TB-Profiler result

Run: ERR4800390
Summary

Run ID: ERR4800390

Sample name:

Date: 01-04-2023 09:47:25

Number of reads: 3163267

Percentage reads mapped: 99.67

Strain: lineage4.3.3

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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 Euro-American (LAM) mainly-LAM None 0.97
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.98
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 0.94 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.98 isoniazid, ethionamide
inhA 1674262 p.Ile21Val missense_variant 0.97 isoniazid
pncA 2288704 p.Val180Phe missense_variant 0.99 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
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 0.99
gyrA 7585 p.Ser95Thr missense_variant 0.96
gyrA 8040 p.Gly247Ser missense_variant 0.98
gyrA 8095 p.Gly265Asp missense_variant 0.97
gyrA 9304 p.Gly668Asp missense_variant 0.97
mshA 576108 p.Ala254Gly missense_variant 0.17
rpoC 764918 p.Val517Leu missense_variant 0.98
rpoC 764995 c.1626C>G synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834346 p.Arg269Cys missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3066313 c.-122T>G upstream_gene_variant 0.98
thyA 3073868 p.Thr202Ala missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.96
clpC1 4038287 c.2418C>T synonymous_variant 0.99
embC 4242182 p.Ala774Ser missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338280 c.241dupA frameshift_variant 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 0.99
gid 4408156 p.Leu16Arg missense_variant 0.89