TB-Profiler result

Run: SRR1165218
Summary

Run ID: SRR1165218

Sample name:

Date: 2024-04-15T19:34:01.577682

Number of reads: 4764973

Percentage reads mapped: 98.78

Median coverage: 114.0

Strain: lineage2.2.2;lineage4.1.1.1

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 0.77
lineage4.1 Euro-American None 0.23
lineage4.1.1.1 Euro-American (X-type) RD183 0.22
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.8
lineage2.2 East-Asian (Beijing) RD105;RD207 0.81
lineage4.1.1 Euro-American (X-type) None 0.24
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
p.His445Asp Assoc w R
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>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.Met306Ile Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA c.517dupG Assoc w R
p.Gly97Cys Assoc w R
streptomycin rrs n.514A>C Assoc w R
gid c.351delG Assoc w R
p.Leu79Ser Uncertain significance Mutation from literature
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.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
ethA p.Ala381Pro 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 761110 p.Asp435Val missense_variant 0.75 rifampicin Assoc w R
rpoB 761139 p.His445Asp missense_variant 0.27 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.77 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.76 capreomycin Assoc w R
amikacin Assoc w R
kanamycin Assoc w R
inhA 1673423 c.-779G>T upstream_gene_variant 0.68 isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288724 c.517dupG frameshift_variant 0.84 pyrazinamide Assoc w R
pncA 2288953 p.Gly97Cys missense_variant 0.22 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.66 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.38 ethambutol Assoc w R
ethA 4326333 p.Ala381Pro missense_variant 0.74 ethionamide Uncertain significance Mutation from literature
gid 4407851 c.351delG frameshift_variant 0.18 streptomycin Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.78 streptomycin 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 1475 p.Asp492Gly missense_variant 0.17 isoniazid
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
fgd1 491742 c.960T>C synonymous_variant 0.78 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.78 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.72 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.23 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.72 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.23 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 0.73 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.76 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.18 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.76 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.76 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.64 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.67 pyrazinamide Not assoc w R
Rv1979c 2221939 p.Arg409Gln missense_variant 0.76 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
ahpC 2726210 c.18T>C synonymous_variant 0.23 isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.77 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641447 p.Thr302Met missense_variant 0.18 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
rpoA 3877553 p.Glu319Lys missense_variant 0.24 rifampicin Not assoc w R
clpC1 4040976 c.-272T>G upstream_gene_variant 0.71 pyrazinamide
glpK 4139947 c.-192C>A upstream_gene_variant 0.81 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240897 c.1035C>G synonymous_variant 0.44 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.45 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.66 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.42 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.69 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
whiB6 4338794 c.-273A>G upstream_gene_variant 0.67 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.78 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.75 streptomycin Not assoc w R