TB-Profiler result

Run: ERR4822359

Summary

Run ID: ERR4822359

Sample name:

Date: 01-04-2023 17:49:37

Number of reads: 2955815

Percentage reads mapped: 99.76

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155169 p.Ser315Arg missense_variant 1.0 isoniazid
ahpC 2726136 c.-57C>T upstream_gene_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
ethA 4326994 c.479delC frameshift_variant 1.0 ethionamide, ethionamide
pncA 2287402 c.414_*1278del frameshift_variant&stop_lost&splice_region_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
gyrB 6677 p.Pro480Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 760574 c.768G>C synonymous_variant 1.0
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 1471861 n.16T>C non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067959 c.-14C>G upstream_gene_variant 1.0
thyA 3074159 c.312delA frameshift_variant 1.0
fbiA 3640354 c.-189C>G upstream_gene_variant 1.0
embC 4240394 p.Glu178Lys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408105 c.80_97delCGGGACCCGGTGTGGAGC disruptive_inframe_deletion 1.0