TB-Profiler result

Run: SRR25827883
Summary

Run ID: SRR25827883

Sample name:

Date: 2024-04-15T20:38:53.114836

Number of reads: 6864269

Percentage reads mapped: 99.1

Median coverage: 237.0

Strain: lineage3;lineage4.2.2.2

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
lineage4.2.2 Euro-American (Ural) None 0.44
lineage3 East-African-Indian RD750 0.55
lineage4.2 Euro-American None 0.47
lineage4 Euro-American None 0.48
lineage4.2.2.2 Euro-American (Ural) None 0.43
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
c.707_708delAC Assoc w R High-level resistance
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol embB p.Gly406Ala Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Cys253* 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
gyrA 7570 p.Ala90Val missense_variant 0.47 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)
gyrA 7582 p.Asp94Gly missense_variant 0.51 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761109 p.Asp435Tyr missense_variant 0.55 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.48 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.47 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.47 isoniazid Assoc w R High-level resistance
katG 2155403 c.707_708delAC frameshift_variant 0.53 isoniazid Assoc w R High-level resistance
ahpC 2726145 c.-48G>A upstream_gene_variant 0.48 isoniazid Uncertain significance Mutation from literature
embB 4247730 p.Gly406Ala missense_variant 0.37 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.5 ethambutol Uncertain significance Mutation from literature
ethA 4326715 p.Cys253* stop_gained 0.46 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
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 8025 p.Asp242His missense_variant 0.52 levofloxacin
moxifloxacin
gyrA 8158 p.Ser286Leu missense_variant 0.54 levofloxacin
moxifloxacin
gyrA 8688 p.Ala463Ser missense_variant 0.45 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 0.6 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576077 c.730C>T synonymous_variant 0.48 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.53 ethionamide Not assoc w R - Interim
Rv0565c 657425 p.Gly16Ser missense_variant 0.41 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.6 rifampicin Not assoc w R
rpoB 761489 c.1683G>A synonymous_variant 0.48 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.52 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.51 rifampicin Not assoc w R
rpoC 764916 p.Leu516Pro missense_variant 0.48 rifampicin Uncertain significance
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 0.53 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpR5 779393 p.Arg135Gln missense_variant 0.44 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.46 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.52 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254743 c.-209C>T upstream_gene_variant 0.55 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1305050 p.Thr707Met missense_variant 0.43 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476561 n.2904C>T non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
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
bacA 2063685 c.1044G>A synonymous_variant 0.48 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.57 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.61 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 2289047 c.195C>T synonymous_variant 0.45 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.56 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.53 isoniazid Not assoc w R
ahpC 2726116 c.-77T>G upstream_gene_variant 0.53 isoniazid Uncertain significance
Rv2477c 2782498 c.1545C>T synonymous_variant 0.49 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
Rv2477c 2783786 p.Arg86His missense_variant 0.48 ethambutol Not assoc w R
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.39 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.41 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568425 c.255T>G synonymous_variant 0.14 streptomycin
amikacin
kanamycin
whiB7 3568428 c.252A>C synonymous_variant 0.18 streptomycin
amikacin
kanamycin
Rv3236c 3613591 c.-475G>A upstream_gene_variant 0.58 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.58 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.57 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 0.64 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.19 ethambutol
whiB6 4338399 p.Trp41Cys missense_variant 0.5 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.59 streptomycin Not assoc w R
gid 4408093 p.Gly37Glu missense_variant 0.53 streptomycin Uncertain significance