TB-Profiler result

Run: SRR22461581
Summary

Run ID: SRR22461581

Sample name:

Date: 2024-10-04T10:22:59.489104

Number of reads: 1877097

Percentage reads mapped: 99.56

Median coverage: 63.0

Strain: lineage4.1.1;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 0.19
lineage4.1 Euro-American None 0.79
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.82
lineage4.3.3 Euro-American (LAM) RD115 0.24
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
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Tyr319Ser Assoc w R
p.Asp354Ala Assoc w R
pyrazinamide pncA p.Gln10Arg Assoc w R
p.Gln10Pro Assoc w R
streptomycin gid p.Pro84Leu Assoc w R - Interim
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 0.25 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.6 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Arg missense_variant 0.27 pyrazinamide Assoc w R
pncA 2289213 p.Gln10Pro missense_variant 0.73 pyrazinamide Assoc w R
embB 4247469 p.Tyr319Ser missense_variant 0.3 ethambutol Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.72 ethambutol Assoc w R
gid 4407952 p.Pro84Leu missense_variant 0.23 streptomycin Assoc w R - Interim
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
gyrB 6052 p.Ile271Met missense_variant 0.94 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7221 p.Ser661Thr missense_variant 0.78 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 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
Rv0565c 657269 p.Ser68Pro missense_variant 0.71 ethionamide Uncertain significance
rpoB 762064 p.Ala753Val missense_variant 0.72 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.2 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.81 rifampicin Not assoc w R
rpoC 767058 p.Thr1230Ile missense_variant 0.87 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.88 linezolid
embR 1416699 p.Leu217Val missense_variant 0.78 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673380 c.-822C>G upstream_gene_variant 0.14 isoniazid
ethionamide
inhA 1673865 c.-337C>T upstream_gene_variant 0.72 isoniazid Uncertain significance
ethionamide Uncertain significance
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.42 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
PPE35 2168998 p.Ile539Val missense_variant 0.24 pyrazinamide Uncertain significance
PPE35 2169725 c.888T>C synonymous_variant 0.17 pyrazinamide
PPE35 2169748 p.Ile289Phe missense_variant 0.14 pyrazinamide
PPE35 2169754 p.Phe287Ile missense_variant 0.12 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3066898 c.-707C>T upstream_gene_variant 0.73 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyA 3073868 p.Thr202Ala missense_variant 0.21 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
mtrA 3627511 c.-162C>G upstream_gene_variant 0.67 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.19 pyrazinamide Not assoc w R
clpC1 4039829 p.Leu292Ile missense_variant 0.15 pyrazinamide
embC 4242182 p.Ala774Ser missense_variant 0.38 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 0.78 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.82 ethambutol Not assoc w R
ethA 4326900 p.Pro192Ser missense_variant 0.82 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
gid 4407980 p.Pro75Ser missense_variant 0.7 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.2 streptomycin Not assoc w R