TB-Profiler result

Run: SAMEA5570051
Summary

Run ID: SAMEA5570051

Sample name:

Date: 2024-04-15T08:49:14.575774

Number of reads: 9765165

Percentage reads mapped: 99.74

Median coverage: 282.0

Strain: lineage4.1.1.3;lineage4.3.4.2

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 0.54
lineage4.1 Euro-American None 0.45
lineage4.1.1.3 Euro-American (X-type) RD193 0.45
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.45
lineage4.3.4 Euro-American (LAM) RD174 0.58
lineage4.3.4.2 Euro-American (LAM) RD174 0.56
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.Met306Ile Assoc w R
p.Gly406Ala Assoc w R
pyrazinamide pncA p.Leu120Pro Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly 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 ald c.992dupC Mutation from literature
ethionamide ethA c.1290delC Assoc w R
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 7582 p.Asp94Gly missense_variant 0.43 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.4 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 2288883 p.Leu120Pro missense_variant 0.44 pyrazinamide Assoc w R
ald 3087810 c.992dupC frameshift_variant 0.41 cycloserine Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.56 ethambutol Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.42 ethambutol Assoc w R
ethA 4326183 c.1290delC frameshift_variant 0.45 ethionamide 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 6140 p.Val301Leu missense_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 13452 p.Gly36Val missense_variant 0.44 isoniazid Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.51 ethionamide Uncertain significance
rpoC 764817 p.Val483Ala missense_variant 0.49 rifampicin Uncertain significance
rpoC 764918 p.Val517Leu missense_variant 0.49 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.49 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.47 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.44 linezolid
fbiC 1302954 c.24G>A synonymous_variant 0.43 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833469 c.-73G>T upstream_gene_variant 0.58 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
katG 2154678 c.1434G>C synonymous_variant 0.41 isoniazid Not assoc w R - Interim
PPE35 2169405 p.Asn403Ser missense_variant 0.43 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726409 p.Asp73His missense_variant 0.43 isoniazid Uncertain significance
ribD 2986827 c.-12G>A upstream_gene_variant 0.43 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.57 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449437 c.936_942delCGCGGCG frameshift_variant 0.42 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.7 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.75 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.61 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 0.47 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.46 ethambutol Not assoc w R
embB 4249678 c.3165C>A synonymous_variant 0.48 ethambutol Not assoc w R - Interim
whiB6 4338247 p.Leu92Ser missense_variant 0.48 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407934 p.Leu90Arg missense_variant 0.41 streptomycin Uncertain significance
gid 4407970 p.Pro78Leu missense_variant 0.58 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.59 streptomycin Not assoc w R