TB-Profiler result

Run: SRR24256301
Summary

Run ID: SRR24256301

Sample name:

Date: 04-02-2024 20:51:29

Number of reads: 3017999

Percentage reads mapped: 99.67

Strain: lineage4.8;lineage2.2.1

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.13)
Fluoroquinolones R gyrA p.Asp94Gly (0.91)
Moxifloxacin R gyrA p.Asp94Gly (0.91)
Ofloxacin R gyrA p.Asp94Gly (0.91)
Levofloxacin R gyrA p.Asp94Gly (0.91)
Ciprofloxacin R gyrA p.Asp94Gly (0.91)
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
lineage2 East-Asian Beijing RD105 0.06
lineage4 Euro-American LAM;T;S;X;H None 0.92
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.9
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.06
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 7582 p.Asp94Gly missense_variant 0.91 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpsL 781687 p.Lys43Arg missense_variant 0.13 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
fgd1 491742 c.960T>C synonymous_variant 0.19
mshA 575907 p.Ala187Val missense_variant 0.22
rpoC 766645 p.Glu1092Asp missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.1
mmpS5 779615 c.-710C>G upstream_gene_variant 0.12
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 0.89
rpsA 1834177 c.636A>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.11
PPE35 2168149 p.Pro822Ser missense_variant 0.91
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247742 p.Leu410Pro missense_variant 0.11
embB 4249354 c.2841G>C synonymous_variant 0.87
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338598 c.-77G>C upstream_gene_variant 0.92