TB-Profiler result

Run: ERR10762311
Summary

Run ID: ERR10762311

Sample name:

Date: 2024-10-05T08:21:53.721934

Number of reads: 4350077

Percentage reads mapped: 99.5

Median coverage: 137.0

Strain: lineage2.2.1;lineage4.2.1

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 0.37
lineage4.2 Euro-American None 0.66
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.33
lineage2.2 East-Asian (Beijing) RD105;RD207 0.38
lineage4 Euro-American None 0.65
lineage4.2.1 Euro-American (TUR) 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.Ser450Trp Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>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 embA c.-16C>T Uncertain significance Mutation from literature
embB p.Asn296His Uncertain significance Mutation from literature
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Asp8Glu Assoc w R
c.-11A>G Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA p.Ser159* Assoc w R
kanamycin eis c.-12C>T Assoc w R
cycloserine ald c.436_437dupGC Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.110delA 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 7582 p.Asp94Ala missense_variant 0.55 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 761155 p.Ser450Trp missense_variant 0.63 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.37 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.32 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.67 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.66 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
tlyA 1918415 p.Ser159* stop_gained 0.67 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289218 p.Asp8Glu missense_variant 0.39 pyrazinamide Assoc w R
pncA 2289252 c.-11A>G upstream_gene_variant 0.62 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.64 kanamycin Assoc w R
ald 3087252 c.436_437dupGC frameshift_variant 0.55 cycloserine Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.39 ethambutol Uncertain significance Mutation from literature
embB 4247399 p.Asn296His missense_variant 0.39 ethambutol Uncertain significance Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 0.62 ethambutol Assoc w R
ethA 4327363 c.110delA frameshift_variant 0.31 ethionamide 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 491247 c.465C>T synonymous_variant 0.65 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.37 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.32 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 619969 p.Val27Ile missense_variant 0.78 kanamycin Uncertain significance
capreomycin Not assoc w R - Interim
amikacin Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.3 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.38 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.3 ethionamide Uncertain significance
rpoB 762391 p.Leu862Arg missense_variant 0.66 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.33 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 0.31 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.36 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.32 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.71 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.37 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833813 p.Leu91Arg missense_variant 0.22 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.35 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
bacA 2063685 c.1044G>A synonymous_variant 0.67 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.61 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.35 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.41 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.62 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086731 c.-89A>G upstream_gene_variant 0.4 cycloserine
ald 3086742 c.-78A>C upstream_gene_variant 0.6 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448859 c.359dupG frameshift_variant 0.42 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.34 pyrazinamide Not assoc w R - Interim
lpqB 3623222 c.1689A>G synonymous_variant 0.56 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.38 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878416 p.Gly31Ala missense_variant 0.34 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.33 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.36 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.7 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.26 ethambutol Not assoc w R
ethA 4326632 p.His281Pro missense_variant 0.69 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.65 ethionamide
whiB6 4338371 p.Thr51Pro missense_variant 0.33 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338594 c.-73T>A upstream_gene_variant 0.3 kanamycin
capreomycin
amikacin
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
gid 4407588 c.615A>G synonymous_variant 0.36 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.34 streptomycin Not assoc w R