TB-Profiler result

Run: ERR4812962
Summary

Run ID: ERR4812962

Sample name:

Date: 01-04-2023 12:26:45

Number of reads: 261654

Percentage reads mapped: 95.83

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.99
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2289090 p.His51Arg missense_variant 1.0 pyrazinamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760749 p.Gly315Arg missense_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777793 p.Ala230Ser missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472463 n.618G>T non_coding_transcript_exon_variant 0.25
rrl 1474092 n.435G>A non_coding_transcript_exon_variant 0.22
rpsA 1834683 p.Ala381Val missense_variant 1.0
tlyA 1917890 c.-50C>A upstream_gene_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102987 p.Ile19Thr missense_variant 0.25
Rv1979c 2222319 c.846C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519111 p.Gln333* stop_gained 0.22
pepQ 2859649 p.Gln257Arg missense_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074330 p.Lys48Glu missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239764 c.-99G>T upstream_gene_variant 0.33
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407768 p.Leu145Phe missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0