TB-Profiler result

Run: SRR6824702
Summary

Run ID: SRR6824702

Sample name:

Date: 2024-10-03T16:37:00.665535

Number of reads: 8031086

Percentage reads mapped: 99.44

Median coverage: 244.0

Strain: lineage2.2.1;lineage4.4.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.14
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.15
lineage2.2 East-Asian (Beijing) RD105;RD207 0.15
lineage4 Euro-American None 0.85
lineage4.4 Euro-American None 0.8
lineage4.4.2 Euro-American None 0.79
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 embB p.Met306Ile Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA c.547_548insC Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
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 0.14 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.13 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.16 isoniazid Assoc w R High-level resistance
pncA 2288694 c.547_548insC frameshift_variant 0.17 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.21 para-aminosalicylic_acid Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.17 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.15 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
gyrB 5302 p.Glu21Asp missense_variant 0.76 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
fgd1 491742 c.960T>C synonymous_variant 0.16 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.15 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.12 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.15 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.14 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.18 rifampicin Not assoc w R
rpoC 764888 p.Leu507Val missense_variant 0.13 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 0.16 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.16 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254131 p.Glu135Ala missense_variant 0.14 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.14 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417236 p.Val38Met missense_variant 0.78 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.13 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 2154177 c.1935G>A synonymous_variant 0.73 isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.13 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.16 pyrazinamide Not assoc w R
Rv1979c 2222165 p.Gly334Arg missense_variant 0.75 bedaquiline
clofazimine
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2783026 p.Asp339Glu missense_variant 0.83 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2752c 3066099 p.Met31Ile missense_variant 0.86 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3074306 p.Ala56Pro missense_variant 0.11 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.93 cycloserine
Rv3083 3448727 p.Leu75Arg missense_variant 0.73 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.17 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.12 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4039058 p.Phe549Leu missense_variant 0.7 pyrazinamide
embC 4238963 c.-900C>T upstream_gene_variant 0.8 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.14 ethambutol Not assoc w R
embA 4243991 c.759T>G synonymous_variant 0.73 ethambutol Not assoc w R - Interim
embA 4245946 p.Ile905Thr missense_variant 0.74 ethambutol
embA 4246508 c.3276G>A synonymous_variant 0.77 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.1 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.8 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.77 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 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.11 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.15 streptomycin Not assoc w R