TB-Profiler result

Run: SRR23861930

Summary

Run ID: SRR23861930

Sample name:

Date: 12-04-2023 10:46:39

Number of reads: 4794904

Percentage reads mapped: 99.67

Strain: lineage4.8

Drug-resistance: RR-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.Leu430Pro (1.00)
Isoniazid
Ethambutol
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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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
mshA 576113 p.Arg256Gly missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778107 p.Ser125Cys 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568416 p.Lys88Asn missense_variant 0.14
whiB7 3568428 c.252A>C synonymous_variant 0.14
clpC1 4040235 p.Gly157Ala missense_variant 0.18
clpC1 4040249 p.Glu152Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246542 p.Ser10Thr missense_variant 0.17
embB 4246552 p.Asn13Lys missense_variant 0.21
embB 4246574 p.Ala21Trp missense_variant 0.14
ethA 4328025 c.-552T>A upstream_gene_variant 0.15
ethR 4328030 p.Ala161Gly missense_variant 0.14
ethA 4328378 c.-905G>C upstream_gene_variant 0.98
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0
whiB6 4337088 c.-187_*1082del transcript_ablation 1.0