TB-Profiler result

Run: SRR998796
Summary

Run ID: SRR998796

Sample name:

Date: 2024-04-15T20:26:05.350917

Number of reads: 3807336

Percentage reads mapped: 99.29

Median coverage: 86.0

Strain: lineage4.1.3

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.92
lineage4.1 Euro-American None 0.93
lineage4 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.Asp435Val Assoc w R
isoniazid inhA p.Ser94Ala Assoc w R - Interim 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 embA c.-16C>G Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Val130Ala Mutation from literature
streptomycin gid p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA p.Ser94Ala Assoc w R - Interim
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 761110 p.Asp435Val missense_variant 0.9 rifampicin Assoc w R
inhA 1674481 p.Ser94Ala missense_variant 0.91 ethionamide Assoc w R - Interim
isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.88 isoniazid Assoc w R High-level resistance
pncA 2288853 p.Val130Ala missense_variant 0.91 pyrazinamide Mutation from literature
embA 4243217 c.-16C>G upstream_gene_variant 0.94 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.94 ethambutol Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.93 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9557 c.2256G>C synonymous_variant 0.93 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.93 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.92 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
rpsL 781421 c.-139C>A upstream_gene_variant 0.9 streptomycin Uncertain significance
rpsL 781750 p.Thr64Met missense_variant 0.94 streptomycin Uncertain significance
fbiC 1304610 c.1680C>T synonymous_variant 0.88 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1305462 c.2532G>T synonymous_variant 0.13 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
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
Rv2680 2996208 p.Ala35Asp missense_variant 0.14 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.92 cycloserine
lpqB 3623291 c.1620C>A synonymous_variant 0.91 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3624660 p.Ala84Gly missense_variant 0.94 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.85 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.95 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 0.14 ethambutol Not assoc w R
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 4338599 c.-78A>C upstream_gene_variant 0.91 capreomycin
amikacin Uncertain significance
kanamycin
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin