TB-Profiler result

Run: ERR10748463
Summary

Run ID: ERR10748463

Sample name:

Date: 2024-10-03T21:45:56.189719

Number of reads: 3447193

Percentage reads mapped: 99.67

Median coverage: 57.0

Strain: lineage4.1.1.1;lineage4.7

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
lineage4.1 Euro-American None 0.2
lineage4.1.1.1 Euro-American (X-type) RD183 0.2
lineage4.7 Euro-American (mainly T) None 0.82
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.2
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 inhA c.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. 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 embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Gly97Asp Assoc w R
streptomycin
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 inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
ethA p.Thr342Lys 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
gyrA 7570 p.Ala90Val missense_variant 0.79 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 0.83 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.79 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155167 p.Ser315Thr missense_variant 0.78 isoniazid Assoc w R High-level resistance
pncA 2288952 p.Gly97Asp missense_variant 0.76 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.75 ethambutol Assoc w R
ethA 4326449 p.Thr342Lys missense_variant 0.89 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 0.27 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.25 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13887 c.-329T>C upstream_gene_variant 0.9 isoniazid
Rv0565c 657497 c.-27G>A upstream_gene_variant 0.86 ethionamide Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 0.83 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.2 rifampicin Not assoc w R
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
rplC 800219 c.-590T>C upstream_gene_variant 0.23 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.63 capreomycin Not assoc w R
linezolid Uncertain significance
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
ald 3086788 c.-32T>C upstream_gene_variant 0.16 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.18 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641447 p.Thr302Met missense_variant 0.15 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
rpoA 3877553 p.Glu319Lys missense_variant 0.2 rifampicin Not assoc w R
embC 4240897 c.1035C>G synonymous_variant 0.17 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.15 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.23 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.9 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 0.22 kanamycin
capreomycin
amikacin
gid 4407704 p.Ala167Pro missense_variant 0.8 streptomycin Uncertain significance