TB-Profiler result

Run: ERR4553771
Summary

Run ID: ERR4553771

Sample name:

Date: 2024-04-15T21:19:10.091916

Number of reads: 2140723

Percentage reads mapped: 99.56

Median coverage: 72.0

Strain: lineage1.2.2.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.98
lineage1.2.2.2 Indo-Oceanic RD239 0.98
lineage1 Indo-Oceanic RD239 0.2
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu452Pro Assoc w R
isoniazid inhA p.Ile21Val Uncertain significance Mutation from literature
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide
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 761161 p.Leu452Pro missense_variant 0.94 rifampicin Assoc w R
inhA 1674262 p.Ile21Val missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 0.94 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
dnaA 237 c.237G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
dnaA 380 p.Thr127Ile missense_variant 0.93 isoniazid Uncertain significance
gyrB 5075 c.-165C>T upstream_gene_variant 0.99 levofloxacin
moxifloxacin
gyrA 7268 c.-34C>T upstream_gene_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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
Rv0010c 13699 c.-141A>G upstream_gene_variant 1.0 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.93 ethionamide
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776555 c.1926C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mmpR5 779392 p.Arg135Trp missense_variant 0.97 clofazimine
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1407467 c.-127C>A upstream_gene_variant 0.99 streptomycin
isoniazid
pyrazinamide
embR 1417554 c.-207C>G upstream_gene_variant 0.73 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
ndh 2102913 p.Ala44Thr missense_variant 0.92 ethionamide Uncertain significance
delamanid
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.96 pyrazinamide Uncertain significance
PPE35 2169071 c.1542A>C synonymous_variant 0.88 pyrazinamide
PPE35 2169199 p.Val472Leu missense_variant 0.94 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.96 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.95 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
Rv2681 2997950 c.1212C>T synonymous_variant 1.0 capreomycin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3086890 p.Ala24Gly missense_variant 0.93 cycloserine
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.97 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.96 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.98 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.94 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407727 p.Met159Arg missense_variant 0.94 streptomycin Uncertain significance