TB-Profiler result

Run: SRR16088240
Summary

Run ID: SRR16088240

Sample name:

Date: 2024-10-04T23:52:04.280750

Number of reads: 3723890

Percentage reads mapped: 99.62

Median coverage: 116.0

Strain: lineage2.2.1;lineage4.1.2.1

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 0.58
lineage4.1 Euro-American None 0.42
lineage4.1.2 Euro-American None 0.42
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.15
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.58
lineage2.2 East-Asian (Beijing) RD105;RD207 0.58
lineage4 Euro-American None 0.45
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Phe Assoc w R
p.His445Gln Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gly406Ala Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethR p.Phe110Leu Uncertain significance Mutation from literature
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 761109 p.Asp435Phe missense_variant 0.16 rifampicin Assoc w R
rpoB 761141 p.His445Gln missense_variant 0.2 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpsL 781687 p.Lys43Arg missense_variant 0.52 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.6 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.62 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.17 isoniazid Assoc w R High-level resistance
embB 4247730 p.Gly406Ala missense_variant 0.63 ethambutol Assoc w R
ethR 4327876 p.Phe110Leu missense_variant 0.24 ethionamide 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
dnaA 1399 p.Gly467Cys missense_variant 0.56 isoniazid 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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13639 c.-81C>G upstream_gene_variant 0.24 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.46 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.6 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.19 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.55 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.61 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.61 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.39 ethionamide Uncertain significance
rpoB 759841 p.Ser12Thr missense_variant 0.15 rifampicin
rpoB 760115 c.309C>T synonymous_variant 0.44 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.59 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.39 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 0.6 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.57 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800200 c.-609C>G upstream_gene_variant 0.23 linezolid
rplC 800889 c.81C>A synonymous_variant 0.33 linezolid Not assoc w R - Interim
Rv1129c 1254214 p.Glu107Asp missense_variant 0.67 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.56 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 0.55 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.56 pyrazinamide Not assoc w R - Interim
rpsA 1834845 c.1313_1315delCCG disruptive_inframe_deletion 0.64 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.99 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 0.56 isoniazid Not assoc w R
katG 2155259 p.Gly285Cys missense_variant 0.59 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.59 pyrazinamide Not assoc w R
PPE35 2168303 c.2310G>T synonymous_variant 0.32 pyrazinamide Not assoc w R - Interim
PPE35 2169776 p.Phe279Leu missense_variant 0.31 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.42 isoniazid
Rv2681 2997153 p.Gly139Arg missense_variant 0.16 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612770 p.Val116Ala missense_variant 0.65 pyrazinamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.68 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 0.43 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840263 c.1158C>T synonymous_variant 0.31 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.4 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.61 ethambutol Not assoc w R
embB 4247086 c.573C>T synonymous_variant 0.31 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.45 ethambutol Not assoc w R
ubiA 4269847 c.-14A>G upstream_gene_variant 0.24 ethambutol Uncertain significance
ethA 4326676 p.Ser266Arg missense_variant 0.53 ethionamide Uncertain significance
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 0.66 streptomycin Not assoc w R
gid 4407654 c.549G>A synonymous_variant 0.66 streptomycin Not assoc w R - Interim
gid 4407927 p.Glu92Asp missense_variant 0.63 streptomycin Not assoc w R