TB-Profiler result

Run: SRR7516324
Summary

Run ID: SRR7516324

Sample name:

Date: 2024-04-14T03:58:08.752106

Number of reads: 2300426

Percentage reads mapped: 99.66

Median coverage: 69.0

Strain: lineage2.2.1;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
lineage2 East-Asian RD105 0.09
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.07
lineage4 Euro-American None 0.95
lineage4.8 Euro-American (mainly T) RD219 0.92
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.Gly406Asp Assoc w R
pyrazinamide
streptomycin gid p.Glu103* Assoc w R
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 0.91 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.92 isoniazid Assoc w R High-level resistance
embB 4247730 p.Gly406Asp missense_variant 0.97 ethambutol Assoc w R
gid 4407896 p.Glu103* stop_gained 0.88 streptomycin 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.96 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.82 rifampicin Not assoc w R
rpoB 761998 p.Leu731Pro missense_variant 0.88 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.91 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.16 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.13 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.96 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.95 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.18 cycloserine
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.92 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.84 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75_-74delGCinsT upstream_gene_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance