TB-Profiler result

Run: SRR1175470
Summary

Run ID: SRR1175470

Sample name:

Date: 21-10-2023 10:14:49

Number of reads: 13562011

Percentage reads mapped: 99.01

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.Val170Phe (1.00), rpoB p.His445Tyr (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Ala146Val (1.00)
Streptomycin R gid p.Gln125* (1.00)
Fluoroquinolones R gyrB p.Asn499Thr (0.15), gyrA p.Ala90Val (0.87)
Moxifloxacin R gyrB p.Asn499Thr (0.15), gyrA p.Ala90Val (0.87)
Ofloxacin R gyrB p.Asn499Thr (0.15), gyrA p.Ala90Val (0.87)
Levofloxacin R gyrB p.Asn499Thr (0.15), gyrA p.Ala90Val (0.87)
Ciprofloxacin R gyrB p.Asn499Thr (0.15), gyrA p.Ala90Val (0.87)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine R ald c.130dupG (1.00)
Ethionamide R fabG1 c.-15C>T (1.00), ethA c.791_792dupTC (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 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
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
gyrB 6735 p.Asn499Thr missense_variant 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.87 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Val missense_variant 1.0 pyrazinamide
ald 3086947 c.130dupG frameshift_variant 1.0 cycloserine
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326681 c.791_792dupTC frameshift_variant 1.0 ethionamide
gid 4407830 p.Gln125* stop_gained 1.0 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 0.99
rpoC 765008 p.Leu547Val missense_variant 1.0
rpoC 766085 p.Pro906Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460992 c.-53A>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 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448500 c.-3_*1408del transcript_ablation 1.0