TB-Profiler result

Run: ERR11465520
Summary

Run ID: ERR11465520

Sample name:

Date: 2024-10-05T13:26:14.877309

Number of reads: 3646939

Percentage reads mapped: 99.62

Median coverage: 79.0

Strain: lineage4.3.3;lineage4.8

Spoligotype:

Drug-resistance: HR-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 0.09
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.87
lineage4.3.3 Euro-American (LAM) RD115 0.15
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
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)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
inhA 1673425 c.-777C>T upstream_gene_variant 0.13 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)
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 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.84 ethionamide Uncertain significance
nusG 734141 c.-113G>A upstream_gene_variant 0.92 rifampicin Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.81 rifampicin Not assoc w R
rpoB 760143 p.Val113Ile missense_variant 0.16 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.16 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 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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.89 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.12 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.87 pyrazinamide Not assoc w R
PPE35 2169149 c.1464G>C synonymous_variant 0.85 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.21 isoniazid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.84 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.15 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.14 cycloserine
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.88 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.83 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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 0.14 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.13 streptomycin Not assoc w R