TB-Profiler result

Run: ERR2516485
Summary

Run ID: ERR2516485

Sample name:

Date: 2024-10-04T21:41:54.687109

Number of reads: 3946586

Percentage reads mapped: 99.67

Median coverage: 81.0

Strain: lineage4.1.2.1;lineage4.3.4.2

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 0.45
lineage4.1 Euro-American None 0.55
lineage4.1.2 Euro-American None 0.57
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.55
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.42
lineage4.3.4.2 Euro-American (LAM) RD174 0.43
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Pro Assoc w R
p.Ser450Leu Assoc w R
rpoC p.Leu527Val Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
p.Met306Ile Assoc w R
pyrazinamide pncA p.Leu182Ser Assoc w R
p.Ile90Thr Assoc w R - Interim
streptomycin
fluoroquinolones
moxifloxacin gyrB p.Asn499Thr Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrB p.Asn499Thr Assoc w R
gyrA p.Ala90Val Assoc w R
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
gyrB 6735 p.Asn499Thr missense_variant 0.59 levofloxacin Assoc w R
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7570 p.Ala90Val missense_variant 0.32 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.62 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761101 p.Gln432Pro missense_variant 0.68 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.5 rifampicin Assoc w R
rpoC 764948 p.Leu527Val missense_variant 0.47 rifampicin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288697 p.Leu182Ser missense_variant 0.56 pyrazinamide Assoc w R
pncA 2288973 p.Ile90Thr missense_variant 0.36 pyrazinamide Assoc w R - Interim
ahpC 2726145 c.-48G>A upstream_gene_variant 0.58 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.29 ethambutol Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.71 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 6140 p.Val301Leu missense_variant 0.44 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
fgd1 491591 p.Lys270Met missense_variant 0.57 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.59 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.43 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.68 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.63 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.45 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.61 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 781276 c.-284A>C upstream_gene_variant 0.63 streptomycin
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
rpsA 1833469 c.-73G>T upstream_gene_variant 0.52 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.59 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.24 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.42 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.49 pyrazinamide Not assoc w R
Rv3236c 3612846 p.Pro91Ser missense_variant 0.48 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.43 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.5 pyrazinamide Not assoc w R
panD 4044181 p.Asp34Gly missense_variant 0.51 pyrazinamide Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.59 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.44 ethambutol Not assoc w R
embB 4248004 p.Gln497His missense_variant 0.47 ethambutol Uncertain significance
ubiA 4269671 p.Val55Leu missense_variant 0.47 ethambutol Uncertain significance
ethA 4326182 p.Phe431Ser missense_variant 0.58 ethionamide Uncertain significance
ethA 4326705 p.Pro257Ala missense_variant 0.38 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 0.55 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 4407691 p.Val171Gly missense_variant 0.54 streptomycin Uncertain significance
gid 4407970 p.Pro78Leu missense_variant 0.42 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.45 streptomycin Not assoc w R