TB-Profiler result

Run: ERR13266770
Summary

Run ID: ERR13266770

Sample name:

Date: 2024-10-04T01:24:39.395166

Number of reads: 6036104

Percentage reads mapped: 99.69

Median coverage: 159.0

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 0.98
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
ahpC c.-81C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
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 7581 p.Asp94Asn missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761110 p.Asp435Val missense_variant 0.98 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
ahpC 2726112 c.-81C>T upstream_gene_variant 0.99 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.98 ethambutol 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
gyrB 5168 c.-72G>A upstream_gene_variant 0.97 levofloxacin
moxifloxacin
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 0.99 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.97 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
Rv1258c 1406504 c.837C>T synonymous_variant 0.98 streptomycin
pyrazinamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.98 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.98 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
pncA 2288743 p.Thr167Pro missense_variant 0.97 pyrazinamide Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.99 capreomycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.98 ethionamide Uncertain significance
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.98 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.97 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326632 p.His281Arg missense_variant 0.98 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 0.99 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R