TB-Profiler result

Run: SRR10430396
Summary

Run ID: SRR10430396

Sample name:

Date: 2024-04-15T19:30:04.851739

Number of reads: 3137985

Percentage reads mapped: 99.54

Median coverage: 95.0

Strain: lineage2.2.1;lineage4.3.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.18
lineage2 East-Asian RD105 0.79
lineage4.3.2 Euro-American (LAM) None 0.17
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.84
lineage4.3.2.1 Euro-American (LAM) RD761 0.14
lineage2.2 East-Asian (Beijing) RD105;RD207 0.84
lineage4 Euro-American None 0.17
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 embB p.Leu74Arg Uncertain significance Mutation from literature
p.Met306Ile Assoc w R
p.Asp328Gly Uncertain significance Mutation from literature
pyrazinamide pncA p.Thr142Ala Assoc w R
p.Lys96Thr Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Gln Assoc w R - Interim
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1047delT 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.81 streptomycin Assoc w R
rpsL 781821 p.Lys88Gln missense_variant 0.16 streptomycin Assoc w R - Interim
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288818 p.Thr142Ala missense_variant 0.8 pyrazinamide Assoc w R
pncA 2288955 p.Lys96Thr missense_variant 0.14 pyrazinamide Assoc w R
embB 4246734 p.Leu74Arg missense_variant 0.87 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.12 ethambutol Assoc w R
embB 4247496 p.Asp328Gly missense_variant 0.85 ethambutol Uncertain significance Mutation from literature
ethA 4326426 c.1047delT frameshift_variant 0.99 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
gyrB 5520 p.Pro94Leu missense_variant 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7222 c.1983C>T synonymous_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8164 p.Ala288Asp missense_variant 0.14 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 0.82 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.78 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.39 ethionamide
isoniazid
ccsA 620625 p.Ile245Met missense_variant 0.77 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.74 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.77 ethionamide Uncertain significance
rpoB 761004 p.Thr400Gly missense_variant 0.17 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.18 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.87 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 0.78 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.79 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpR5 779120 p.Leu44Pro missense_variant 0.22 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 0.83 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.78 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.8 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.85 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.14 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.81 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.98 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 0.86 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.78 pyrazinamide Not assoc w R
PPE35 2170871 c.-259A>C upstream_gene_variant 0.77 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290107 c.-866T>A upstream_gene_variant 0.2 pyrazinamide
Rv2752c 3064974 p.Asn406Lys missense_variant 0.87 ethambutol
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.22 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.79 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 0.84 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640407 c.-136G>A upstream_gene_variant 0.17 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.19 pyrazinamide 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 0.84 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.82 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 0.77 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.78 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.24 streptomycin Not assoc w R