TB-Profiler result

Run: ERR3077948
Summary

Run ID: ERR3077948

Sample name:

Date: 2024-03-25T23:00:01.418501

Number of reads: 1949837

Percentage reads mapped: 99.4

Median coverage: 60.0

Strain: lineage1.1.2;lineage3.1.1

Spoligotype:

Drug-resistance: MDR-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 0.38
lineage1.1.2 Indo-Oceanic RD239 0.61
lineage3.1.1 East-African-Indian RD750 0.39
lineage1.1 Indo-Oceanic RD239 0.59
lineage1 Indo-Oceanic RD239 0.6
lineage3.1 East-African-Indian RD750 0.27
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asp Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gly406Ser Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Ala46Val Assoc w R - Interim
streptomycin rrs n.517C>T Assoc w R
gid c.115delC Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
rpoB 761139 p.His445Asp missense_variant 0.28 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.72 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.62 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289105 p.Ala46Val missense_variant 0.69 pyrazinamide Assoc w R - Interim
embB 4247429 p.Met306Val missense_variant 0.6 ethambutol Assoc w R
embB 4247729 p.Gly406Ser missense_variant 0.34 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.38 ethambutol Uncertain significance Mutation from literature
gid 4408087 c.115delC frameshift_variant 0.29 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 0.59 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.55 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.62 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 0.68 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.64 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
Rv0565c 657081 c.390G>A synonymous_variant 0.55 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.59 ethionamide
hadA 732154 c.225G>C synonymous_variant 0.61 isoniazid Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.67 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.42 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.35 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 0.55 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.59 rifampicin Not assoc w R
rpoC 764585 p.Leu406Phe missense_variant 0.24 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.51 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_variant 0.64 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 1.0 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 800250 c.-559C>G upstream_gene_variant 0.6 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.51 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
embR 1417019 p.Cys110Tyr missense_variant 0.66 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.66 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.71 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.53 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.51 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 0.48 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 0.71 pyrazinamide Uncertain significance
PPE35 2168435 c.2178C>T synonymous_variant 0.59 pyrazinamide
PPE35 2170461 p.Gly51Glu missense_variant 0.38 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.62 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 2289047 c.195C>T synonymous_variant 0.32 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.31 pyrazinamide
pncA 2289472 c.-231G>A upstream_gene_variant 0.65 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.58 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.62 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.33 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.34 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 2996383 c.-356C>A upstream_gene_variant 0.79 capreomycin
Rv2681 2996912 c.174C>T synonymous_variant 0.73 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.67 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
fbiD 3339741 c.624G>A synonymous_variant 0.58 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.67 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.6 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 4040517 p.Val63Ala missense_variant 0.66 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.48 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.68 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
glpK 4138622 c.1134C>T synonymous_variant 0.41 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 4240172 p.Val104Met missense_variant 0.42 ethambutol Not assoc w R
embC 4240756 c.894G>T synonymous_variant 0.64 ethambutol
embC 4241042 p.Asn394Asp missense_variant 0.64 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.39 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.37 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 0.68 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.62 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.71 ethambutol Not assoc w R
embB 4249673 p.Ser1054Pro missense_variant 0.62 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.46 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.58 ethambutol Not assoc w R
ethA 4326453 p.Ala341Thr missense_variant 0.65 ethionamide
ethA 4328209 c.-736C>A upstream_gene_variant 0.71 ethionamide
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 0.63 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
whiB6 4338846 c.-325T>G upstream_gene_variant 0.49 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.54 streptomycin Not assoc w R
gid 4407935 p.Leu90Val missense_variant 0.72 streptomycin Uncertain significance
gid 4407944 p.Gln87Glu missense_variant 0.69 streptomycin Uncertain significance