TB-Profiler result

Run: ERR4553841
Summary

Run ID: ERR4553841

Sample name:

Date: 01-04-2023 06:22:33

Number of reads: 2013626

Percentage reads mapped: 99.76

Strain: lineage4

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
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
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
gyrB 6061 p.Ser274Arg missense_variant 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.33
rpoB 759628 c.-179C>T upstream_gene_variant 1.0
rpoC 764673 p.Gln435Pro missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407255 p.Ala29Glu missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673393 c.-809G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169779 c.834A>C synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289256 c.-15A>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.38
fprA 3474299 p.Asp98Gly missense_variant 1.0
panD 4043957 p.Asp109Asn missense_variant 0.98
embC 4240409 p.Pro183Ala missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269311 p.Trp175Gly missense_variant 1.0
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0