs n.1402C>T Assoc w R - Interim
cycloserine
ethionamide ethA c.479delC 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
gyrA 7570 p.Ala90Val missense_variant 1.0 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
gyrA 7572 p.Ser91Pro missense_variant 1.0 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin Assoc w R
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 1.0 amikacin Assoc w R - Interim
kanamycin Assoc w R - Interim
capreomycin Assoc w R
katG 2155169 p.Ser315Arg missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2287402 c.414_*1278del frameshift_variant&stop_lost&splice_region_variant 1.0 pyrazinamide Assoc w R
ahpC 2726136 c.-57C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol Assoc w R
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol Assoc w R
ethA 4326994 c.479delC frameshift_variant 1.0 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
gyrB 6677 p.Pro480Ser missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 760574 c.768G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
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
Rv1129c 1254520 c.8_14dupGGAGTAA frameshift_variant&stop_gained 1.0 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
rrs 1471861 n.16T>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin 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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223724 c.-560C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
thyX 3067959 c.-14C>G upstream_gene_variant 1.0 para-aminosalicylic_acid
thyA 3074159 c.312delA frameshift_variant 1.0 para-aminosalicylic_acid
fbiA 3640354 c.-189C>G upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
glpK 4139183 c.572dupG frameshift_variant 0.15 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4240394 p.Glu178Lys missense_variant 1.0 ethambutol 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
gid 4408105 c.80_97delCGGGACCCGGTGTGGAGC disruptive_inframe_deletion 1.0 streptomycin