TB-Profiler result

Run: SRR3742667
Summary

Run ID: SRR3742667

Sample name:

Date: 2024-10-04T23:42:36.579389

Number of reads: 24260

Percentage reads mapped: 0.27

Median coverage: 0.0

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 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
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
rpoB 762909 p.Ile1035Leu missense_variant 1.0 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 762920 c.-450C>G upstream_gene_variant 1.0 rifampicin
rpoB 762923 c.3117C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 1.0 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 1.0 rifampicin Uncertain significance
rpoC 762953 c.-417G>A upstream_gene_variant 1.0 rifampicin
rpoC 762965 c.-405T>C upstream_gene_variant 1.0 rifampicin
rpoB 762989 c.3183G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762990 p.Phe1062Leu missense_variant 1.0 rifampicin
rpoB 762995 c.3189G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 763005 p.Cys1067Val missense_variant 1.0 rifampicin
rpoB 763013 c.3207C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 763014 p.Met1070Leu missense_variant 1.0 rifampicin
rpoB 763017 p.Gln1071Glu missense_variant 1.0 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764611 c.1242G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 1.0 rifampicin
rpoC 764640 p.Tyr424Phe missense_variant 1.0 rifampicin
rpoC 764650 c.1281G>C synonymous_variant 1.0 rifampicin
rpoC 764663 p.Val432Thr missense_variant 1.0 rifampicin
rpoC 764668 c.1299C>G synonymous_variant 1.0 rifampicin
rpoC 764672 p.Gln435Glu missense_variant 1.0 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 1.0 rifampicin
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472129 n.284G>T non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472135 n.290C>G non_coding_transcript_exon_variant 0.92 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.92 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.92 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472153 n.308G>C non_coding_transcript_exon_variant 0.92 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.9 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.73 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.96 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472706 n.861C>G non_coding_transcript_exon_variant 0.5 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.66 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.7 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473130 n.1285G>T non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473193 n.1348G>T non_coding_transcript_exon_variant 0.73 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473195 n.1350T>A non_coding_transcript_exon_variant 0.72 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473201 n.1356_1360delACGCTinsTGAC non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476238 n.2581T>C non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1476246 n.2589G>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.98 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476266 n.2609G>A non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1476279 n.2622G>C non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.99 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 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.99 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>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.97 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.98 capreomycin
linezolid
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid