TB-Profiler result

Run: ERR8975589
Summary

Run ID: ERR8975589

Sample name:

Date: 2024-04-15T12:01:41.613981

Number of reads: 3149113

Percentage reads mapped: 99.61

Median coverage: 103.0

Strain: lineage2.2.1;lineage4.1.1.1

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 0.38
lineage4.1 Euro-American None 0.69
lineage4.1.1.1 Euro-American (X-type) RD183 0.61
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.33
lineage2.2 East-Asian (Beijing) RD105;RD207 0.35
lineage4 Euro-American None 0.65
lineage4.1.1 Euro-American (X-type) None 0.64
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Leu 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.Thr394Ala Uncertain significance Mutation from literature
p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA c.439dupG Assoc w R
streptomycin rpsL p.Lys43Arg 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)
ofloxacin
levofloxacin gyrA p.Ala90Val 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 7570 p.Ala90Val missense_variant 0.38 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 761140 p.His445Leu missense_variant 0.37 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.3 streptomycin Assoc w R
inhA 1673432 c.-770T>C upstream_gene_variant 0.31 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 2154932 p.Thr394Ala missense_variant 0.58 isoniazid Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.37 isoniazid Assoc w R High-level resistance
pncA 2288802 c.439dupG frameshift_variant 0.45 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.36 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.34 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.37 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.34 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.35 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.32 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.63 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.28 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.76 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 0.34 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.41 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.35 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.72 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.5 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.35 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 0.28 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 0.31 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.3 pyrazinamide Not assoc w R
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 0.68 isoniazid Not assoc w R - Interim
ald 3086739 c.-81G>A upstream_gene_variant 0.35 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.4 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 0.42 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641447 p.Thr302Met missense_variant 0.69 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
rpoA 3877553 p.Glu319Lys missense_variant 0.73 rifampicin Not assoc w R
embC 4240897 c.1035C>G synonymous_variant 0.63 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 0.6 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.32 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.63 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.29 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
gid 4407588 c.615A>G synonymous_variant 0.38 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.38 streptomycin Not assoc w R