TB-Profiler result

Run: SRR28498635
Summary

Run ID: SRR28498635

Sample name:

Date: 2024-10-04T01:17:22.413647

Number of reads: 3380952

Percentage reads mapped: 99.59

Median coverage: 91.0

Strain: lineage4.3.4.1;lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.24
lineage4.3.4.1 Euro-American (LAM) RD174 0.21
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.78
lineage4.3.4 Euro-American (LAM) RD174 0.23
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
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
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 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.19 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13310 c.249T>C synonymous_variant 0.77 isoniazid Not assoc w R - Interim
fgd1 491424 c.650_655delCCGCTG disruptive_inframe_deletion 0.72 pretomanid
delamanid
clofazimine
mshA 575915 p.Asp190Asn missense_variant 0.82 isoniazid Uncertain significance
ethionamide Uncertain significance
rpoC 763783 c.414G>A synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.26 rifampicin Not assoc w R
rpoC 765325 c.1956C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 778965 c.-485G>T upstream_gene_variant 0.8 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 0.22 pyrazinamide 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 0.78 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.18 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168147 p.Pro822Ser missense_variant 0.23 pyrazinamide Not assoc w R
Rv1979c 2223123 c.42G>A synonymous_variant 0.22 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2746540 c.1059G>A synonymous_variant 0.26 para-aminosalicylic_acid
Rv2477c 2784541 c.-499G>A upstream_gene_variant 0.76 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.68 capreomycin
Rv2681 2996821 p.Gly28Ala missense_variant 0.25 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.27 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.21 cycloserine
Rv3083 3448322 c.-182G>A upstream_gene_variant 0.77 ethionamide
Rv3236c 3612009 p.Ala370Thr missense_variant 0.28 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.17 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840710 c.711A>G synonymous_variant 0.21 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.18 pyrazinamide Not assoc w R
embC 4240373 c.511C>T synonymous_variant 0.84 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246904 p.Val131Met missense_variant 0.79 ethambutol Uncertain significance
whiB6 4338550 c.-29A>T upstream_gene_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin 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 0.27 kanamycin
capreomycin
amikacin
whiB6 4338735 c.-214C>G upstream_gene_variant 0.27 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.2 streptomycin Not assoc w R