TB-Profiler result

Run: ERR11082702
Summary

Run ID: ERR11082702

Sample name:

Date: 11-04-2023 02:35:30

Number of reads: 8019389

Percentage reads mapped: 99.65

Strain: lineage4.8

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
Rifampicin R rpoB p.His445Tyr (1.00)
Isoniazid R fabG1 c.-17G>T (1.00), fabG1 c.-15C>T (1.00), ahpC c.-48G>A (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide
Streptomycin R rrs n.514A>C (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-17G>T (1.00), fabG1 c.-15C>T (1.00)
Clofazimine
Para-aminosalicylic_acid R folC p.Ile43Ser (1.00)
Delamanid
Bedaquiline
Linezolid
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
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
folC 2747471 p.Ile43Ser missense_variant 1.0 para-aminosalicylic_acid
embB 4247431 p.Met306Ile 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
gyrB 5078 c.-162_-161insG upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.32
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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154334 p.Gly593Ser missense_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.17
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
rpoA 3878618 c.-111A>C upstream_gene_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.41
ubiA 4269864 c.-31C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0