TB-Profiler result

Run: ERR11252512
Summary

Run ID: ERR11252512

Sample name:

Date: 2024-05-22T08:49:55.650943

Number of reads: 3155721

Percentage reads mapped: 99.75

Median coverage: 97.0

Strain: lineage1.2.2.2;lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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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 0.9
lineage1.2.2 Indo-Oceanic RD239 0.09
lineage1.2.2.2 Indo-Oceanic RD239 0.1
lineage4 Euro-American None 0.92
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.91
lineage1 Indo-Oceanic RD239 0.05
lineage4.3.4 Euro-American (LAM) RD174 0.89
lineage4.3.4.2 Euro-American (LAM) RD174 0.92
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
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
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 5075 c.-165C>T upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6140 p.Val301Leu missense_variant 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6745 c.1506T>C synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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
rpoC 763552 c.183C>T synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.93 rifampicin Not assoc w R
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
rplC 800357 c.-452C>A upstream_gene_variant 0.12 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.14 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417491 c.-144C>T upstream_gene_variant 0.91 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
ndh 2102240 p.Arg268His missense_variant 0.14 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.11 pyrazinamide Not assoc w R
Rv1979c 2222098 p.Thr356Lys missense_variant 0.14 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.16 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726051 c.-142G>A upstream_gene_variant 0.12 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.86 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.92 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.86 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.95 pyrazinamide Not assoc w R
clpC1 4040719 c.-15A>G upstream_gene_variant 0.12 pyrazinamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245670 p.Ala813Gly missense_variant 0.1 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.13 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.1 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.19 ethionamide Not assoc w R - Interim
ethA 4326298 c.1176G>T synonymous_variant 0.89 ethionamide
ethA 4326433 c.1041G>A synonymous_variant 0.14 ethionamide
ethA 4326439 p.Asn345Lys missense_variant 0.13 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.16 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.91 streptomycin Not assoc w R