TB-Profiler result

Run: SRR28046141
Summary

Run ID: SRR28046141

Sample name:

Date: 2024-05-22T09:56:51.761491

Number of reads: 8101509

Percentage reads mapped: 99.52

Median coverage: 218.0

Strain: lineage4.4

Spoligotype:

Drug-resistance: Pre-XDR-TB

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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.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Asp354Ala Assoc w R
pyrazinamide pncA p.Thr100Pro Assoc w R - Interim
p.Thr76Pro Assoc w R
c.-11A>G Assoc w R
streptomycin gid c.115delC Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.237dupG Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761110 p.Asp435Val missense_variant 0.98 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288944 p.Thr100Pro missense_variant 0.22 pyrazinamide Assoc w R - Interim
pncA 2289016 p.Thr76Pro missense_variant 0.29 pyrazinamide Assoc w R
pncA 2289252 c.-11A>G upstream_gene_variant 0.41 pyrazinamide Assoc w R
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol Assoc w R
ethA 4327236 c.237dupG frameshift_variant 1.0 ethionamide Assoc w R
gid 4408087 c.115delC 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 760315 p.Val170Gly missense_variant 1.0 rifampicin Uncertain significance
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
rrs 1471618 n.-228G>C upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
PPE35 2170558 p.Ala19Pro missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714523 p.His270Gln missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726762 c.570C>G synonymous_variant 1.0 isoniazid
folC 2747480 p.Glu40Val missense_variant 1.0 para-aminosalicylic_acid
pepQ 2859521 c.898C>T synonymous_variant 1.0 clofazimine
bedaquiline
Rv2752c 3065715 c.477T>C synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3066452 c.-261T>G upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448946 c.445dupT frameshift_variant 1.0 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878619 c.-112A>C upstream_gene_variant 0.17 rifampicin
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 4243324 p.Val31Ala missense_variant 1.0 ethambutol Uncertain significance
embB 4247028 p.Leu172Arg missense_variant 0.25 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.12 ethambutol
embB 4247548 c.1035C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
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
ethA 4326509 p.Ala322Val missense_variant 1.0 ethionamide 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