TB-Profiler result

Run: SRR993002
Summary

Run ID: SRR993002

Sample name:

Date: 2024-04-16T01:33:48.700729

Number of reads: 1739901

Percentage reads mapped: 98.46

Median coverage: 14.0

Strain: lineage4

Spoligotype:

Drug-resistance: HR-TB

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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
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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
katG 2155168 p.Ser315Thr missense_variant 0.62 isoniazid Assoc w R High-level resistance
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 7585 p.Ser95Thr missense_variant 0.86 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.6 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.62 rifampicin Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.5 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.62 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1475223 n.1566G>A non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.83 isoniazid Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.57 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.6 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.73 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.69 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877704 c.804G>C synonymous_variant 0.5 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.64 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.6 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.3 capreomycin
amikacin
kanamycin