TB-Profiler result

Run: ERR038755
Summary

Run ID: ERR038755

Sample name:

Date: 2024-10-04T16:09:10.316071

Number of reads: 18083318

Percentage reads mapped: 99.46

Median coverage: 314.5

Strain: lineage4.1.1.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.1.3 Euro-American (X-type) RD193 1.0
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) 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.Ser450Leu Assoc w R
p.Leu452Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
c.-11C>A Uncertain significance Mutation from literature
pyrazinamide
streptomycin gid c.115delC Assoc w R
c.102delG Assoc w R
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 0.29 rifampicin Assoc w R
rpoB 761161 p.Leu452Pro missense_variant 0.33 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embA 4243217 c.-16C>T upstream_gene_variant 0.41 ethambutol Uncertain significance Mutation from literature
embA 4243222 c.-11C>A upstream_gene_variant 0.57 ethambutol Uncertain significance Mutation from literature
gid 4408087 c.115delC frameshift_variant 0.24 streptomycin Assoc w R
gid 4408100 c.102delG frameshift_variant 0.44 streptomycin 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
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
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
mmaA3 737453 c.696dupG frameshift_variant 0.22 isoniazid
rpoC 765150 p.Gly594Glu missense_variant 1.0 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 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1475615 n.1958C>T non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
rpsA 1833684 p.Arg48Pro missense_variant 1.0 pyrazinamide
rpsA 1834130 p.Glu197Lys missense_variant 1.0 pyrazinamide Uncertain significance
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
thyX 3067901 c.45C>T synonymous_variant 0.99 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
rpoA 3877964 p.Arg182Trp missense_variant 0.18 rifampicin Uncertain significance
embC 4241292 p.Leu477Arg missense_variant 0.62 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.99 ethambutol Not assoc w R
embA 4243622 c.390G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247106 p.Pro198His missense_variant 0.6 ethambutol
embB 4249408 c.2895G>A synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326279 p.Ser399Pro missense_variant 1.0 ethionamide 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 4407862 p.Ile114Asn missense_variant 0.19 streptomycin Uncertain significance