TB-Profiler result

Run: SRR23861971
Summary

Run ID: SRR23861971

Sample name:

Date: 12-04-2023 12:53:19

Number of reads: 4672253

Percentage reads mapped: 99.69

Strain: lineage4.8

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 inhA p.Ser94Ala (1.00)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrB p.Asp461Asn (0.30), gyrB p.Asn499Thr (0.56)
Moxifloxacin R gyrB p.Asp461Asn (0.30), gyrB p.Asn499Thr (0.56)
Ofloxacin R gyrB p.Asp461Asn (0.30), gyrB p.Asn499Thr (0.56)
Levofloxacin R gyrB p.Asp461Asn (0.30), gyrB p.Asn499Thr (0.56)
Ciprofloxacin R gyrB p.Asp461Asn (0.30), gyrB p.Asn499Thr (0.56)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R inhA p.Ser94Ala (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 6620 p.Asp461Asn missense_variant 0.3 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrB 6735 p.Asn499Thr missense_variant 0.56 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
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
mshA 576093 p.Pro249Arg missense_variant 0.17
mshA 576100 p.Asp251Glu missense_variant 0.17
mshA 576101 p.Arg252Gly missense_variant 0.17
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 0.99
rrs 1471786 n.-60T>G upstream_gene_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568416 p.Lys88His missense_variant 0.14
whiB7 3568428 c.252A>C synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247395 c.882C>T synonymous_variant 1.0
embB 4247965 c.1452C>T synonymous_variant 1.0
ethR 4328030 p.Ala161Gly missense_variant 0.18
ethR 4328045 p.Leu166Gln missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0