TB-Profiler result

Run: SRR28351401
Summary

Run ID: SRR28351401

Sample name:

Date: 2024-05-22T15:36:26.050326

Number of reads: 9458197

Percentage reads mapped: 99.78

Median coverage: 276.0

Strain: lineage2.2.1;lineage4.2.1

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 0.31
lineage4.2 Euro-American None 0.65
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.29
lineage2.2 East-Asian (Beijing) RD105;RD207 0.29
lineage4 Euro-American None 0.67
lineage4.2.1 Euro-American (TUR) None 0.69
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 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 embA c.-16C>T Uncertain significance Mutation from literature
embB p.Ser297Ala Uncertain significance Mutation from literature
pyrazinamide pncA p.Val21Ala Not assoc w R - Interim Mutation from literature
streptomycin rpsL p.Lys88Arg Assoc w R
gid c.115delC Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 0.77 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.66 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.69 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 0.62 isoniazid Assoc w R High-level resistance
pncA 2289180 p.Val21Ala missense_variant 0.72 pyrazinamide Not assoc w R - Interim Mutation from literature
eis 2715344 c.-12C>T upstream_gene_variant 0.54 kanamycin Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 0.48 ethambutol Uncertain significance Mutation from literature
embB 4247402 p.Ser297Ala missense_variant 0.5 ethambutol Uncertain significance Mutation from literature
gid 4408087 c.115delC frameshift_variant 0.26 streptomycin 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
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 491247 c.465C>T synonymous_variant 0.69 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.28 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.43 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 619969 p.Val27Ile missense_variant 0.41 capreomycin Not assoc w R - Interim
amikacin Not assoc w R
kanamycin Uncertain significance
ccsA 620625 p.Ile245Met missense_variant 0.57 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.25 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.22 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.21 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.74 rifampicin Uncertain significance
rpoC 766645 p.Glu1092Asp missense_variant 0.38 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 0.41 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.35 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.29 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.67 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.27 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.41 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.39 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.31 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
bacA 2063685 c.1044G>A synonymous_variant 0.61 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.68 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.38 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.17 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.85 pyrazinamide Uncertain significance
Rv1979c 2222112 c.1052dupT frameshift_variant 0.15 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2783650 c.393C>T synonymous_variant 0.34 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ald 3086742 c.-78A>C upstream_gene_variant 0.79 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.37 pyrazinamide Not assoc w R - Interim
lpqB 3623222 c.1689A>G synonymous_variant 0.48 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.53 bedaquiline Uncertain significance
rifampicin 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 0.58 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.56 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.46 ethambutol Not assoc w R
ethA 4326632 p.His281Pro missense_variant 0.75 ethionamide Uncertain significance
ethA 4327406 p.Leu23Arg missense_variant 0.21 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.66 ethionamide
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 0.23 streptomycin Not assoc w R
gid 4407890 p.Val105Leu missense_variant 0.71 streptomycin
gid 4407927 p.Glu92Asp missense_variant 0.29 streptomycin Not assoc w R