TB-Profiler result

Run: SRR5341329

Summary

Run ID: SRR5341329

Sample name:

Date: 20-10-2023 18:48:11

Number of reads: 5766712

Percentage reads mapped: 97.86

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.Leu452Pro (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Ala146Glu (0.31), pncA c.390_391dupGG (0.18), pncA c.390_391dupGG (0.18), pncA p.Trp68Gly (0.15)
Streptomycin R rpsL p.Lys43Arg (0.98)
Fluoroquinolones R gyrB p.Asn499Lys (1.00)
Moxifloxacin R gyrB p.Asn499Lys (1.00)
Ofloxacin R gyrB p.Asn499Lys (1.00)
Levofloxacin R gyrB p.Asn499Lys (1.00)
Ciprofloxacin R gyrB p.Asn499Lys (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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 6736 p.Asn499Lys missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Glu missense_variant 0.31 pyrazinamide
pncA 2288850 c.390_391dupGG frameshift_variant 0.18 pyrazinamide, pyrazinamide
pncA 2289040 p.Trp68Gly missense_variant 0.15 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 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
rplC 801021 c.213C>T synonymous_variant 0.86
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 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064537 p.Val552Gly missense_variant 1.0
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326842 p.Tyr211Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0