TB-Profiler result

Run: SRR21276937
Summary

Run ID: SRR21276937

Sample name:

Date: 2024-04-16T11:03:35.615944

Number of reads: 8178675

Percentage reads mapped: 99.27

Median coverage: 271.0

Strain: lineage4.4.2

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 0.99
lineage4.4 Euro-American None 0.98
lineage4.4.2 Euro-American None 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB c.1296_1304delATTCATGGA Assoc w R
c.1296_1304delATTCATGGA Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA c.-1787_*5293del Assoc w R
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 761100 c.1296_1304delATTCATGGA disruptive_inframe_deletion 0.97 rifampicin Assoc w R
rifampicin Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2283387 c.-1787_*5293del transcript_ablation 0.93 pyrazinamide 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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.12 ethionamide Not assoc w R
isoniazid Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 1.0 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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2783873 p.Pro57Leu missense_variant 0.99 ethambutol Uncertain significance
moxifloxacin
streptomycin Uncertain significance
levofloxacin
kanamycin
rifampicin Uncertain significance
amikacin
Rv2681 2998044 p.Asp436Asn missense_variant 0.99 capreomycin
Rv2752c 3066099 p.Met31Ile missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.99 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878641 c.-135delG upstream_gene_variant 1.0 rifampicin Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4243119 p.Trp1086* stop_gained 0.99 ethambutol
embC 4243146 c.3284A>G stop_lost&splice_region_variant 1.0 ethambutol
embA 4246508 c.3276G>A synonymous_variant 0.99 ethambutol Not assoc w R
embB 4247249 p.Gly246Arg missense_variant 0.95 ethambutol Uncertain significance
aftB 4268918 c.-82G>T upstream_gene_variant 0.97 ethambutol
ubiA 4268928 c.906C>T synonymous_variant 0.97 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.99 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407898 p.Arg102Pro missense_variant 1.0 streptomycin Uncertain significance