TB-Profiler result

Run: ERR13285126
Summary

Run ID: ERR13285126

Sample name:

Date: 2024-10-04T04:58:20.464728

Number of reads: 4828719

Percentage reads mapped: 99.79

Median coverage: 134.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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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
lineage4.8 Euro-American (mainly T) RD219 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB c.1312_1314delAAC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
c.1312_1314delAAC Mutation from literature
p.Ser450Leu Assoc w R
isoniazid katG c.-13141_799del Assoc w R High-level resistance
ahpC c.-57C>T Uncertain significance Mutation from literature
ethambutol embB p.Gly406Ser Assoc w R
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
rpoB 761114 c.1312_1314delAAC conservative_inframe_deletion 0.14 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rifampicin Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 0.84 rifampicin Assoc w R
katG 2155312 c.-13141_799del frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
ahpC 2726136 c.-57C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
embB 4247729 p.Gly406Ser missense_variant 0.73 ethambutol Assoc w R
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 759939 p.Pro45Ser missense_variant 0.39 rifampicin Uncertain significance
rpoB 761528 p.Asp574Glu missense_variant 0.15 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254358 c.177G>T synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
Rv1129c 1254624 c.-90G>C upstream_gene_variant 0.4 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3066788 c.-597G>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv3083 3448507 c.5_*1407del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
rpoA 3877949 p.Thr187Ala missense_variant 0.21 rifampicin Uncertain significance
clpC1 4040071 p.Pro212Ala missense_variant 0.89 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4407642 c.552_560delTGATGTCAG disruptive_inframe_deletion 1.0 streptomycin