TB-Profiler result

Run: ERR1213939
Summary

Run ID: ERR1213939

Sample name:

Date: 2024-04-15T06:25:14.921520

Number of reads: 6545501

Percentage reads mapped: 97.96

Median coverage: 88.0

Strain: lineage2.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.2
lineage2 East-Asian RD105 0.81
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.81
lineage2.2 East-Asian (Beijing) RD105;RD207 0.81
lineage4 Euro-American None 0.18
lineage4.3.3 Euro-American (LAM) RD115 0.2
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.Val155Ala Assoc w R - Interim
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
rpoB 761155 p.Ser450Leu missense_variant 0.22 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.17 isoniazid Assoc w R High-level resistance
pncA 2288778 p.Val155Ala missense_variant 0.22 pyrazinamide Assoc w R - Interim
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.14 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
fgd1 491742 c.960T>C synonymous_variant 0.8 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.7 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.78 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.89 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.91 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.74 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.76 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.79 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.73 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.79 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471777 n.-69C>T upstream_gene_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 0.86 pyrazinamide Not assoc w R - Interim
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 0.78 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.91 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
pncA 2289559 c.-318T>G upstream_gene_variant 0.74 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.23 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.21 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.87 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625941 c.673C>T synonymous_variant 0.79 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.77 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627336 p.Arg5Thr missense_variant 0.79 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3627574 c.-961A>G upstream_gene_variant 0.18 bedaquiline
rifampicin
rpoA 3877967 p.Thr181Ala missense_variant 0.17 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.19 pyrazinamide Not assoc w R
embC 4242241 c.2379C>T synonymous_variant 0.58 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.69 ethambutol Not assoc w R
embB 4249447 c.2934G>A synonymous_variant 0.21 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.77 ethambutol 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 4407588 c.615A>G synonymous_variant 0.83 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.81 streptomycin Not assoc w R