TB-Profiler result

Run: ERR11775987
Summary

Run ID: ERR11775987

Sample name:

Date: 2024-05-22T18:19:57.758328

Number of reads: 6667408

Percentage reads mapped: 99.57

Median coverage: 210.0

Strain: lineage4.1.2.1;lineage4.3.4.1

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 0.13
lineage4.1 Euro-American None 0.85
lineage4.1.2 Euro-American None 0.86
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.87
lineage4.3.4.1 Euro-American (LAM) RD174 0.12
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.16
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8715 p.Pro472Ser missense_variant 0.13 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13367 c.192C>T synonymous_variant 0.15 isoniazid Not assoc w R - Interim
fgd1 491591 p.Lys270Met missense_variant 0.87 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.85 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.86 ethionamide Uncertain significance
rpoB 759608 c.-199C>T upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.18 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.88 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
sigE 1364434 p.Arg8Trp missense_variant 0.13 pyrazinamide Not assoc w R
Rv1258c 1407586 c.-246G>A upstream_gene_variant 0.9 streptomycin
isoniazid
pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.82 isoniazid
ahpC 2726323 p.Pro44Arg missense_variant 0.16 isoniazid Uncertain significance
pepQ 2859830 p.Gly197Arg missense_variant 0.19 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.12 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.12 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.18 capreomycin
Rv2752c 3066299 c.-108C>T upstream_gene_variant 0.86 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.13 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448598 p.Ile32Thr missense_variant 0.16 ethionamide Uncertain significance
Rv3236c 3612768 p.Ala117Pro missense_variant 0.14 pyrazinamide Uncertain significance
lpqB 3624392 c.519C>T synonymous_variant 0.85 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627756 c.-407A>T upstream_gene_variant 0.83 bedaquiline
rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.13 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.93 ethambutol Not assoc w R
embC 4240682 p.Asp274Asn missense_variant 0.87 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.88 ethambutol Not assoc w R
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 4408156 p.Leu16Arg missense_variant 0.17 streptomycin Not assoc w R