TB-Profiler result

Run: SRR7829587
Summary

Run ID: SRR7829587

Sample name:

Date: 2024-10-04T17:06:21.832713

Number of reads: 3686752

Percentage reads mapped: 95.66

Median coverage: 104.0

Strain: lineage4.1.2

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
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 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.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Glu405Asp Uncertain significance Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys88Gln Assoc w R - Interim
fluoroquinolones
moxifloxacin gyrA p.Asp94Tyr Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Tyr Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>T Assoc w R - Interim
capreomycin rrs n.1402C>T Assoc w R
kanamycin rrs n.1402C>T Assoc w R - Interim
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 7581 p.Asp94Tyr missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781821 p.Lys88Gln missense_variant 1.0 streptomycin Assoc w R - Interim
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 1.0 amikacin Assoc w R - Interim
capreomycin Assoc w R
kanamycin Assoc w R - Interim
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247728 p.Glu405Asp missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
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 7323 p.Pro8Ala missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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
Rv0010c 13625 c.-67T>C upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
Rv0565c 656832 c.639G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_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 776659 p.Asp608Asn missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
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
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
PPE35 2168501 p.Phe704Leu missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
Rv2680 2996136 p.Ser11Asn missense_variant 0.13 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625581 c.1033C>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4247121 p.Ser203Leu missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269088 p.Ala249Val missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269341 p.Gly165Ser missense_variant 1.0 ethambutol Uncertain significance
ethA 4327307 p.Asp56Ala missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin