TB-Profiler result

Run: ERR10748381
Summary

Run ID: ERR10748381

Sample name:

Date: 2024-10-03T19:43:46.118934

Number of reads: 928695

Percentage reads mapped: 99.89

Median coverage: 42.0

Strain: lineage3;lineage4.1.1.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.27
lineage4.1 Euro-American None 0.74
lineage4.1.1.3 Euro-American (X-type) RD193 0.75
lineage4 Euro-American None 0.74
lineage4.1.1 Euro-American (X-type) None 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.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Val139Met Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.597delC Assoc w R
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 0.74 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.78 streptomycin Assoc w R
katG 2155167 p.Ser315Thr missense_variant 0.74 isoniazid Assoc w R High-level resistance
pncA 2288827 p.Val139Met missense_variant 0.69 pyrazinamide Assoc w R
ahpC 2726145 c.-48G>A upstream_gene_variant 0.73 isoniazid Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.75 ethambutol Assoc w R
ethA 4326876 c.597delC frameshift_variant 0.76 ethionamide 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 6608 p.Val457Leu missense_variant 0.67 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 8056 p.Arg252Leu missense_variant 0.25 levofloxacin Not assoc w R - Interim
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.22 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.21 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.8 ethionamide Uncertain significance
hadA 732145 c.216C>T synonymous_variant 0.22 isoniazid Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.26 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.24 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.75 rifampicin Not assoc w R
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 0.33 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
rplC 800219 c.-590T>C upstream_gene_variant 0.77 linezolid
rplC 801354 c.546G>A synonymous_variant 0.72 linezolid Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.22 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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 0.21 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.19 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.21 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.32 pyrazinamide
Rv2477c 2782498 c.1545C>T synonymous_variant 0.18 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2752c 3065025 c.1167G>A synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
thyA 3074424 c.48G>T synonymous_variant 0.19 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449616 p.Met371Ile missense_variant 0.75 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.32 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
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 0.56 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.87 ethambutol Not assoc w R
ethA 4328212 c.-740delC upstream_gene_variant 0.31 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
gid 4407588 c.615A>G synonymous_variant 0.33 streptomycin Not assoc w R