TB-Profiler result

Run: ERR8975807
Summary

Run ID: ERR8975807

Sample name:

Date: 20-10-2023 15:55:21

Number of reads: 8127233

Percentage reads mapped: 99.71

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.Ser450Leu (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Met175Val (1.00)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (1.00)
Cycloserine
Ethionamide R ethA c.867_934delGGACCAGCGATTGTGCTTGGTGCCCAACGGCGACCTGTTCCGGGCCATTCGTCACGGGAAGGTCGAGG (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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288719 p.Met175Val missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326539 c.867_934delGGACCAGCGATTGTGCTTGGTGCCCAACGGCGACCTGTTCCGGGCCATTCGTCACGGGAAGGTCGAGG frameshift_variant 1.0 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 1.0
gyrA 7581 p.Asp94Arg missense_variant 0.51
rpoC 765862 p.Phe831Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779127 c.139dupG frameshift_variant 0.54
mmpR5 779392 p.Arg135Trp missense_variant 0.5
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 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169149 c.1464G>C synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288949 p.Ala98Val missense_variant 1.0
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_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
ethA 4326539 c.866_934delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT disruptive_inframe_deletion 1.0