TB-Profiler result

Run: SRR24255983
Summary

Run ID: SRR24255983

Sample name:

Date: 20-03-2024 12:23:17

Number of reads: 3253616

Percentage reads mapped: 99.5

Strain: lineage4.2.1.1

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.Asp435Val (0.86)
Isoniazid R fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-12C>T (0.12), embB p.Gly406Ser (0.96)
Pyrazinamide R pncA p.Ser32Ile (0.94)
Streptomycin R rpsL p.Lys88Arg (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1401A>G (0.91)
Amikacin R rrs n.1401A>G (0.91)
Capreomycin R rrs n.1401A>G (0.91)
Kanamycin R rrs n.1401A>G (0.91)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
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 0.99
lineage4.2 Euro-American H;T;LAM None 0.92
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.06
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.91
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.92
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 761110 p.Asp435Val missense_variant 0.86 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.91 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289147 p.Ser32Ile missense_variant 0.94 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.12 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.96 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.11
rpoC 766645 p.Glu1092Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776802 p.Met560Thr missense_variant 0.97
mmpL5 777451 p.Val344Leu missense_variant 0.85
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 2169879 p.Phe245Cys missense_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065958 c.234G>A synonymous_variant 0.96
ald 3086742 c.-78A>C upstream_gene_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.19
ddn 3987092 p.Glu83Asp missense_variant 0.9
clpC1 4040786 c.-82G>A upstream_gene_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 0.85
embA 4243460 c.228C>T synonymous_variant 0.11
ethA 4327529 c.-56T>G upstream_gene_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 0.97