TB-Profiler result

Run: ERR4553515
Summary

Run ID: ERR4553515

Sample name:

Date: 01-04-2023 06:12:07

Number of reads: 1213963

Percentage reads mapped: 99.7

Strain: lineage4

Drug-resistance: MDR-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
rpoB 761089 p.Ser428Thr missense_variant 1.0 rifampicin
rpoB 761140 p.His445Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 1.0
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 0.3
rpoB 759628 c.-179C>T upstream_gene_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
rrl 1475228 n.1571A>G non_coding_transcript_exon_variant 0.14
inhA 1673393 c.-809G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168498 c.2115G>C synonymous_variant 0.14
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 0.29
fbiD 3339744 c.627A>T synonymous_variant 0.38
fprA 3474299 p.Asp98Gly missense_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.67
panD 4043957 p.Asp109Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248441 p.Thr643Ile missense_variant 1.0
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0