TB-Profiler result

Run: ERR4813120
Summary

Run ID: ERR4813120

Sample name:

Date: 2024-10-04T17:48:28.947301

Number of reads: 3040675

Percentage reads mapped: 99.64

Median coverage: 98.0

Strain: lineage4.1.1;lineage4.3.2

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
lineage4.3 Euro-American (LAM) None 0.26
lineage4.3.2 Euro-American (LAM) None 0.27
lineage4.1 Euro-American None 0.77
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.73
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Pro Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Asp354Ala Assoc w R
pyrazinamide pncA p.Thr160Pro Assoc w R
p.Gln10Pro Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
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.Asp94Asn missense_variant 0.72 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761101 p.Gln432Pro missense_variant 0.29 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.68 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.75 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288764 p.Thr160Pro missense_variant 0.27 pyrazinamide Assoc w R
pncA 2289213 p.Gln10Pro missense_variant 0.7 pyrazinamide Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.76 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
gyrB 6052 p.Ile271Met missense_variant 0.7 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7221 p.Ser661Thr missense_variant 0.74 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
Rv0565c 657269 p.Ser68Pro missense_variant 0.76 ethionamide Uncertain significance
nusG 734420 p.Ala56Val missense_variant 0.3 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.25 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.74 rifampicin Not assoc w R
rpoC 765926 p.Thr853Ala missense_variant 0.34 rifampicin Uncertain significance
rpoC 767058 p.Thr1230Ile missense_variant 0.72 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 0.71 linezolid
embR 1416699 p.Leu217Val missense_variant 0.69 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.23 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
inhA 1673865 c.-337C>T upstream_gene_variant 0.64 isoniazid Uncertain significance
ethionamide 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
eis 2715727 c.-395G>A upstream_gene_variant 0.34 kanamycin
amikacin
Rv2752c 3066898 c.-707C>T upstream_gene_variant 0.73 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyA 3073868 p.Thr202Ala missense_variant 0.25 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 0.78 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.24 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.76 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.7 ethambutol Not assoc w R
ethA 4326900 p.Pro192Ser missense_variant 0.75 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 4407721 p.Ala161Gly missense_variant 0.24 streptomycin Uncertain significance
gid 4407980 p.Pro75Ser missense_variant 0.67 streptomycin Uncertain significance
gid 4408050 p.Asn51Lys missense_variant 0.33 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.39 streptomycin Not assoc w R