TB-Profiler result

Run: SRR28393525
Summary

Run ID: SRR28393525

Sample name:

Date: 2024-10-04T17:19:44.045795

Number of reads: 19500191

Percentage reads mapped: 99.58

Median coverage: 570.0

Strain: lineage4.1.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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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 0.3
lineage4.1 Euro-American None 0.66
lineage4.1.2 Euro-American None 0.65
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.65
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.31
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Tyr319Ser Assoc w R
pyrazinamide pncA p.Gln10Arg Assoc w R
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
rpoB 761110 p.Asp435Val missense_variant 0.28 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.24 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Arg missense_variant 0.28 pyrazinamide Assoc w R
embB 4247469 p.Tyr319Ser missense_variant 0.32 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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.3 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 13783 c.-225T>A upstream_gene_variant 0.68 isoniazid
fgd1 491591 p.Lys270Met missense_variant 0.65 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.61 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.68 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.68 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.31 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.66 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 781276 c.-284A>C upstream_gene_variant 0.63 streptomycin
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
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.33 pyrazinamide Uncertain significance
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
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 0.67 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.33 isoniazid
Rv2477c 2783921 p.Gly41Glu missense_variant 0.33 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2477c 2784613 c.-571T>C upstream_gene_variant 0.26 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.13 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.15 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.13 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.29 para-aminosalicylic_acid
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
clpC1 4038287 c.2418C>T synonymous_variant 0.32 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.68 ethambutol Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.31 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.67 ethambutol Not assoc w R
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
gid 4408156 p.Leu16Arg missense_variant 0.32 streptomycin Not assoc w R