TB-Profiler result

Run: ERR11082913

Summary

Run ID: ERR11082913

Sample name:

Date: 11-04-2023 12:08:31

Number of reads: 4583319

Percentage reads mapped: 99.7

Strain: lineage4.8

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.Phe424Val (1.00), rpoB p.Leu430Pro (1.00), rpoB p.Ser450Trp (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide
Streptomycin R gid c.200_214delATATCGGTAGCGGAG (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine
Ethionamide R ethA p.Tyr438* (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
rpoB 761076 p.Phe424Val missense_variant 1.0 rifampicin
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpoB 761155 p.Ser450Trp missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326160 p.Tyr438* stop_gained 1.0 ethionamide
gid 4407988 c.200_214delATATCGGTAGCGGAG disruptive_inframe_deletion 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 1.0
mshA 576108 p.Ala254Gly missense_variant 0.25
rpoB 759627 c.-180A>C upstream_gene_variant 0.98
rpoC 766744 p.Gln1125His 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 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169503 c.1109delG frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289109 p.Val45Met missense_variant 1.0
Rv2752c 3067180 c.-989C>A upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.14
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243228 c.-5G>A upstream_gene_variant 1.0
embB 4246582 c.69T>C synonymous_variant 0.12
embB 4246584 p.Arg24Pro missense_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0