TB-Profiler result

Run: ERR2516678
Summary

Run ID: ERR2516678

Sample name:

Date: 2024-10-04T23:02:41.068096

Number of reads: 2846799

Percentage reads mapped: 99.76

Median coverage: 59.0

Strain: lineage4

Spoligotype:

Drug-resistance: MDR-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
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Thr400Ala Uncertain significance Mutation from literature
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Trp119Gly Assoc w R - Interim
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA c.966_968dupGAC 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
rpoB 761004 p.Thr400Ala missense_variant 1.0 rifampicin Uncertain significance Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.36 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288887 p.Trp119Gly missense_variant 1.0 pyrazinamide Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol Assoc w R
ethA 4326505 c.966_968dupGAC disruptive_inframe_insertion 0.98 ethionamide 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
mshA 575837 c.490C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
Rv0565c 656770 p.Pro234Leu missense_variant 0.55 ethionamide Uncertain significance
Rv0565c 656919 c.549_551delCGT disruptive_inframe_deletion 0.35 ethionamide
rpoB 761889 p.Val695Leu missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777875 c.605delG frameshift_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpR5 779181 c.198dupG frameshift_variant 1.0 bedaquiline Assoc w R
clofazimine Assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 1.0 linezolid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 0.98 kanamycin
capreomycin
streptomycin
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 2063075 c.1653dupC frameshift_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
ndh 2101831 c.1212G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
katG 2156173 c.-62C>A upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726141 c.-52C>A upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv2752c 3065517 c.675C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
thyA 3074495 c.-24C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
Rv3083 3449722 p.Cys407Arg missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3612219 p.Val300Ile missense_variant 1.0 pyrazinamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4328317 c.-844C>T upstream_gene_variant 1.0 ethionamide
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 1.0 kanamycin
capreomycin
amikacin
gid 4407967 p.Leu79Trp missense_variant 1.0 streptomycin Uncertain significance