TB-Profiler result

Run: SRR13837734
Summary

Run ID: SRR13837734

Sample name:

Date: 2025-03-08T11:04:27.486862

Number of reads: 2936538

Percentage reads mapped: 100.0

Median coverage: 98.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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
isoniazid
ethambutol
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
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 5922 p.Glu228Gly missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7242 p.Lys668Thr missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
ccsA 620360 p.Tyr157Ser missense_variant 0.99 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
hadA 732060 p.Gly44Val missense_variant 1.0 isoniazid Uncertain significance
hadA 732292 c.363C>T synonymous_variant 1.0 isoniazid Uncertain significance
nusG 734239 c.-14delG upstream_gene_variant 1.0 rifampicin Uncertain significance
mmaA3 738003 p.Met49Ile missense_variant 1.0 isoniazid Uncertain significance
rpoB 761356 c.1550_1551insA frameshift_variant 1.0 rifampicin Uncertain significance
rpoC 763347 c.-23C>G upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoC 766025 p.Val886Met missense_variant 1.0 rifampicin Uncertain significance
mmpL5 776145 p.Ala779Gly missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776954 p.Lys509Asn missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 801231 c.423C>A synonymous_variant 1.0 linezolid Uncertain significance
sigE 1364454 c.42G>A synonymous_variant 1.0 pyrazinamide Uncertain significance
atpE 1460916 c.-129G>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
rrl 1476201 n.2544C>G non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
katG 2155137 c.975G>C synonymous_variant 1.0 isoniazid Uncertain significance
PPE35 2168892 p.Thr574Lys missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222852 p.Ala105Thr missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
ribD 2987259 p.Leu141Val missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2752c 3065161 p.Asn344Thr missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3065830 p.Ile121Thr missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3067100 c.-909G>A upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
fbiD 3339117 c.-1C>T upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv3083 3448661 p.Val53Ala missense_variant 0.99 ethionamide Uncertain significance
Rv3236c 3612041 p.Val359Glu missense_variant 1.0 pyrazinamide Uncertain significance
lpqB 3623964 p.Gly316Val missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
lpqB 3624582 p.Ala110Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiA 3640418 c.-125C>A upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rpoA 3877877 p.Ala211Ser missense_variant 1.0 rifampicin Uncertain significance
clpC1 4039250 c.1455C>G synonymous_variant 1.0 pyrazinamide Uncertain significance
embC 4242113 c.2251C>T synonymous_variant 1.0 ethambutol Uncertain significance
embB 4246367 c.-147C>T upstream_gene_variant 0.99 ethambutol Uncertain significance
whiB6 4338567 c.-46C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4408302 c.-101delC upstream_gene_variant 1.0 streptomycin Uncertain significance