TB-Profiler result

Run: ERR1034680
Summary

Run ID: ERR1034680

Sample name:

Date: 2024-04-14T15:59:59.649901

Number of reads: 5642518

Percentage reads mapped: 99.58

Median coverage: 95.0

Strain: lineage4.1.2.1;lineage4.3.4.1

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 0.87
lineage4.1 Euro-American None 0.12
lineage4.1.2 Euro-American None 0.11
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.13
lineage4.3.4.1 Euro-American (LAM) RD174 0.89
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.88
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
p.Ser450Leu Assoc w R
rpoC p.Gly332Arg Uncertain significance Mutation from literature
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
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.18 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761110 p.Asp435Val missense_variant 0.84 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.17 rifampicin Assoc w R
rpoC 764363 p.Gly332Arg missense_variant 0.26 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.11 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155167 p.Ser315Thr missense_variant 0.87 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 0.16 pyrazinamide Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.87 streptomycin 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
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 7587 c.286C>T synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.16 ethionamide Not assoc w R
isoniazid Not assoc w R
hadA 732111 p.Cys61Ser missense_variant 0.12 isoniazid Uncertain significance
rpoC 764863 c.1494G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.85 rifampicin Not assoc w R
rpoC 766628 p.Arg1087Gly missense_variant 0.13 rifampicin
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
sigE 1364434 p.Arg8Trp missense_variant 0.86 pyrazinamide Not assoc w R
sigE 1364940 c.528C>A synonymous_variant 0.97 pyrazinamide
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 0.15 isoniazid
ahpC 2726323 p.Pro44Arg missense_variant 0.86 isoniazid Uncertain significance
Rv2477c 2784613 c.-571T>C upstream_gene_variant 0.69 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ribD 2986729 c.-110G>A upstream_gene_variant 0.92 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.84 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.83 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.87 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.14 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGC frameshift_variant&missense_variant 0.15 ethambutol
ubiA 4269133 p.Gly234Val missense_variant 0.89 ethambutol Uncertain significance
ubiA 4269296 p.Met180Val missense_variant 0.14 ethambutol Uncertain significance
ethA 4326344 p.Ile377Ser missense_variant 0.13 ethionamide
whiB6 4338594 c.-75_-73delGCTinsCC upstream_gene_variant 1.0 capreomycin Uncertain significance
amikacin Not assoc w R
kanamycin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 0.99 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.84 streptomycin Not assoc w R