TB-Profiler result

Run: ERR4800367
Summary

Run ID: ERR4800367

Sample name:

Date: 2024-04-15T09:18:54.215667

Number of reads: 3479858

Percentage reads mapped: 99.58

Median coverage: 99.0

Strain: lineage2.2.1;lineage4.8

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 0.73
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.66
lineage2.2 East-Asian (Beijing) RD105;RD207 0.68
lineage4 Euro-American None 0.3
lineage4.8 Euro-American (mainly T) RD219 0.29
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Asp63Gly Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.906A>G Uncertain significance Mutation from literature
gid c.102delG Assoc w R
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
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 0.28 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
gyrA 7581 p.Asp94Asn missense_variant 0.64 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.39 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.33 streptomycin Assoc w R
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.77 streptomycin Uncertain significance Mutation from literature
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.23 capreomycin Assoc w R
amikacin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R High-level resistance
pncA 2289054 p.Asp63Gly missense_variant 0.26 pyrazinamide Assoc w R - Interim
embB 4247429 p.Met306Val missense_variant 0.35 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.77 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
gyrB 5332 c.93C>T synonymous_variant 0.34 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.68 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8168 p.Glu289Asp missense_variant 0.3 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 0.58 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.65 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.77 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.72 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.23 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.75 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.78 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.34 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.71 rifampicin Not assoc w R
rpoC 765862 p.Phe831Leu missense_variant 0.35 rifampicin Uncertain significance
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 0.69 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.68 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.7 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.64 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406738 c.603C>T synonymous_variant 0.72 streptomycin
isoniazid
pyrazinamide
Rv1258c 1406760 c.580_581insC frameshift_variant 0.68 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Not assoc w R
inhA 1673406 c.-796C>G upstream_gene_variant 0.31 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.61 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.68 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 0.62 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.73 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.26 pyrazinamide Not assoc w R
PPE35 2169424 p.Ser397Pro missense_variant 0.71 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2747470 p.Ile43Ala missense_variant 0.29 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.3 capreomycin
Rv2752c 3065773 p.Glu140Gly missense_variant 0.33 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.64 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.71 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.65 pyrazinamide Not assoc w R - Interim
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.3 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.7 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.71 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.29 pyrazinamide 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 0.74 ethambutol Not assoc w R
embA 4245417 p.Gly729Arg missense_variant 0.4 ethambutol Uncertain significance
embB 4249109 p.Pro866Thr missense_variant 0.77 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.73 ethambutol Not assoc w R
ubiA 4269296 p.Met180Val missense_variant 0.29 ethambutol Uncertain significance
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 0.64 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.71 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.71 streptomycin Not assoc w R