TB-Profiler result

Run: ERR3287689

Summary

Run ID: ERR3287689

Sample name:

Date: 2024-03-25T20:37:15.664158

Number of reads: 3846514

Percentage reads mapped: 99.61

Median coverage: 119.0

Strain: lineage4.1.1;lineage4.1.2.1

Spoligotype:

Drug-resistance: HR-TB


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 0.53
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.53
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.49
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.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. 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
pyrazinamide
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)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
thyA p.His207Arg Mutation from literature
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 0.51 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
inhA 1673432 c.-770T>C upstream_gene_variant 0.46 isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
katG 2155168 p.Ser315Thr missense_variant 0.57 isoniazid Assoc w R High-level resistance
thyX 3067961 c.-16C>T upstream_gene_variant 0.53 para-aminosalicylic_acid Mutation from literature
thyA 3073852 p.His207Arg missense_variant 0.53 para-aminosalicylic_acid 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 6052 p.Ile271Met missense_variant 0.51 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7055 p.Gly606Ser missense_variant 0.5 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7221 p.Ser661Thr missense_variant 0.5 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 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 0.58 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.5 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.46 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.51 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.44 linezolid
embR 1416699 p.Leu217Val missense_variant 0.41 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.57 isoniazid
Rv2752c 3066898 c.-707C>T upstream_gene_variant 0.49 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3074588 c.-117A>G upstream_gene_variant 0.47 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612846 p.Pro91Ser missense_variant 0.55 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627511 c.-162C>G upstream_gene_variant 0.43 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.55 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 1.0 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.5 ethambutol Not assoc w R
ethA 4326116 p.Thr453Ile missense_variant 0.43 ethionamide 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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407916 p.Arg96Leu missense_variant 0.51 streptomycin Uncertain significance
gid 4408009 p.Val65Asp missense_variant 0.47 streptomycin