TB-Profiler result

Run: ERR3273089
Summary

Run ID: ERR3273089

Sample name:

Date: 01-04-2023 01:10:41

Number of reads: 2985642

Percentage reads mapped: 99.36

Strain: lineage4.5

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
lineage4.5 Euro-American H;T RD122 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2154973 p.Thr380Ile missense_variant 1.0 isoniazid
pncA 2288869 p.Val125Phe missense_variant 0.22 pyrazinamide
pncA 2288934 p.Tyr103Cys missense_variant 0.17 pyrazinamide
pncA 2289114 p.His43Pro missense_variant 0.45 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 0.64 isoniazid
embB 4247429 p.Met306Val 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoC 766485 p.Val1039Ala missense_variant 0.21
rpoC 766789 c.3420G>A synonymous_variant 0.98
rpoC 766825 p.Lys1152Asn missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472176 n.331G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154047 p.Trp689Gly missense_variant 1.0
katG 2156199 c.-88G>A upstream_gene_variant 0.99
katG 2156258 c.-148_-147insA upstream_gene_variant 0.99
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859673 p.Ile249Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878333 p.Val59Leu missense_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 0.98
clpC1 4038318 p.Pro796Leu missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269284 p.Ser184Ala missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407766 p.Thr146Lys missense_variant 0.17