TB-Profiler result

Run: ERR4796343
Summary

Run ID: ERR4796343

Sample name:

Date: 01-04-2023 06:48:42

Number of reads: 3052081

Percentage reads mapped: 99.7

Strain: lineage4.8

Drug-resistance: 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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rplC 801268 p.Cys154Arg missense_variant 1.0 linezolid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288719 p.Met175Val missense_variant 1.0 pyrazinamide
embB 4249518 p.His1002Arg missense_variant 1.0 ethambutol
ethA 4326906 c.567dupG frameshift_variant 1.0 ethionamide, ethionamide
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 8176 p.Arg292Leu missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
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 1472753 n.908A>C non_coding_transcript_exon_variant 1.0
rrl 1474001 n.344C>T 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
pncA 2289969 c.-728G>C upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethR 4326844 c.-705G>C upstream_gene_variant 1.0
whiB6 4338362 p.Arg54Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408061 p.His48Asn missense_variant 1.0
Rv3083 3448498 c.-5_*1408del transcript_ablation 1.0