TB-Profiler result

Run: ERR13286085
Summary

Run ID: ERR13286085

Sample name:

Date: 2024-10-04T06:37:07.824305

Number of reads: 4907002

Percentage reads mapped: 99.83

Median coverage: 155.0

Strain: lineage4.3.2.1;lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.89
lineage4.3.2 Euro-American (LAM) None 0.88
lineage4.3.2.1 Euro-American (LAM) RD761 0.88
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.1
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.11 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.13 ethambutol Assoc w R
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 Drugs Confidence
gyrB 5520 p.Pro94Leu missense_variant 0.88 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7222 c.1983C>T synonymous_variant 0.88 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.88 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.92 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
nusG 734141 c.-113G>A upstream_gene_variant 0.12 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.86 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.83 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.85 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156109 c.3G>T synonymous_variant 0.94 isoniazid
PPE35 2169149 c.1464G>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.91 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.91 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.93 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.9 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.12 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.95 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.91 streptomycin Not assoc w R