TB-Profiler result

Run: ERR4799013
Summary

Run ID: ERR4799013

Sample name:

Date: 2024-04-14T16:30:19.872089

Number of reads: 3275780

Percentage reads mapped: 99.43

Median coverage: 90.0

Strain: lineage1.1.2;lineage3

Spoligotype:

Drug-resistance: HR-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 0.06
lineage1.1.2 Indo-Oceanic RD239 0.87
lineage1.1 Indo-Oceanic RD239 0.85
lineage1 Indo-Oceanic RD239 0.87
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
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 0.88 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
katG 2155168 p.Ser315Thr missense_variant 0.16 isoniazid Assoc w R High-level resistance
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 5076 c.-164_-163insT upstream_gene_variant 0.87 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.88 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.8 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.84 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.97 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.82 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.9 rifampicin Not assoc w R
nusG 734555 p.Asn101Ser missense_variant 0.84 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.14 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.99 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.86 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.87 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.82 rifampicin Not assoc w R
rpoC 765358 p.Met663Ile missense_variant 0.89 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 0.98 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 0.89 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.96 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 0.86 ethambutol Not assoc w R
embR 1417051 c.297G>A synonymous_variant 0.86 ethambutol Not assoc w R - Interim
embR 1417554 c.-207C>G upstream_gene_variant 0.84 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.84 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.82 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.8 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.95 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 0.88 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 0.96 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.97 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.74 pyrazinamide Uncertain significance
PPE35 2168604 p.Pro670Leu missense_variant 0.14 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.96 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
pncA 2290018 c.-777C>T upstream_gene_variant 0.89 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.85 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.88 isoniazid
folC 2746927 c.672C>T synonymous_variant 0.84 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.12 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
Rv2681 2996912 c.174C>T synonymous_variant 0.82 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.85 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
Rv2752c 3065317 p.Ala292Asp missense_variant 0.86 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.88 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.93 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.9 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878875 c.-368C>T upstream_gene_variant 0.9 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.9 pyrazinamide Not assoc w R - Interim
panD 4045263 c.-982C>A upstream_gene_variant 0.81 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.93 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 0.85 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.78 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.77 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.84 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.85 ethambutol Not assoc w R
aftB 4267636 p.Arg401Trp missense_variant 0.82 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 0.87 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.76 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 0.81 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.97 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.92 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.8 streptomycin Not assoc w R
gid 4408144 p.Arg20Pro missense_variant 0.87 streptomycin Uncertain significance