TB-Profiler result

Run: ERR108465
Summary

Run ID: ERR108465

Sample name:

Date: 2024-04-15T20:47:15.238012

Number of reads: 6584342

Percentage reads mapped: 99.56

Median coverage: 140.0

Strain: lineage4.1.2;lineage4.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.8
lineage4.1.2 Euro-American None 0.8
lineage4.2 Euro-American None 0.18
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.18
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethR p.Phe110Leu 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
rpsL 781687 p.Lys43Arg missense_variant 0.13 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid Assoc w R High-level resistance
ethR 4327876 p.Phe110Leu missense_variant 0.84 ethionamide 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
Rv0010c 13639 c.-81C>G upstream_gene_variant 0.78 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.84 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.84 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.84 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.83 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
rplC 800200 c.-609C>G upstream_gene_variant 0.81 linezolid
rplC 800204 c.-605T>C upstream_gene_variant 0.19 linezolid
rplC 800889 c.81C>A synonymous_variant 0.83 linezolid 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
bacA 2063685 c.1044G>A synonymous_variant 0.21 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2168303 c.2310G>T synonymous_variant 0.79 pyrazinamide Not assoc w R - Interim
PPE35 2169776 p.Phe279Leu missense_variant 0.82 pyrazinamide Uncertain significance
PPE35 2169879 p.Phe245Cys missense_variant 0.16 pyrazinamide Uncertain significance
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 0.84 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.48 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.16 capreomycin
ald 3086742 c.-78A>C upstream_gene_variant 0.17 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625403 p.Val404Ala missense_variant 0.16 bedaquiline Uncertain significance
rifampicin Uncertain significance
alr 3840263 c.1158C>T synonymous_variant 0.85 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.8 ethambutol Not assoc w R
embB 4247086 c.573C>T synonymous_variant 0.83 ethambutol Not assoc w R - Interim
embB 4249594 c.3081G>A synonymous_variant 0.14 ethambutol Not assoc w R - Interim
ubiA 4269847 c.-14A>G upstream_gene_variant 0.81 ethambutol Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.13 ethionamide
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