TB-Profiler result

Run: SRR15465773
Summary

Run ID: SRR15465773

Sample name:

Date: 2024-10-05T09:00:39.846274

Number of reads: 3390974

Percentage reads mapped: 99.18

Median coverage: 91.0

Strain: lineage3;lineage4.1.1.3

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 0.8
lineage4.1 Euro-American None 0.18
lineage4.1.1.3 Euro-American (X-type) RD193 0.19
lineage4 Euro-American None 0.2
lineage4.1.1 Euro-American (X-type) None 0.18
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Asn Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.His445Asp Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Leu Assoc w R
pyrazinamide pncA p.Asp136Tyr Uncertain significance Mutation from literature
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 rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
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 0.14 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761109 p.Asp435Asn missense_variant 0.77 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761139 p.His445Asp missense_variant 0.88 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.13 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.15 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2288836 p.Asp136Tyr missense_variant 0.14 pyrazinamide Uncertain significance Mutation from literature
embB 4247429 p.Met306Leu missense_variant 0.78 ethambutol 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
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 0.84 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575283 c.-65C>G upstream_gene_variant 0.81 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.27 ethionamide Uncertain significance
hadA 732110 p.Cys61Ser missense_variant 0.79 isoniazid Uncertain significance
rpoB 759694 c.-113C>T upstream_gene_variant 0.19 rifampicin Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.81 rifampicin Not assoc w R
rpoB 761314 p.Phe503Ser missense_variant 0.12 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.8 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.9 rifampicin Not assoc w R
rpoC 764229 p.Gln287Arg missense_variant 0.75 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.22 rifampicin Not assoc w R
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 0.83 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253566 c.969A>G synonymous_variant 0.84 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.74 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1416814 c.534G>A synonymous_variant 0.75 ethambutol Not assoc w R
embR 1417773 c.-426G>A upstream_gene_variant 0.2 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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 0.75 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.76 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
pncA 2289047 c.195C>T synonymous_variant 0.82 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.9 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.79 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.76 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568857 c.-178C>T upstream_gene_variant 0.78 kanamycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
streptomycin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044023 c.259C>T synonymous_variant 0.81 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.82 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.86 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4139633 c.123C>A synonymous_variant 0.89 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
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
embC 4242803 p.Val981Leu missense_variant 0.11 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.23 ethambutol Not assoc w R
ethA 4326632 p.His281Arg missense_variant 0.13 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
gid 4407588 c.615A>G synonymous_variant 0.73 streptomycin Not assoc w R
gid 4407787 p.Val139Gly missense_variant 0.76 streptomycin