TB-Profiler result

Run: ERR3132157
Summary

Run ID: ERR3132157

Sample name:

Date: 2024-03-24T18:43:53.025653

Number of reads: 3516951

Percentage reads mapped: 99.46

Median coverage: 180.0

Strain: lineage1.2.1.2.1;lineage4.1.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.2 Indo-Oceanic RD239 0.93
lineage4.1.2 Euro-American None 0.05
lineage4 Euro-American None 0.09
lineage1 Indo-Oceanic RD239 0.93
lineage1.2.1.2.1 Indo-Oceanic RD239 0.93
lineage1.2.1 Indo-Oceanic RD239 0.93
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Thr400Ala Uncertain significance Mutation from literature
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Ser94Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser140Asn Uncertain significance Mutation from literature
ethambutol embB p.Gln497Pro Uncertain significance Mutation from literature
pyrazinamide
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ser94Ala Assoc w R - Interim
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 761004 p.Thr400Ala missense_variant 0.93 rifampicin Uncertain significance Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 0.95 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.96 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.93 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA 1674481 p.Ser94Ala missense_variant 0.94 ethionamide Assoc w R - Interim
isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155693 p.Ser140Asn missense_variant 0.11 isoniazid Uncertain significance Mutation from literature
embB 4248003 p.Gln497Pro missense_variant 0.94 ethambutol Uncertain significance Mutation from literature
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 1302 c.1302C>A synonymous_variant 0.91 isoniazid Not assoc w R
gyrB 6112 p.Met291Ile missense_variant 0.94 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 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9260 c.1959G>C synonymous_variant 0.92 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 13175 c.384T>C synonymous_variant 0.93 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.92 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.91 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.94 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575368 c.21T>C synonymous_variant 0.92 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.92 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.92 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.92 rifampicin Not assoc w R
rpoC 763531 c.162G>C synonymous_variant 0.97 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.97 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.97 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 0.94 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.91 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406312 c.1029T>C synonymous_variant 0.92 streptomycin Not assoc w R
isoniazid Not assoc w R
pyrazinamide Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.92 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.97 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.93 ethambutol
atpE 1460907 c.-138T>C upstream_gene_variant 0.95 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674162 c.-40C>T upstream_gene_variant 0.97 ethionamide Uncertain significance
isoniazid Not assoc w R
tsnR 1853974 c.369C>T synonymous_variant 0.91 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 0.89 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 0.92 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.94 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.93 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 2288875 p.Arg123Gly missense_variant 0.94 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.95 isoniazid
kasA 2519048 p.Gly312Ser missense_variant 0.93 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.91 isoniazid
Rv2680 2996003 c.-101_-50delGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN upstream_gene_variant 0.94 capreomycin
Rv2680 2996003 c.-101_-51delTGACCTCCGCCGGCGACGATGCAGAGCGCAGCGATGAGGAGGAGCGGCGCT upstream_gene_variant 0.25 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339417 c.300A>G synonymous_variant 0.92 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.86 ethionamide Uncertain significance
whiB7 3568488 c.191delG frameshift_variant 0.95 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.95 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640557 c.15T>C synonymous_variant 0.93 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.93 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.92 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 4138951 p.Gln269* stop_gained 0.93 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.92 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.93 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243580 c.348G>A synonymous_variant 0.92 ethambutol Not assoc w R
embA 4244420 c.1188G>C synonymous_variant 0.94 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.96 ethambutol Not assoc w R
embB 4247480 p.Phe323Leu missense_variant 0.94 ethambutol Uncertain significance
embB 4247578 c.1065G>A synonymous_variant 0.91 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.9 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.91 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.93 ethambutol Not assoc w R
ubiA 4269864 c.-32delG upstream_gene_variant 0.91 ethambutol Not assoc w R
whiB6 4338361 p.Arg54Gln missense_variant 0.9 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin 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 0.9 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 0.93 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.93 streptomycin Not assoc w R