TB-Profiler result

Run: ERR4813822
Summary

Run ID: ERR4813822

Sample name:

Date: 2024-10-03T15:35:28.577471

Number of reads: 2950269

Percentage reads mapped: 99.63

Median coverage: 89.0

Strain: lineage4.1.2.1;lineage4.3.4

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
lineage4.3 Euro-American (LAM) None 0.07
lineage4.1 Euro-American None 0.91
lineage4.1.2 Euro-American None 0.88
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.89
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.12
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 c.1338_1339dupCC Assoc w R High-level resistance
c.1327_1328delCC Assoc w R High-level resistance
ahpC c.-54C>T Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94His Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94His Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
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
gyrA 7581 p.Asp94His missense_variant 0.82 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.9 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2154772 c.1338_1339dupCC frameshift_variant 0.78 isoniazid Assoc w R High-level resistance
katG 2154783 c.1327_1328delCC frameshift_variant 0.91 isoniazid Assoc w R High-level resistance
ahpC 2726139 c.-54C>T upstream_gene_variant 0.31 isoniazid Uncertain significance Mutation from literature
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 5076 c.-164_-163insTC upstream_gene_variant 0.9 levofloxacin
moxifloxacin
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
fgd1 491591 p.Lys270Met missense_variant 0.86 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.93 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.91 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.92 rifampicin Not assoc w R
rpoC 764521 c.1152T>C synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.11 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.9 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781276 c.-284A>C upstream_gene_variant 0.9 streptomycin
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 kanamycin
capreomycin
streptomycin
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.92 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.14 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.22 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087630 p.Gln271Glu missense_variant 0.23 cycloserine
ald 3087648 c.830_831dupGC frameshift_variant 0.6 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.14 pyrazinamide Not assoc w R
Rv3236c 3612847 c.270G>A synonymous_variant 0.91 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.12 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.86 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.93 ethambutol Not assoc w R
embA 4243225 c.-8C>A upstream_gene_variant 0.87 ethambutol Uncertain significance
embB 4248880 c.2367G>T synonymous_variant 0.9 ethambutol Not assoc w R - Interim
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 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.12 streptomycin Not assoc w R