TB-Profiler result

Run: SRR25827324
Summary

Run ID: SRR25827324

Sample name:

Date: 2024-10-03T14:27:30.156673

Number of reads: 9878982

Percentage reads mapped: 99.35

Median coverage: 137.0

Strain: lineage2.2.1;lineage3;lineage4

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
lineage3 East-African-Indian RD750 0.74
lineage2 East-Asian RD105 0.24
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.23
lineage2.2 East-Asian (Beijing) RD105;RD207 0.23
lineage4 Euro-American None 0.07
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
rpoC p.Leu527Val Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Gly132Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
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 7582 p.Asp94Gly missense_variant 0.25 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoC 764948 p.Leu527Val missense_variant 0.7 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.17 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.11 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.66 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 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13905 c.-347G>T upstream_gene_variant 0.66 isoniazid
fgd1 491742 c.960T>C synonymous_variant 0.95 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.28 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.16 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.13 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.96 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.23 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.85 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.68 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.97 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 0.93 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.28 bedaquiline Not assoc w R
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253952 p.Ala195Pro missense_variant 0.75 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.92 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 0.22 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.92 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 0.95 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.93 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.2 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.18 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.63 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.71 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.78 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.79 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.92 cycloserine
ald 3087862 p.Gly348Glu missense_variant 0.64 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.24 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.91 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.3 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878614 c.-107A>C upstream_gene_variant 0.12 rifampicin
panD 4044872 c.-591C>T upstream_gene_variant 0.74 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.77 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.66 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 0.27 ethambutol Not assoc w R
embA 4245131 c.1899G>A synonymous_variant 0.64 ethambutol Not assoc w R - Interim
embB 4246544 p.Thr11Pro missense_variant 0.4 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.33 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.36 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.37 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.44 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.45 ethambutol Not assoc w R - Interim
aftB 4268753 c.84T>G synonymous_variant 0.17 ethambutol Not assoc w R - Interim
whiB6 4338194 p.Arg110Trp missense_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 0.93 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.28 streptomycin Not assoc w R
gid 4407742 p.Arg154Pro missense_variant 0.65 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.2 streptomycin Not assoc w R