TB-Profiler result

Run: SRR25827478
Summary

Run ID: SRR25827478

Sample name:

Date: 15-03-2024 16:27:12

Number of reads: 26986684

Percentage reads mapped: 99.02

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 c.1312_1314delAAC (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embA c.-16C>T (1.00)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
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 761114 c.1312_1314delAAC conservative_inframe_deletion 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_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
rpoB 760848 p.Thr348Pro missense_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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169085 p.Ser510Ala missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288835 p.Asp136Ala missense_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
rpoA 3878614 c.-107A>C upstream_gene_variant 0.14
rpoA 3878618 c.-111A>C upstream_gene_variant 0.14
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.22
embB 4247033 p.Ser174Arg missense_variant 0.14
embB 4247039 p.Phe176Val missense_variant 0.16
embB 4247873 p.Ala454Thr missense_variant 0.82
ubiA 4269317 p.Ser173Ala missense_variant 0.85
whiB6 4338595 c.-75delG upstream_gene_variant 1.0