TB-Profiler result

Run: SRR1013532
Summary

Run ID: SRR1013532

Sample name:

Date: 2024-05-17T14:27:34.203957

Number of reads: 160081

Percentage reads mapped: 2.74

Median coverage: 3.0

Strain: lineage4.3.2;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
lineage4.3 Euro-American (LAM) None 0.06
lineage4.3.2 Euro-American (LAM) None 0.15
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 0.88
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
rpoC 764617 c.1248C>T synonymous_variant 0.85 rifampicin
rpoC 764623 c.1254C>G synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764647 c.1278C>T synonymous_variant 0.84 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764658 c.1289_1290insTAC disruptive_inframe_insertion 0.79 rifampicin
rpoC 764662 c.1295_1297delTCG disruptive_inframe_deletion 1.0 rifampicin
rpoC 764671 c.1302G>A synonymous_variant 0.79 rifampicin
rpoC 764672 p.Gln435Thr missense_variant 1.0 rifampicin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.98 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.98 kanamycin
amikacin
streptomycin Uncertain significance
capreomycin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.97 kanamycin
amikacin
streptomycin Uncertain significance
capreomycin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.97 kanamycin
amikacin
streptomycin Uncertain significance
capreomycin
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.96 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.9 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.98 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.91 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.91 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.91 kanamycin
amikacin
streptomycin
capreomycin
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.8 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.91 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
amikacin Not assoc w R
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.95 kanamycin
amikacin
streptomycin
capreomycin
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin
capreomycin Uncertain significance
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin
capreomycin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
capreomycin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.96 capreomycin
linezolid
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.82 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.82 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.77 capreomycin
linezolid