TB-Profiler result

Run: SRR11972175
Summary

Run ID: SRR11972175

Sample name:

Date: 2024-04-13T22:14:55.616294

Number of reads: 379312

Percentage reads mapped: 49.42

Median coverage: 5.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 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
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.92 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>C non_coding_transcript_exon_variant 0.75 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472608 n.763T>A non_coding_transcript_exon_variant 0.75 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472612 n.767G>A non_coding_transcript_exon_variant 0.75 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472615 n.770C>T non_coding_transcript_exon_variant 0.75 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472620 n.775A>G non_coding_transcript_exon_variant 0.82 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472634 n.789T>C non_coding_transcript_exon_variant 0.9 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472639 n.794G>A non_coding_transcript_exon_variant 0.9 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472643 n.798A>T non_coding_transcript_exon_variant 0.9 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472644 n.799C>G non_coding_transcript_exon_variant 0.9 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.85 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.86 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.94 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475869 n.2212C>T non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.5 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.97 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.86 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.84 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.56 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
embC 4241958 p.Arg699Leu missense_variant 1.0 ethambutol Uncertain significance