TB-Profiler result

Run: SRR21276933
Summary

Run ID: SRR21276933

Sample name:

Date: 2024-10-05T11:47:56.835474

Number of reads: 9899931

Percentage reads mapped: 98.72

Median coverage: 282.0

Strain: lineage2.2.1

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
lineage2 East-Asian RD105 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.99
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
isoniazid katG p.Ser315Asn Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Met1000Arg Uncertain significance Mutation from literature
pyrazinamide pncA p.Val139Ala Assoc w R
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Ala504Val Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA p.Asp89Asn Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Ala504Val Assoc w R - Interim
gyrA p.Asp89Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid folC p.Ile43Thr Mutation from literature
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
gyrB 6750 p.Ala504Val missense_variant 0.71 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7566 p.Asp89Asn missense_variant 0.19 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.87 streptomycin Assoc w R
katG 2155168 p.Ser315Asn missense_variant 0.98 isoniazid Assoc w R High-level resistance
pncA 2288826 p.Val139Ala missense_variant 0.73 pyrazinamide Assoc w R
folC 2747471 p.Ile43Thr missense_variant 0.97 para-aminosalicylic_acid Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.96 ethambutol Uncertain significance Mutation from literature
embB 4249512 p.Met1000Arg missense_variant 0.97 ethambutol Uncertain significance Mutation from literature
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 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 574925 c.-423C>G upstream_gene_variant 0.97 isoniazid
ethionamide
mshA 575907 p.Ala187Val missense_variant 0.99 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 0.96 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.98 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766346 p.Glu993Lys missense_variant 0.84 rifampicin
rpoC 766488 p.Pro1040Arg missense_variant 0.98 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.99 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.97 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254111 p.Thr142Pro missense_variant 0.96 levofloxacin
moxifloxacin
isoniazid
rifampicin
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.98 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 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
rpsA 1834177 c.636A>C synonymous_variant 0.98 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 0.98 isoniazid Not assoc w R
katG 2156245 c.-134G>C upstream_gene_variant 0.9 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.98 pyrazinamide Not assoc w R
PPE35 2169632 c.981C>A synonymous_variant 0.88 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2288723 c.519G>A synonymous_variant 0.97 pyrazinamide
pncA 2289107 c.126_134delTCACGTCGT disruptive_inframe_deletion 0.22 pyrazinamide
thyA 3073740 p.Glu244Asp missense_variant 0.94 para-aminosalicylic_acid
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 3625898 p.Val239Ala missense_variant 0.97 rifampicin
bedaquiline
mtrB 3626562 p.Pro18Ser missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840258 p.Tyr388Cys missense_variant 0.81 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.99 ethambutol Not assoc w R
whiB6 4338596 c.-76_-75delAGinsGA upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
whiB6 4338598 c.-77G>C upstream_gene_variant 0.91 kanamycin
capreomycin
amikacin Uncertain significance
whiB6 4338599 c.-78A>C upstream_gene_variant 0.91 kanamycin
capreomycin
amikacin Uncertain significance
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 0.98 streptomycin Not assoc w R