TB-Profiler result

Run: SRR15316025
Summary

Run ID: SRR15316025

Sample name:

Date: 2024-10-05T00:56:30.579317

Number of reads: 6109418

Percentage reads mapped: 99.56

Median coverage: 185.0

Strain: lineage4.5

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
lineage4.5 Euro-American RD122 1.0
lineage4 Euro-American None 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 p.His445Asp Assoc w R
isoniazid katG p.Ser315Gly Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin rrs n.514A>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Ser91Pro Assoc w R
p.Asp94Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1307delC 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
gyrA 7570 p.Ala90Val missense_variant 1.0 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 7572 p.Ser91Pro missense_variant 0.51 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 7581 p.Asp94Asn missense_variant 0.3 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin Assoc w R
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 0.99 streptomycin Uncertain significance Mutation from literature
katG 2155167 p.Ser315Gly missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol Assoc w R
ethA 4326166 c.1307delC frameshift_variant 0.98 ethionamide 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 7892 c.591G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13572 c.-14G>T upstream_gene_variant 1.0 isoniazid
ccsA 620029 c.139C>T synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620566 p.Asp226Asn missense_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
Rv0565c 657057 p.Phe138Leu missense_variant 0.98 ethionamide
rpoB 759648 c.-159_-158insT upstream_gene_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777254 c.1227G>A synonymous_variant 0.99 bedaquiline
clofazimine
mmpL5 777640 c.832_840dupGCCATCTTC conservative_inframe_insertion 0.99 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Not assoc w R
rplC 800678 c.-131C>T upstream_gene_variant 0.98 linezolid
rplC 801053 p.Ala82Gly missense_variant 0.99 linezolid
Rv1129c 1254133 c.387_401dupCGCCACCGAGGAACT disruptive_inframe_insertion 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
embR 1417934 c.-587C>T upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
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
bacA 2063157 c.1572C>T synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin
amikacin Not assoc w R - Interim
katG 2155142 p.Thr324Ala missense_variant 0.99 isoniazid
PPE35 2170568 p.Ile15Met missense_variant 1.0 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
pncA 2288860 p.Val128Phe missense_variant 0.99 pyrazinamide
ahpC 2726146 c.-47_-46insT upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv3236c 3613591 c.-475G>C upstream_gene_variant 1.0 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.99 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248004 p.Gln497His missense_variant 0.99 ethambutol Uncertain significance
embB 4248548 p.Ala679Thr missense_variant 0.99 ethambutol Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin