TB-Profiler result

Run: SRR21747017
Summary

Run ID: SRR21747017

Sample name:

Date: 2024-10-04T09:51:39.778813

Number of reads: 2266021

Percentage reads mapped: 99.66

Median coverage: 121.0

Strain: lineage2.2.1;lineage4.5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.15
lineage2 East-Asian RD105 0.86
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.84
lineage2.2 East-Asian (Beijing) RD105;RD207 0.85
lineage4 Euro-American None 0.16
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
pyrazinamide pncA p.Val163Ala Assoc w R - Interim
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
rpoB 761155 p.Ser450Leu missense_variant 0.13 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid Assoc w R High-level resistance
pncA 2288754 p.Val163Ala missense_variant 0.1 pyrazinamide Assoc w R - Interim
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 7892 c.591G>A synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.92 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.13 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.73 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.91 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.91 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.85 rifampicin Not assoc w R
rpoC 764248 c.879C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764944 p.His525Gln missense_variant 0.15 rifampicin Uncertain significance
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 0.88 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.8 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406586 p.Thr252Asn missense_variant 0.15 streptomycin
pyrazinamide
isoniazid
Rv1258c 1406760 c.580_581insC frameshift_variant 0.81 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1406796 p.Gly182Val missense_variant 0.19 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1475764 n.2107A>G non_coding_transcript_exon_variant 0.11 capreomycin
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.87 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 0.83 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.85 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.18 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
Rv2477c 2782956 c.1087C>T synonymous_variant 0.11 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2681 2997619 p.Val294Ala missense_variant 0.78 capreomycin
thyA 3074582 c.-111T>G upstream_gene_variant 0.91 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.84 cycloserine
whiB7 3569220 c.-541C>T upstream_gene_variant 0.88 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.83 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 0.92 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3879070 c.-563G>A upstream_gene_variant 0.12 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.18 pyrazinamide Not assoc w R
glpK 4139183 c.570_572dupGGG disruptive_inframe_insertion 0.86 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.85 ethambutol Not assoc w R
embB 4247573 p.Asp354Asn missense_variant 0.21 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.8 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.81 ethionamide 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 1.0 kanamycin
capreomycin
amikacin
whiB6 4338949 c.-428G>A upstream_gene_variant 0.92 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.89 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.85 streptomycin Not assoc w R