TB-Profiler result

Run: SRR5486893
Summary

Run ID: SRR5486893

Sample name:

Date: 2024-10-04T15:29:09.456545

Number of reads: 6607165

Percentage reads mapped: 99.64

Median coverage: 193.0

Strain: lineage4.1.2.1;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
lineage4.1 Euro-American None 0.26
lineage4.1.2 Euro-American None 0.27
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.26
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.74
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Tyr Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA c.152dupA Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 761139 p.His445Tyr missense_variant 0.67 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.79 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.74 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.7 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.71 isoniazid Assoc w R High-level resistance
pncA 2289089 c.152dupA frameshift_variant 0.73 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.8 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.76 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.25 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9208 p.Lys636Thr missense_variant 0.74 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13624 c.-66C>T upstream_gene_variant 0.77 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.31 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.23 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.12 ethionamide Uncertain significance
rpoB 760106 c.300G>A synonymous_variant 0.26 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.26 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.31 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 781276 c.-284A>C upstream_gene_variant 0.21 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.29 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1305156 c.2226G>A synonymous_variant 0.14 pretomanid
delamanid
clofazimine
embR 1417985 c.-638C>A upstream_gene_variant 0.78 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.72 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.27 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.74 pyrazinamide Not assoc w R
PPE35 2168373 p.Pro747Leu missense_variant 0.24 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.3 isoniazid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.69 capreomycin
Rv2752c 3066286 c.-95C>G upstream_gene_variant 0.71 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 0.25 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.34 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3641713 p.Leu60Gln missense_variant 0.19 pretomanid
delamanid
clofazimine
embC 4239298 c.-565C>T upstream_gene_variant 0.24 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.26 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 0.26 kanamycin
capreomycin
amikacin