TB-Profiler result

Run: SRR12416829
Summary

Run ID: SRR12416829

Sample name:

Date: 2024-10-05T02:15:44.716106

Number of reads: 5484039

Percentage reads mapped: 90.49

Median coverage: 133.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 0.99
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.Ile491Thr Uncertain significance Mutation from literature
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.Gln127Pro Uncertain significance Mutation from literature
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
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
rpoB 761155 p.Ser450Leu missense_variant 0.91 rifampicin Assoc w R
rpoC 764841 p.Ile491Thr missense_variant 0.86 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.93 streptomycin Assoc w R
inhA 1673423 c.-779G>T upstream_gene_variant 0.99 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 2155732 p.Gln127Pro missense_variant 0.97 isoniazid Uncertain significance Mutation from literature
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.95 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
dnaA 1092 c.1092T>C synonymous_variant 0.14 isoniazid Not assoc w R - Interim
dnaA 1098 c.1098A>G synonymous_variant 0.14 isoniazid
dnaA 1104 c.1104T>C synonymous_variant 0.14 isoniazid
dnaA 1110 c.1110T>C synonymous_variant 0.13 isoniazid
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 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.98 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.99 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.99 ethionamide Uncertain significance
rpoB 760223 c.417T>C synonymous_variant 0.15 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760283 c.477G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760328 c.522G>C synonymous_variant 0.13 rifampicin
rpoB 761015 c.1209G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.13 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764858 c.1489T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254242 p.Glu98Gly missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254612 c.-78G>A upstream_gene_variant 0.99 levofloxacin
moxifloxacin
isoniazid
rifampicin
fbiC 1302874 c.-57G>A upstream_gene_variant 0.18 pretomanid
delamanid
clofazimine
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833410 c.-132G>A upstream_gene_variant 1.0 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834012 c.471G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834465 c.924T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.13 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834495 c.954G>A synonymous_variant 0.13 pyrazinamide
rpsA 1834499 c.958C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.13 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2519206 c.1092C>T synonymous_variant 0.13 isoniazid
Rv2681 2997439 p.Trp234Ser missense_variant 1.0 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide 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 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626972 c.-359A>G upstream_gene_variant 0.16 rifampicin
bedaquiline
mtrB 3626987 c.-374C>G upstream_gene_variant 0.16 rifampicin
bedaquiline
mtrB 3627005 c.-392G>C upstream_gene_variant 0.16 rifampicin
bedaquiline
mtrB 3627008 c.-395G>C upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrB 3627011 c.-398T>G upstream_gene_variant 0.17 rifampicin
bedaquiline
alr 3841614 c.-194C>G upstream_gene_variant 1.0 cycloserine
rpoA 3878076 c.432C>T synonymous_variant 0.13 rifampicin
rpoA 3878094 c.414C>G synonymous_variant 0.14 rifampicin
rpoA 3878103 c.405A>G synonymous_variant 0.15 rifampicin
rpoA 3878106 c.402G>C synonymous_variant 0.14 rifampicin
rpoA 3878193 c.315T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3878205 c.303T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878217 c.291A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878232 c.276G>C synonymous_variant 0.13 rifampicin
rpoA 3878247 c.261G>C synonymous_variant 0.15 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878276 c.232C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878284 p.Glu75Ala missense_variant 0.13 rifampicin
rpoA 3878292 c.216T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>C synonymous_variant 0.16 rifampicin
rpoA 3878313 c.195G>T synonymous_variant 0.16 rifampicin
rpoA 3878878 c.-371T>C upstream_gene_variant 0.13 rifampicin Uncertain significance
rpoA 3878890 c.-383C>G upstream_gene_variant 0.15 rifampicin
rpoA 3878909 c.-402A>G upstream_gene_variant 0.16 rifampicin
rpoA 3878914 c.-407T>C upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878917 c.-410G>C upstream_gene_variant 0.14 rifampicin
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.99 ethambutol Not assoc w R
embB 4248220 c.1707A>C synonymous_variant 0.13 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.99 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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R