TB-Profiler result

Run: ERR2510548
Summary

Run ID: ERR2510548

Sample name:

Date: 2024-06-18T07:51:10.452779

Number of reads: 2374544

Percentage reads mapped: 99.4

Median coverage: 74.0

Strain: lineage1.1.2;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
lineage1.1.2 Indo-Oceanic RD239 0.89
lineage1.1 Indo-Oceanic RD239 0.93
lineage4 Euro-American None 0.1
lineage1 Indo-Oceanic RD239 0.92
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu452Pro Assoc w R
isoniazid inhA p.Ile21Val Uncertain significance Mutation from literature
katG p.Ser315Asn Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin gid c.351delG 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)
ofloxacin
levofloxacin gyrA p.Ala90Val 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 7570 p.Ala90Val missense_variant 0.97 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761161 p.Leu452Pro missense_variant 0.91 rifampicin Assoc w R
inhA 1674262 p.Ile21Val missense_variant 0.83 isoniazid Uncertain significance Mutation from literature
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid Assoc w R High-level resistance
gid 4407851 c.351delG frameshift_variant 0.86 streptomycin 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
gyrB 6112 p.Met291Ile missense_variant 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7158 c.1931_1933delCCG disruptive_inframe_deletion 0.89 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.81 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.91 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
gyrA 9629 c.2328C>T synonymous_variant 0.9 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13298 p.Ile87Met missense_variant 0.89 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.85 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.95 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.88 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.93 rifampicin Not assoc w R
nusG 734214 c.-40T>C upstream_gene_variant 0.96 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.97 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.84 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.96 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 0.94 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.95 linezolid 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
embR 1417019 p.Cys110Tyr missense_variant 0.88 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.91 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.89 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853597 c.-9G>C upstream_gene_variant 0.13 linezolid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.93 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.96 linezolid Not assoc w R
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 2062922 p.Ile603Val missense_variant 0.85 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.95 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.91 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.84 pyrazinamide Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.13 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.87 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 0.87 isoniazid
eis 2714773 p.Pro187Arg missense_variant 0.12 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.81 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.85 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.87 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.9 cycloserine
ald 3086950 p.Ala44Val missense_variant 0.81 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.92 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.91 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.22 pyrazinamide Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.88 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.91 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.87 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.83 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242992 p.Thr1044Pro missense_variant 0.13 ethambutol Uncertain significance
embA 4243848 p.Val206Met missense_variant 0.94 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.81 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.91 ethambutol Not assoc w R
embB 4248026 p.Ala505Thr missense_variant 0.86 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.92 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.9 ethambutol Not assoc w R
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 4338603 c.-82C>T upstream_gene_variant 0.87 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 0.92 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.91 streptomycin Not assoc w R