TB-Profiler result

Run: SRR25827460
Summary

Run ID: SRR25827460

Sample name:

Date: 02-02-2024 04:28:53

Number of reads: 10147903

Percentage reads mapped: 98.63

Strain: lineage4.8

Drug-resistance: Pre-XDR-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.His445Leu (0.90)
Isoniazid R fabG1 c.-15C>T (0.89), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Asp328Tyr (0.93)
Pyrazinamide R pncA c.104delT (0.89)
Streptomycin R rpsL p.Lys43Arg (0.95)
Fluoroquinolones R gyrA p.Ala90Val (0.90)
Moxifloxacin R gyrA p.Ala90Val (0.90)
Ofloxacin R gyrA p.Ala90Val (0.90)
Levofloxacin R gyrA p.Ala90Val (0.90)
Ciprofloxacin R gyrA p.Ala90Val (0.90)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.89)
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 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
gyrA 7570 p.Ala90Val missense_variant 0.9 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Leu missense_variant 0.9 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.95 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.89 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289137 c.104delT frameshift_variant 0.89 pyrazinamide
embB 4247495 p.Asp328Tyr missense_variant 0.93 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
mmpL5 775639 p.Ile948Val 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 0.94
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.91
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747481 p.Glu40Lys missense_variant 0.91
Rv3083 3448693 p.Tyr64Asp missense_variant 0.94
clpC1 4039729 p.Asp326Asn missense_variant 0.92
embC 4240061 p.Phe67Val missense_variant 0.93
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247015 p.Ser168Ala missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.14