TB-Profiler result

Run: SRR28393374
Summary

Run ID: SRR28393374

Sample name:

Date: 2024-05-22T12:53:18.559886

Number of reads: 5042643

Percentage reads mapped: 99.58

Median coverage: 148.0

Strain: lineage4.1.2.1

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 0.76
lineage4.1.2 Euro-American None 0.74
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.76
lineage4 Euro-American 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
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ahpC c.-54C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA c.335delA Assoc w R
p.Ile5Thr Uncertain significance Mutation from literature
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
ethA p.Asp58Ala Uncertain significance Mutation from literature
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 1.0 rifampicin Assoc w R
inhA 1673423 c.-779G>T upstream_gene_variant 0.16 ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.81 isoniazid Assoc w R High-level resistance
pncA 2288906 c.335delA frameshift_variant 0.18 pyrazinamide Assoc w R
pncA 2289228 p.Ile5Thr missense_variant 0.73 pyrazinamide Uncertain significance Mutation from literature
ahpC 2726139 c.-54C>T upstream_gene_variant 0.8 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.77 ethambutol Assoc w R
ethA 4327301 p.Asp58Ala missense_variant 0.72 ethionamide 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 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 0.81 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.78 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.71 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.71 rifampicin Not assoc w R
rpoB 761407 p.Val534Gly missense_variant 0.32 rifampicin Uncertain significance
rpoB 761889 p.Val695Leu missense_variant 0.17 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.74 rifampicin Not assoc w R
rpoC 765617 p.Glu750Gln missense_variant 0.75 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.75 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.29 linezolid Not assoc w R - Interim
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
katG 2153911 p.Leu734Arg missense_variant 0.21 isoniazid Uncertain significance
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.21 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.76 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.6 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.18 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.16 capreomycin
Rv2752c 3065517 c.675C>T synonymous_variant 0.26 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.75 cycloserine
Rv3083 3448439 c.-64delA upstream_gene_variant 0.23 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 0.75 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.79 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 0.8 ethambutol Not assoc w R
ethA 4328317 c.-844C>T upstream_gene_variant 0.28 ethionamide
whiB6 4338440 p.Glu28* stop_gained 0.74 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 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 4408064 p.Arg47Gly missense_variant 0.73 streptomycin