TB-Profiler result

Run: ERR13261230
Summary

Run ID: ERR13261230

Sample name:

Date: 2025-02-11T14:32:50.312197

Number of reads: 3076218

Percentage reads mapped: 99.84

Median coverage: 87.0

Strain: lineage4.3.3;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
lineage4.3 Euro-American (LAM) None 0.09
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.88
lineage4.3.3 Euro-American (LAM) RD115 0.05
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.Gly406Ala Assoc w R
pyrazinamide pncA p.Leu182Trp Assoc w R
streptomycin gid p.Leu79Ser Uncertain significance Mutation from literature
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
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 0.79 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.93 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.88 isoniazid Assoc w R High-level resistance
pncA 2288697 p.Leu182Trp missense_variant 0.89 pyrazinamide Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.85 ethambutol Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.91 streptomycin 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 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.93 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.92 rifampicin Not assoc w R
rpoC 766487 p.Pro1040Ser missense_variant 0.88 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.97 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.16 isoniazid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.88 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
kasA 2518919 p.Gly269Ser missense_variant 0.15 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.19 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.89 capreomycin
Rv2680 2996052 c.-53G>A upstream_gene_variant 0.5 capreomycin
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.9 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.17 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.11 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.89 pyrazinamide Not assoc w R
clpC1 4040444 c.261C>T synonymous_variant 0.94 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269794 p.Val14Leu missense_variant 0.89 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.19 streptomycin Not assoc w R