TB-Profiler result

Run: SRR5341216
Summary

Run ID: SRR5341216

Sample name:

Date: 21-10-2023 01:28:11

Number of reads: 1260039

Percentage reads mapped: 99.28

Strain: lineage4.1.2;lineage3

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (0.63)
Ethambutol
Pyrazinamide
Streptomycin R gid c.102delG (0.66)
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
lineage3 East-African-Indian CAS RD750 0.3
lineage4 Euro-American LAM;T;S;X;H None 0.68
lineage4.1 Euro-American T;X;H None 0.59
lineage4.1.2 Euro-American T;H None 0.66
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
katG 2155168 p.Ser315Thr missense_variant 0.63 isoniazid
gid 4408100 c.102delG frameshift_variant 0.66 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.63
rpoB 760115 c.309C>T synonymous_variant 0.71
rpoB 761421 p.Asn539His missense_variant 0.28
rpoC 763031 c.-339T>C upstream_gene_variant 0.34
rpoC 764263 c.894G>A synonymous_variant 0.48
rpoC 765150 p.Gly594Glu missense_variant 0.6
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.37
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.48
PPE35 2170048 p.Leu189Val missense_variant 0.61
PPE35 2170053 p.Thr187Ser missense_variant 0.58
Rv1979c 2221988 p.Leu393Ile missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.52
thyX 3067423 c.523C>T synonymous_variant 0.36
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449566 p.Gly355Arg missense_variant 0.77
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.96
embC 4242075 p.Arg738Gln missense_variant 0.29
embC 4242329 p.Glu823Lys missense_variant 0.75
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.82
ethA 4327728 c.-255C>T upstream_gene_variant 0.58
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.38