TB-Profiler result

Run: SRR25827342
Summary

Run ID: SRR25827342

Sample name:

Date: 2024-10-05T12:07:01.873713

Number of reads: 16136543

Percentage reads mapped: 99.48

Median coverage: 454.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Pre-XDR-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 0.92
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
rpoC p.Asp747Ala Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA p.Thr76Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Gly88Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Gly88Ala Assoc w R - Interim
p.Asp94Gly Assoc w R
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
gyrA 7564 p.Gly88Ala missense_variant 0.88 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.11 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoC 765609 p.Asp747Ala missense_variant 0.87 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.95 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R High-level resistance
pncA 2289016 p.Thr76Pro missense_variant 0.87 pyrazinamide Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.94 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
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.92 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.9 rifampicin Not assoc w R
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.91 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.11 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.88 pyrazinamide 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.91 capreomycin
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.93 pyrazinamide Not assoc w R
rpoA 3878619 c.-112A>C upstream_gene_variant 0.14 rifampicin
clpC1 4039729 p.Asp326Asn missense_variant 0.91 pyrazinamide Not assoc w R
embC 4240054 c.192C>T synonymous_variant 0.85 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.29 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.2 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.19 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.18 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.23 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.18 ethambutol Not assoc w R - Interim
embB 4247028 p.Leu172Arg missense_variant 0.17 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.11 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R