TB-Profiler result

Run: ERR13266803
Summary

Run ID: ERR13266803

Sample name:

Date: 2025-02-11T18:59:31.526347

Number of reads: 6280747

Percentage reads mapped: 99.43

Median coverage: 167.0

Strain: lineage1.2.2.2;lineage3

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 0.16
lineage1.2.2 Indo-Oceanic RD239 0.81
lineage1.2.2.2 Indo-Oceanic RD239 0.81
lineage1 Indo-Oceanic RD239 0.82
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin gid c.362delA 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 761140 p.His445Leu missense_variant 0.21 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.22 isoniazid Assoc w R High-level resistance
gid 4407840 c.362delA frameshift_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
gyrB 5075 c.-165C>T upstream_gene_variant 0.85 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.75 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.76 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 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8525 c.1224C>T synonymous_variant 0.77 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13198 p.Thr121Ala missense_variant 0.79 isoniazid Uncertain significance
Rv0010c 13298 p.Ile87Met missense_variant 0.78 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.81 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.83 isoniazid Not assoc w R
Rv0010c 13548 p.Thr4Ile missense_variant 0.8 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.86 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 619869 c.-22C>A upstream_gene_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.13 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.79 ethionamide
hadA 732245 p.Asp106Asn missense_variant 0.84 isoniazid Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.8 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.25 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.15 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 0.8 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.8 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpR5 779275 p.Arg96Trp missense_variant 0.17 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.82 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254747 c.-213C>A upstream_gene_variant 0.86 levofloxacin
moxifloxacin
isoniazid
rifampicin
embR 1417019 p.Cys110Tyr missense_variant 0.83 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.82 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.83 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473009 n.1164T>A non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473949 n.292C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1474065 n.408C>T non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.75 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.99 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 0.78 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin 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 2168742 p.Gly624Asp missense_variant 0.83 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.82 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2222706 c.458_459insA frameshift_variant 0.79 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.75 bedaquiline Uncertain significance
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.16 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.2 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.82 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.81 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.2 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.2 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.79 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.83 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.83 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
fbiA 3640390 c.-153A>C upstream_gene_variant 0.85 pretomanid
delamanid
clofazimine
rpoA 3878817 c.-310T>A upstream_gene_variant 0.83 rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.79 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.12 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.84 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.84 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.81 ethambutol Not assoc w R
embC 4241150 p.Ile430Val missense_variant 0.85 ethambutol
embC 4242075 p.Arg738Gln missense_variant 0.14 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.86 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.89 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.83 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.78 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.82 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.86 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.82 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.84 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.82 streptomycin Not assoc w R