TB-Profiler result

Run: SRR1172844
Summary

Run ID: SRR1172844

Sample name:

Date: 2024-10-03T22:30:21.090297

Number of reads: 166105

Percentage reads mapped: 50.66

Median coverage: 3.0

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 0.99
lineage4.9 Euro-American (H37Rv-like) None 0.76
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
rpoB 760328 c.522G>C synonymous_variant 0.6 rifampicin
rpoC 763702 c.333C>G synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 763732 c.363C>G synonymous_variant 0.54 rifampicin
rpoC 764131 c.762T>C synonymous_variant 0.67 rifampicin
rpoC 764215 c.846A>G synonymous_variant 0.55 rifampicin
rplC 800867 p.Ser20Asn missense_variant 0.7 linezolid
rplC 800874 c.66A>G synonymous_variant 0.7 linezolid
rplC 800875 p.Val23Ile missense_variant 0.7 linezolid
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.7 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.71 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.62 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.86 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.64 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.7 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674582 c.381T>C synonymous_variant 0.7 isoniazid
ethionamide
inhA 1674601 p.Leu134Thr missense_variant 0.7 isoniazid
ethionamide
rpsA 1833661 c.120A>G synonymous_variant 0.62 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.6 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.82 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.6 pyrazinamide Not assoc w R - Interim
embA 4245137 c.1905T>C synonymous_variant 0.6 ethambutol
embA 4245146 c.1914G>A synonymous_variant 0.55 ethambutol
embA 4245149 c.1917C>G synonymous_variant 0.55 ethambutol
embA 4245153 p.Ile641Val missense_variant 0.58 ethambutol