TB-Profiler result

Run: SRR15315964
Summary

Run ID: SRR15315964

Sample name:

Date: 2024-10-04T02:25:45.371394

Number of reads: 5633973

Percentage reads mapped: 99.54

Median coverage: 173.0

Strain: lineage4.4

Spoligotype:

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.4 Euro-American None 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.His445Asp Assoc w R
isoniazid katG p.Asn138His Uncertain significance Mutation from literature
ahpC c.-81C>T Uncertain significance Mutation from literature
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.His1002Arg Uncertain significance Mutation from literature
pyrazinamide pncA c.391dupG Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
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 eis c.-12C>T Assoc w R
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid thyX c.-16C>T 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 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
katG 2155700 p.Asn138His missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
pncA 2288850 c.391dupG frameshift_variant 0.99 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.99 kanamycin Assoc w R
ahpC 2726112 c.-81C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4249518 p.His1002Arg missense_variant 1.0 ethambutol 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
gyrB 5416 c.177C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 0.99 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 491718 c.936A>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
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
Rv1129c 1254519 p.Val6Ile missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254623 c.-89C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3066099 p.Met31Ile missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3074479 c.-8T>C upstream_gene_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245449 c.2217G>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embA 4246508 c.3276G>A synonymous_variant 0.99 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269375 c.459G>A 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 1.0 kanamycin
capreomycin
amikacin