TB-Profiler result

Run: ERR8025443
Summary

Run ID: ERR8025443

Sample name:

Date: 2024-10-03T19:08:22.532454

Number of reads: 15591263

Percentage reads mapped: 99.52

Median coverage: 266.0

Strain: lineage2.2.2;lineage4.1.1.3

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.69
lineage4.1 Euro-American None 0.32
lineage4.1.1.3 Euro-American (X-type) RD193 0.32
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.68
lineage2.2 East-Asian (Beijing) RD105;RD207 0.67
lineage4 Euro-American None 0.33
lineage4.1.1 Euro-American (X-type) None 0.32
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.Ser450Leu 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
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Ala Assoc w R
pyrazinamide pncA c.517dupG Assoc w R
c.296delA Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.514A>C Assoc w R
gid p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Asn Assoc w R
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
c.597delC Assoc w R
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 7570 p.Ala90Val missense_variant 0.63 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)
gyrA 7581 p.Asp94Asn missense_variant 0.35 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761110 p.Asp435Val missense_variant 0.6 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.38 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.35 streptomycin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.7 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.71 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673423 c.-779G>T upstream_gene_variant 0.7 ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
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)
katG 2155167 p.Ser315Thr missense_variant 0.36 isoniazid Assoc w R High-level resistance
pncA 2288724 c.517dupG frameshift_variant 0.64 pyrazinamide Assoc w R
pncA 2288945 c.296delA frameshift_variant 0.27 pyrazinamide Assoc w R
ahpC 2726145 c.-48G>A upstream_gene_variant 0.39 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.67 ethambutol Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.35 ethambutol Assoc w R
ethA 4326333 p.Ala381Pro missense_variant 0.64 ethionamide Uncertain significance Mutation from literature
ethA 4326876 c.597delC frameshift_variant 0.29 ethionamide Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.69 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
gyrB 6608 p.Val457Leu missense_variant 0.3 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 0.69 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.71 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.71 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.33 ethionamide Uncertain significance
rpoB 761268 p.Ile488Val missense_variant 0.31 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.66 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.32 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 0.69 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.68 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.35 linezolid
rplC 801354 c.546G>A synonymous_variant 0.35 linezolid Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.72 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.66 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 2154724 p.Arg463Leu missense_variant 0.75 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.74 pyrazinamide Not assoc w R
Rv1979c 2221939 p.Arg409Gln missense_variant 0.69 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
thyA 3074039 p.Pro145Ala missense_variant 0.24 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449616 p.Met371Ile missense_variant 0.31 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.77 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040976 c.-272T>G upstream_gene_variant 0.67 pyrazinamide
glpK 4139947 c.-192C>A upstream_gene_variant 0.67 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.34 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.63 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.27 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.59 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
whiB6 4338794 c.-273A>G upstream_gene_variant 0.6 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.7 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.71 streptomycin Not assoc w R