TB-Profiler result

Run: SRR25827360
Summary

Run ID: SRR25827360

Sample name:

Date: 2024-04-15T03:57:22.797139

Number of reads: 16432873

Percentage reads mapped: 99.07

Median coverage: 450.0

Strain: lineage3;lineage4

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
lineage3 East-African-Indian RD750 0.82
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.07
lineage4 Euro-American None 0.11
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Tyr Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Lys Assoc w R
pyrazinamide
streptomycin gid p.Leu79Ser Uncertain significance Mutation from literature
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 0.15 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Tyr missense_variant 0.73 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.25 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid Assoc w R High-level resistance
embB 4248002 p.Gln497Lys missense_variant 0.81 ethambutol Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.14 streptomycin 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
gyrB 6963 p.Arg575His missense_variant 0.79 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.87 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.91 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.88 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.81 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.83 rifampicin Not assoc w R
rpoB 762909 p.Ile1035Val missense_variant 0.77 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.89 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 0.91 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776181 p.Asp767Ala missense_variant 0.79 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.89 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.89 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.91 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 0.9 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.95 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289365 c.-125delC upstream_gene_variant 0.84 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.84 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.83 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.89 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.87 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841578 c.-158G>A upstream_gene_variant 0.73 cycloserine
alr 3841590 c.-170G>A upstream_gene_variant 0.79 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.84 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.86 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.81 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.17 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.16 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.11 ethambutol
embB 4246563 p.Leu17Trp missense_variant 0.12 ethambutol Uncertain significance
embB 4247028 p.Leu172Arg missense_variant 0.16 ethambutol
aftB 4268719 p.Asn40Asp missense_variant 0.74 ethambutol Uncertain significance
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 0.91 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.89 streptomycin Not assoc w R
gid 4408070 p.Trp45Arg missense_variant 0.78 streptomycin Uncertain significance