TB-Profiler result

Run: ERR192070
Summary

Run ID: ERR192070

Sample name:

Date: 2024-04-16T06:51:09.743092

Number of reads: 126939

Percentage reads mapped: 3.78

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 0.85
lineage4.9 Euro-American (H37Rv-like) None 0.79
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 764602 c.1233C>T synonymous_variant 0.63 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.63 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.65 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.65 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.65 rifampicin Not assoc w R - Interim
rpoC 764644 c.1275G>C synonymous_variant 0.65 rifampicin Not assoc w R - Interim
rpoC 764647 c.1278C>T synonymous_variant 0.65 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.65 rifampicin Not assoc w R - Interim
rpoC 764659 c.1290C>T synonymous_variant 0.67 rifampicin
rpoC 764663 p.Val432Thr missense_variant 0.65 rifampicin
rpoC 764668 c.1299C>T synonymous_variant 0.68 rifampicin Not assoc w R - Interim
rpoC 764672 c.1303_1305delCAGinsGA frameshift_variant&missense_variant 0.68 rifampicin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.97 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.97 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472712 n.867G>A non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
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 1472781 n.936C>T non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.97 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476246 n.2589G>A non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.95 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476266 n.2609G>A non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476279 n.2622G>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1476404 n.2747G>A non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.98 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476474 n.2817C>T non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.97 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.92 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid