TB-Profiler result

Run: SRR1167335
Summary

Run ID: SRR1167335

Sample name:

Date: 2024-04-15T22:13:22.288535

Number of reads: 4762843

Percentage reads mapped: 99.17

Median coverage: 105.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: MDR-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 1.0
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 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.Leu452Pro Assoc w R
isoniazid inhA c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A. 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 embB p.Met306Val Assoc w R
pyrazinamide pncA c.456dupC Assoc w R
streptomycin gid c.160_290del Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A
ethA c.825dupG Assoc w R
c.-11A>G Uncertain significance Mutation from literature
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
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin Assoc w R
inhA 1673432 c.-770T>A upstream_gene_variant 1.0 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>A
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288785 c.456dupC frameshift_variant 1.0 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol Assoc w R
ethA 4326648 c.825dupG frameshift_variant 0.14 ethionamide Assoc w R
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide Uncertain significance Mutation from literature
gid 4407912 c.160_290del frameshift_variant 1.0 streptomycin 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
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 8040 p.Gly247Ser 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
rpoC 764995 c.1626C>G synonymous_variant 0.99 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 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1417152 c.195dupC frameshift_variant 0.12 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 1.0 isoniazid
Rv2752c 3065824 p.Pro123Leu missense_variant 0.99 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4040457 c.246_247dupCC frameshift_variant 0.11 pyrazinamide
ubiA 4269296 p.Met180Val missense_variant 0.99 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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R