TB-Profiler result

Run: ERR4799203
Summary

Run ID: ERR4799203

Sample name:

Date: 2024-10-05T09:55:01.498443

Number of reads: 5613163

Percentage reads mapped: 99.8

Median coverage: 144.0

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) RD219 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Tyr319Ser Assoc w R
pyrazinamide pncA c.-9_27delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC Assoc w R
c.-8_27delGTGGACGTATGCGGGCGTTGATCATCGTCGACGTG Assoc w R
streptomycin gid c.423_432delGTTGGACAAG 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
cycloserine
ethionamide
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 7570 p.Ala90Val missense_variant 0.99 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 761155 p.Ser450Leu missense_variant 0.98 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R High-level resistance
pncA 2289214 c.-9_27delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC start_lost&conservative_inframe_deletion 0.99 pyrazinamide Assoc w R
pncA 2289214 c.-8_27delGTGGACGTATGCGGGCGTTGATCATCGTCGACGTG start_lost&conservative_inframe_deletion 0.99 pyrazinamide Assoc w R
embB 4247469 p.Tyr319Ser missense_variant 0.99 ethambutol Assoc w R
gid 4407770 c.423_432delGTTGGACAAG frameshift_variant 0.97 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
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.96 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.97 rifampicin Not assoc w R
rpoC 764660 p.Val431Met missense_variant 0.98 rifampicin Uncertain significance
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
sigE 1364337 c.-76G>A upstream_gene_variant 0.94 pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.94 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.98 capreomycin
Rv2752c 3065022 c.1169dupC frameshift_variant 0.94 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.99 ethionamide Uncertain significance
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.97 pyrazinamide Not assoc w R
fbiB 3642530 c.996A>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine Not assoc w R - Interim
rpoA 3878590 c.-84delC upstream_gene_variant 0.94 rifampicin Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.98 pyrazinamide Not assoc w R
embC 4241662 c.1800G>C synonymous_variant 0.96 ethambutol
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