TB-Profiler result

Run: SRR18715352
Summary

Run ID: SRR18715352

Sample name:

Date: 2024-10-03T20:41:08.386798

Number of reads: 3168707

Percentage reads mapped: 99.74

Median coverage: 90.0

Strain: lineage4.3.3;lineage4.8

Spoligotype:

Drug-resistance: HR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.24
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.74
lineage4.3.3 Euro-American (LAM) RD115 0.26
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)
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.54 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.74 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)
ahpC 2726145 c.-48G>A upstream_gene_variant 0.56 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.29 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmaA3 737495 c.646_654delACGATCGAG conservative_inframe_deletion 0.49 isoniazid
rpoC 764995 c.1626C>G synonymous_variant 0.2 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
rpsL 781676 c.117C>T synonymous_variant 0.54 streptomycin Not assoc w R - Interim
rplC 800437 c.-372G>C upstream_gene_variant 0.17 linezolid Uncertain significance
fbiC 1305105 c.2175G>A synonymous_variant 0.5 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.19 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834836 p.Met432Thr missense_variant 0.25 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.29 linezolid Not assoc w R
tlyA 1917811 c.-129T>C upstream_gene_variant 0.24 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155751 p.Gly121Ser missense_variant 0.64 isoniazid Uncertain significance
katG 2156196 c.-85C>T upstream_gene_variant 0.17 isoniazid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.24 pyrazinamide 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 2518919 p.Gly269Ser missense_variant 0.31 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.16 para-aminosalicylic_acid
Rv2477c 2784408 c.-366G>A upstream_gene_variant 0.62 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.23 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.25 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.21 cycloserine
Rv3083 3448322 c.-182G>A upstream_gene_variant 0.21 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 0.26 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.25 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
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 0.17 kanamycin
capreomycin
amikacin
whiB6 4338863 c.-342C>G upstream_gene_variant 0.55 kanamycin
capreomycin
amikacin
gid 4407992 p.Gly71Arg missense_variant 0.2 streptomycin Uncertain significance
gid 4408061 p.His48Tyr missense_variant 0.2 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.32 streptomycin Not assoc w R