TB-Profiler result

Run: SRR921502
Summary

Run ID: SRR921502

Sample name:

Date: 2024-04-16T04:01:39.818752

Number of reads: 6380870

Percentage reads mapped: 96.88

Median coverage: 105.0

Strain: lineage2.1;lineage2.2.1

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
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.24
lineage2.2 East-Asian (Beijing) RD105;RD207 0.25
lineage2.1 East-Asian (non-Beijing) None 0.73
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Tyr Assoc w R
isoniazid katG c.861_866delACCCGA Mutation from literature
ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol embA c.-16C>G Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
p.Glu504Asp Uncertain significance Mutation from literature
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Lys96Gln Assoc w R
p.Phe94Leu Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Asn499Thr Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA p.Ala90Val Assoc w R 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 gyrB p.Asn499Thr Assoc w R
gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA p.Lys200* Assoc w R
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
gyrB 6735 p.Asn499Thr missense_variant 0.76 levofloxacin Assoc w R
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7570 p.Ala90Val missense_variant 0.21 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.68 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Tyr missense_variant 0.84 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.73 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.3 kanamycin Assoc w R
amikacin Assoc w R
capreomycin Assoc w R
katG 2155245 c.861_866delACCCGA disruptive_inframe_deletion 0.24 isoniazid Mutation from literature
pncA 2288956 p.Lys96Gln missense_variant 0.73 pyrazinamide Assoc w R
pncA 2288962 p.Phe94Leu missense_variant 0.25 pyrazinamide Assoc w R
ahpC 2726141 c.-52C>T upstream_gene_variant 0.76 isoniazid Uncertain significance Mutation from literature
embA 4243217 c.-16C>G upstream_gene_variant 0.25 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.19 ethambutol Assoc w R
embB 4248025 p.Glu504Asp missense_variant 0.75 ethambutol Uncertain significance Mutation from literature
embB 4249583 p.Asp1024Asn missense_variant 0.74 ethambutol Uncertain significance Mutation from literature
ethA 4326876 p.Lys200* stop_gained 0.19 ethionamide Assoc w R
gid 4408100 c.102delG frameshift_variant 0.25 streptomycin 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
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575793 c.448_450dupATC conservative_inframe_insertion 0.65 ethionamide
isoniazid
mshA 575907 p.Ala187Val missense_variant 0.24 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.32 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 656356 p.Val372Asp missense_variant 0.27 ethionamide
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765121 c.1752G>A synonymous_variant 0.77 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.23 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.38 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800617 c.-192C>T upstream_gene_variant 0.74 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1304443 p.Ala505Thr missense_variant 0.71 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.16 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
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
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2154851 p.Gly421Ser missense_variant 0.74 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide 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
pncA 2289309 c.-68C>G upstream_gene_variant 0.66 pyrazinamide
Rv2477c 2783790 p.Val85Ile missense_variant 0.81 ethambutol Not assoc w R
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2680 2995875 c.-230G>C upstream_gene_variant 0.85 capreomycin
Rv2752c 3064689 c.1503C>T synonymous_variant 0.15 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3065197 p.Asp332Gly missense_variant 0.2 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv2752c 3065616 c.576C>T synonymous_variant 0.72 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.25 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.32 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640349 c.-194A>C upstream_gene_variant 0.76 clofazimine
pretomanid
delamanid
clpC1 4039502 c.1203C>T synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
clpC1 4040841 c.-138_-137delGCinsT upstream_gene_variant 0.74 pyrazinamide
clpC1 4040928 c.-224T>C upstream_gene_variant 0.23 pyrazinamide
glpK 4138392 p.Thr455Asn missense_variant 0.58 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138717 p.Glu347Gln missense_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.27 ethambutol Not assoc w R
embA 4246088 c.2856A>G synonymous_variant 0.76 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
ethA 4327208 p.Ala89Glu missense_variant 0.74 ethionamide Uncertain significance
whiB6 4338473 p.Arg17Gly missense_variant 0.27 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.2 streptomycin Not assoc w R