TB-Profiler result

Run: ERR4797284
Summary

Run ID: ERR4797284

Sample name:

Date: 2024-04-16T02:26:45.476957

Number of reads: 4232004

Percentage reads mapped: 99.5

Median coverage: 117.0

Strain: lineage1.1.2;lineage2.2.1

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
lineage2 East-Asian RD105 0.11
lineage1.1 Indo-Oceanic RD239 0.88
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.08
lineage2.2 East-Asian (Beijing) RD105;RD207 0.08
lineage1 Indo-Oceanic RD239 0.9
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid
ethambutol
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)
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 0.15 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)
rpoB 761155 p.Ser450Leu missense_variant 0.13 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.14 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
dnaA 1519 p.Arg507Cys missense_variant 0.94 isoniazid Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.87 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.86 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7153 c.1914G>C synonymous_variant 0.89 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.85 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
Rv0010c 13298 p.Ile87Met missense_variant 0.92 isoniazid Not assoc w R
Rv0010c 13353 p.Ala69Val missense_variant 0.95 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 0.9 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575091 c.-257G>A upstream_gene_variant 0.9 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575907 p.Ala187Val missense_variant 0.14 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620553 c.663T>C synonymous_variant 0.11 capreomycin Not assoc w R
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.12 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.92 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.94 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.87 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.87 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.19 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.87 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpR5 779323 p.Ala112Ser missense_variant 0.83 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpR5 779414 p.Leu142Arg missense_variant 0.17 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.96 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406503 p.Val280Leu missense_variant 0.93 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.88 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.9 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.93 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475300 n.1643G>T non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.84 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.85 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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.87 pyrazinamide Uncertain significance
PPE35 2169813 c.794_799dupACAACT conservative_inframe_insertion 0.83 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.95 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 0.89 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.88 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.88 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.89 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 1.0 cycloserine
ald 3087824 c.1005G>A synonymous_variant 0.92 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.94 ethionamide Uncertain significance
whiB7 3568795 c.-116A>G upstream_gene_variant 0.11 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.15 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.89 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.12 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640211 c.-332T>G upstream_gene_variant 0.19 clofazimine
pretomanid
delamanid
clpC1 4040517 p.Val63Ala missense_variant 0.96 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 4239480 c.-383G>A upstream_gene_variant 0.95 ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.87 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.86 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 0.9 ethambutol Not assoc w R
embA 4245385 p.Thr718Ile missense_variant 0.92 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.92 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.87 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.16 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.1 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.93 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.88 ethambutol Not assoc w R
whiB6 4338224 c.297delC frameshift_variant 0.87 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 4338603 c.-82C>T upstream_gene_variant 0.9 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 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.87 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.14 streptomycin Not assoc w R