TB-Profiler result

Run: SRR22179535
Summary

Run ID: SRR22179535

Sample name:

Date: 2024-10-04T18:17:27.434714

Number of reads: 7931925

Percentage reads mapped: 99.77

Median coverage: 227.0

Strain: lineage2.2.1;lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) None 0.79
lineage2 East-Asian RD105 0.21
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.19
lineage2.2 East-Asian (Beijing) RD105;RD207 0.22
lineage4 Euro-American None 0.8
lineage4.3.4 Euro-American (LAM) RD174 0.81
lineage4.3.4.2 Euro-American (LAM) RD174 0.8
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 c.45_46insA Assoc w R High-level resistance
ethambutol
pyrazinamide
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 0.19 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.21 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.2 streptomycin Assoc w R
katG 2156066 c.45_46insA frameshift_variant 0.21 isoniazid Assoc w R High-level resistance
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 6817 c.1578G>A synonymous_variant 0.78 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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 0.21 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.18 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.21 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.23 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.2 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.29 rifampicin Not assoc w R
rpoC 763501 p.Asp44Glu missense_variant 0.21 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.84 rifampicin Not assoc w R
rpoC 766275 p.Ala969Asp missense_variant 0.26 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 0.17 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.18 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.18 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800248 c.-561C>T upstream_gene_variant 0.83 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.23 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 0.24 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 0.25 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 0.2 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.2 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
Rv2752c 3066237 c.-47_-46delCCinsTT upstream_gene_variant 0.16 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyA 3073868 p.Thr202Ala missense_variant 0.85 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.85 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.19 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 0.17 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.88 pyrazinamide Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.27 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4239763 c.-100C>T upstream_gene_variant 0.77 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 0.23 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.18 ethambutol Not assoc w R
whiB6 4338440 c.81_82insC frameshift_variant 0.14 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 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.15 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.19 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.85 streptomycin Not assoc w R