TB-Profiler result

Run: ERR4821747

Summary

Run ID: ERR4821747

Sample name:

Date: 2024-10-04T21:52:46.254759

Number of reads: 189973

Percentage reads mapped: 4.15

Median coverage: 1.0

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 0.96
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 760244 c.438G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 760253 c.447T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 760263 p.Met153Leu missense_variant 1.0 rifampicin
rpoB 760266 p.Met154Gln missense_variant 1.0 rifampicin
rpoB 760274 p.Glu156Asp missense_variant 1.0 rifampicin Uncertain significance
rpoB 762879 p.Met1025Leu missense_variant 0.89 rifampicin Uncertain significance
rpoC 762896 c.-474G>C upstream_gene_variant 0.94 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.98 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoC 762947 c.-423C>G upstream_gene_variant 0.95 rifampicin
rpoB 762962 c.3156C>T synonymous_variant 0.95 rifampicin Not assoc w R - Interim
rpoC 762980 c.-390T>C upstream_gene_variant 0.93 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.9 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.88 rifampicin Not assoc w R - Interim
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
rpoB 763038 p.Thr1078Ala missense_variant 1.0 rifampicin
rpoC 763052 c.-318G>C upstream_gene_variant 1.0 rifampicin
rpoC 763053 c.-317_-315delTTGinsCTC upstream_gene_variant 1.0 rifampicin
rpoC 763058 c.-312C>G upstream_gene_variant 1.0 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 763075 p.Thr1090Ile missense_variant 1.0 rifampicin
rpoB 763077 p.Val1091Leu missense_variant 1.0 rifampicin
rpoB 763115 c.3309T>C synonymous_variant 0.97 rifampicin Not assoc w R - Interim
rpoB 763126 p.Pro1107Gln missense_variant 0.96 rifampicin
rpoC 763133 c.-237G>C upstream_gene_variant 0.95 rifampicin
rpoB 763136 c.3330C>T synonymous_variant 0.95 rifampicin Not assoc w R - Interim
rpoC 763148 c.-222G>C upstream_gene_variant 0.93 rifampicin
rpoC 763462 c.93G>C synonymous_variant 1.0 rifampicin
rpoC 763483 c.114G>C synonymous_variant 1.0 rifampicin
rpoC 763486 c.117T>G synonymous_variant 0.95 rifampicin
rpoC 763492 c.123G>C synonymous_variant 0.95 rifampicin Not assoc w R - Interim
rpoC 763504 c.135C>T synonymous_variant 0.96 rifampicin
rpoC 763511 p.Cys48Gly missense_variant 0.95 rifampicin
rpoC 763517 p.Lys50Gln missense_variant 0.96 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.96 rifampicin Not assoc w R - Interim
rpoC 763531 c.162G>C synonymous_variant 0.96 rifampicin Not assoc w R
rpoC 763532 p.Thr55Ser missense_variant 0.96 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.96 rifampicin Not assoc w R - Interim
rpoC 763550 p.Tyr61Ala missense_variant 0.93 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.88 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.88 rifampicin Not assoc w R - Interim
rpoC 763589 p.Ile74Val missense_variant 0.94 rifampicin
rpoC 763609 c.240C>G synonymous_variant 0.88 rifampicin
rpoC 763660 c.291T>C synonymous_variant 0.92 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoC 763699 c.330G>C synonymous_variant 0.93 rifampicin
rpoC 763708 c.339G>C synonymous_variant 0.93 rifampicin
rpoC 763709 c.340C>T synonymous_variant 0.93 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.93 rifampicin
rpoC 763727 p.Leu120Met missense_variant 0.93 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.93 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.89 rifampicin
rpoC 763751 p.Ile128Val missense_variant 0.91 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.79 rifampicin
rpoC 764593 c.1224C>T synonymous_variant 0.95 rifampicin
rpoC 764602 c.1233C>T synonymous_variant 0.97 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.98 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoC 764660 p.Val431Ile missense_variant 0.99 rifampicin
rpoC 764692 c.1323C>T synonymous_variant 0.96 rifampicin Not assoc w R - Interim
rpoC 764706 p.Leu446Gln missense_variant 0.95 rifampicin Uncertain significance
rpoC 764713 c.1344G>C synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpsL 781751 c.192G>C synonymous_variant 0.83 streptomycin
rpsL 781754 c.195G>C synonymous_variant 0.92 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.89 streptomycin
rpsL 781794 p.Met79Leu missense_variant 0.9 streptomycin
rpsL 781814 c.255C>T synonymous_variant 0.96 streptomycin
rpsL 781817 c.258G>T synonymous_variant 0.96 streptomycin
rpsL 781829 c.270G>C synonymous_variant 0.96 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.96 streptomycin
rpsL 781841 c.282C>T synonymous_variant 0.95 streptomycin
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance