TB-Profiler result

Run: SRR24256314
Summary

Run ID: SRR24256314

Sample name:

Date: 04-02-2024 21:03:00

Number of reads: 4622075

Percentage reads mapped: 99.72

Strain: lineage4.3.3;lineage2.2.1

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.Ser450Leu (0.89)
Isoniazid R fabG1 c.-15C>T (0.97), katG p.Ser315Thr (0.93)
Ethambutol R embB p.Tyr319Ser (0.92)
Pyrazinamide R pncA c.233dupG (0.91), pncA c.233dupG (0.91)
Streptomycin R rrs n.514A>C (0.88)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.97)
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 0.11
lineage4 Euro-American LAM;T;S;X;H None 0.92
lineage4.3 Euro-American (LAM) mainly-LAM None 0.93
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.09
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.08
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.91
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 761155 p.Ser450Leu missense_variant 0.89 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.88 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.97 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.93 isoniazid
pncA 2289008 c.233dupG frameshift_variant 0.91 pyrazinamide, pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.92 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 8040 p.Gly247Ser missense_variant 0.87
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.12
rpoB 761998 p.Leu731Pro missense_variant 0.92
rpoC 764995 c.1626C>G synonymous_variant 0.93
rpoC 766645 p.Glu1092Asp missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.93
fbiC 1304962 p.Trp678Gly missense_variant 0.88
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.19
katG 2156196 c.-85C>T upstream_gene_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.93
folC 2746340 p.Ala420Val missense_variant 0.95
ribD 2986827 c.-12G>A upstream_gene_variant 0.92
thyA 3073868 p.Thr202Ala missense_variant 0.9
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.89
clpC1 4038968 c.1737G>A synonymous_variant 0.9
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.11
gid 4407927 p.Glu92Asp missense_variant 0.11
gid 4408156 p.Leu16Arg missense_variant 0.85
gid 4408325 c.-123C>A upstream_gene_variant 0.84