TB-Profiler result

Run: ERR13286216
Summary

Run ID: ERR13286216

Sample name:

Date: 2025-07-16T14:55:26.478730

Number of reads: 4370472

Percentage reads mapped: 99.73

Median coverage: 139.0

Strain: lineage2.2.1.1;lineage4.4.1.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 29.08
lineage2.2 East-Asian (Beijing) RD105;RD207 28.97
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 28.78
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 31.3
lineage4 Euro-American None 69.38
lineage4.4 Euro-American None 66.39
lineage4.4.1 Euro-American (S-type) None 68.75
lineage4.4.1.1 Euro-American None 69.98
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.His445Tyr Assoc w R
isoniazid inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. 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 pncA p.Val130Gly Assoc w R - Interim
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ser91Pro Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
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
gyrA 7572 p.Ser91Pro missense_variant 0.72 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761110 p.Asp435Val missense_variant 0.71 rifampicin Assoc w R
rpoB 761139 p.His445Tyr missense_variant 0.31 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.77 streptomycin Assoc w R
inhA 1673432 c.-770T>C upstream_gene_variant 0.73 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.69 isoniazid Assoc w R High-level resistance
pncA 2288853 p.Val130Gly missense_variant 0.75 pyrazinamide Assoc w R - Interim
embB 4247730 p.Gly406Ala missense_variant 0.69 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
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 9138 p.Gln613Glu missense_variant 0.76 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 0.29 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
mshA 575907 p.Ala187Val missense_variant 0.32 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.29 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.32 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.28 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.31 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 0.35 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.3 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 777416 c.1065G>T synonymous_variant 0.74 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.27 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781301 c.-259C>T upstream_gene_variant 0.35 streptomycin Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.25 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.4 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
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
ndh 2102990 p.Val18Ala missense_variant 0.66 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.35 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.3 pyrazinamide Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 0.74 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.66 pyrazinamide Not assoc w R
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.32 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2714846 p.Val163Ile missense_variant 0.24 amikacin Not assoc w R
kanamycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3448506 p.Met1? start_lost 0.71 ethionamide Uncertain significance
Rv3083 3448608 c.105G>A synonymous_variant 0.76 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.73 amikacin Not assoc w R
kanamycin Not assoc w R
streptomycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.75 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.24 pyrazinamide 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 0.4 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.67 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 0.32 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.26 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.27 ethambutol Not assoc w R
ethA 4326359 p.Met372Arg missense_variant 0.68 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 0.32 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.31 streptomycin Not assoc w R