TB-Profiler result

Run: SRR26159048
Summary

Run ID: SRR26159048

Sample name:

Date: 2024-10-04T19:56:24.262114

Number of reads: 211332

Percentage reads mapped: 98.52

Median coverage: 0.0

Strain: lineage4.9

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
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.77 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.82 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.23 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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rrs 1472298 n.454_461delTCCGGGTT non_coding_transcript_exon_variant 0.97 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472309 n.464_465insACT non_coding_transcript_exon_variant 0.87 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472313 n.468_469delGAinsTGAG non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.46 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.49 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.99 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid
rrl 1476035 n.2378G>A non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476105 n.2448_2449delGAinsT non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.93 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid
inhA 1674136 c.-66T>G upstream_gene_variant 1.0 isoniazid
ethionamide
inhA 1674141 c.-61T>C upstream_gene_variant 1.0 isoniazid
ethionamide
inhA 1674153 c.-49G>C upstream_gene_variant 1.0 isoniazid
ethionamide
inhA 1674171 c.-31T>C upstream_gene_variant 1.0 isoniazid
ethionamide
inhA 1674183 c.-19_-18insAATCACC upstream_gene_variant 0.96 isoniazid
ethionamide
inhA 1674187 c.-15A>G upstream_gene_variant 0.94 isoniazid
ethionamide
inhA 1674191 c.-11_-10insAAGCACATT upstream_gene_variant 1.0 isoniazid
ethionamide
inhA 1674199 c.-3C>G upstream_gene_variant 1.0 isoniazid Uncertain significance
ethionamide
inhA 1674205 p.Thr2Ala missense_variant 1.0 isoniazid Uncertain significance
ethionamide
inhA 1674216 c.15G>C synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674219 p.Asp6Glu missense_variant 1.0 isoniazid
ethionamide
inhA 1674229 p.Ile10Val missense_variant 1.0 isoniazid
ethionamide
inhA 1674237 c.36T>C synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674243 c.42A>G synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674279 c.78A>G synonymous_variant 0.71 isoniazid
ethionamide
inhA 1674280 p.Arg27Lys missense_variant 0.65 isoniazid
ethionamide
inhA 1674285 c.84A>C synonymous_variant 0.55 isoniazid
ethionamide
inhA 1674295 p.Gln32Ala missense_variant 0.39 isoniazid
ethionamide
inhA 1674300 c.99C>G synonymous_variant 0.38 isoniazid
ethionamide
inhA 1674303 c.102C>G synonymous_variant 0.37 isoniazid
ethionamide
inhA 1674307 c.106C>T synonymous_variant 0.34 isoniazid
ethionamide
inhA 1674321 c.120G>A synonymous_variant 0.3 isoniazid
ethionamide
inhA 1674342 c.141T>C synonymous_variant 0.24 isoniazid
ethionamide
inhA 1674537 c.336C>T synonymous_variant 0.2 isoniazid
ethionamide
inhA 1674542 p.Ala114Glu missense_variant 0.19 isoniazid
ethionamide
inhA 1674576 c.375T>C synonymous_variant 0.23 isoniazid
ethionamide
inhA 1674585 c.384T>C synonymous_variant 0.23 isoniazid
ethionamide
inhA 1674589 p.Met130Leu missense_variant 0.23 isoniazid
ethionamide
inhA 1674849 c.648G>A synonymous_variant 0.18 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 0.95 capreomycin Not assoc w R
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.63 streptomycin Not assoc w R