TB-Profiler result

Run: ERR5866510
Summary

Run ID: ERR5866510

Sample name:

Date: 2024-10-04T16:36:37.115241

Number of reads: 7129965

Percentage reads mapped: 99.53

Median coverage: 147.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.98
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 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.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Ala146Thr Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
rpoB 761155 p.Ser450Leu missense_variant 0.95 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288806 p.Ala146Thr missense_variant 1.0 pyrazinamide 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
dnaA 1495 p.Thr499Ala missense_variant 0.97 isoniazid Uncertain significance
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 8040 p.Gly247Ser missense_variant 0.98 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
rpoB 761461 p.Arg552His missense_variant 0.97 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.95 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
Rv1129c 1254536 c.-2A>G upstream_gene_variant 0.99 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
fbiC 1303095 c.165G>A synonymous_variant 0.99 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rpsA 1834836 p.Met432Thr missense_variant 0.99 pyrazinamide Not assoc w R - Interim
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
katG 2156196 c.-85C>T upstream_gene_variant 0.99 isoniazid 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 0.98 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.99 para-aminosalicylic_acid
folC 2747470 p.Ile43Ala missense_variant 0.99 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.96 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.98 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.99 pyrazinamide Not assoc w R - Interim
panD 4045227 c.-946G>A upstream_gene_variant 0.99 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247495 p.Asp328His missense_variant 0.99 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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407743 p.Arg154Trp missense_variant 0.99 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.99 streptomycin Not assoc w R