TB-Profiler result

Run: ERR4553510
Summary

Run ID: ERR4553510

Sample name:

Date: 2024-10-05T00:29:27.915194

Number of reads: 1493398

Percentage reads mapped: 99.67

Median coverage: 46.0

Strain: lineage4

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.3 Indo-Oceanic RD239 0.18
lineage1.1.3.3 Indo-Oceanic RD239 0.19
lineage4 Euro-American None 0.75
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
pyrazinamide pncA p.Leu19Arg Uncertain significance Mutation from literature
streptomycin rpsL p.Lys43Arg 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 0.68 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.68 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289186 p.Leu19Arg missense_variant 0.66 pyrazinamide Uncertain significance Mutation from literature
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 6061 p.Ser274Arg missense_variant 0.75 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13641 c.-83A>G upstream_gene_variant 0.62 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.34 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
hadA 732127 p.Lys66Asn missense_variant 0.68 isoniazid Uncertain significance
nusG 734407 p.Val52Leu missense_variant 0.28 rifampicin
rpoB 759628 c.-179C>T upstream_gene_variant 0.7 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.25 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.12 rifampicin Not assoc w R
rpoC 767123 p.Val1252Leu missense_variant 0.33 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.3 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.28 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1407255 p.Ala29Glu missense_variant 0.67 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473293 n.1448G>C non_coding_transcript_exon_variant 0.52 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
inhA 1673393 c.-809G>A upstream_gene_variant 0.73 isoniazid Uncertain significance
ethionamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 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 0.33 isoniazid Not assoc w R
katG 2156146 c.-35A>G upstream_gene_variant 0.21 isoniazid Uncertain significance
PPE35 2169779 c.834A>C synonymous_variant 0.67 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
Rv1979c 2223712 c.-548G>A upstream_gene_variant 0.26 bedaquiline
clofazimine
pncA 2289256 c.-15A>C upstream_gene_variant 0.57 pyrazinamide Uncertain significance
folC 2746365 c.1234C>T synonymous_variant 0.22 para-aminosalicylic_acid
Rv2681 2997944 c.1206C>T synonymous_variant 0.24 capreomycin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.3 cycloserine
lpqB 3623435 c.1476G>A synonymous_variant 0.33 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 0.38 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4043957 p.Asp109Asn missense_variant 0.72 pyrazinamide Uncertain significance
embC 4238922 c.-941G>A upstream_gene_variant 0.34 ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.27 ethambutol Not assoc w R
embC 4241736 p.Val625Ala missense_variant 0.16 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.2 ethambutol Not assoc w R
embB 4248516 p.Val668Ala missense_variant 0.11 ethambutol Uncertain significance
ethA 4328317 c.-844C>T upstream_gene_variant 0.69 ethionamide
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 1.0 kanamycin
capreomycin
amikacin