TB-Profiler result

Run: ERR4797100
Summary

Run ID: ERR4797100

Sample name:

Date: 2024-10-05T03:12:37.904933

Number of reads: 5036776

Percentage reads mapped: 99.59

Median coverage: 104.0

Strain: lineage1.1.2;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 0.8
lineage1.1.2 Indo-Oceanic RD239 0.18
lineage1.1 Indo-Oceanic RD239 0.12
lineage1 Indo-Oceanic RD239 0.18
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val 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)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Leu Assoc w R
pyrazinamide pncA p.Asp12Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.906A>G Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 761110 p.Asp435Val missense_variant 0.73 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.18 streptomycin Assoc w R
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance Mutation from literature
inhA 1673425 c.-777C>T upstream_gene_variant 0.84 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)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289207 p.Asp12Ala missense_variant 0.82 pyrazinamide Assoc w R
embB 4247429 p.Met306Leu missense_variant 0.81 ethambutol 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
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 0.31 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
gyrA 9360 p.Asp687Asn missense_variant 0.14 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13298 p.Ile87Met missense_variant 0.35 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
Rv0565c 657081 c.390G>A synonymous_variant 0.9 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.11 ethionamide
rpoB 759546 c.-261A>G upstream_gene_variant 0.13 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.82 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.27 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.82 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765857 p.Glu830Gln missense_variant 0.22 rifampicin Uncertain significance
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
mmpL5 776395 p.Phe696Leu missense_variant 0.16 bedaquiline Uncertain significance
clofazimine Not assoc w R
mmpL5 777626 c.855C>T synonymous_variant 0.81 bedaquiline Not assoc w R - Interim
clofazimine 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 0.23 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
embR 1417554 c.-207C>G upstream_gene_variant 0.12 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.18 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854045 p.Tyr147Cys missense_variant 0.12 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 0.16 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2103184 c.-142G>T upstream_gene_variant 0.8 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2156187 c.-76G>A upstream_gene_variant 0.65 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170785 c.-173T>C upstream_gene_variant 0.25 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.96 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.68 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.19 isoniazid
eis 2714545 p.Glu263Val missense_variant 0.48 kanamycin
amikacin
eis 2715016 p.Arg106His missense_variant 0.18 kanamycin Uncertain significance
amikacin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.28 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.7 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.8 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
Rv2681 2996912 c.174C>T synonymous_variant 0.28 capreomycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448440 c.-64A>C upstream_gene_variant 0.83 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.13 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
alr 3841473 c.-53G>A upstream_gene_variant 0.89 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.19 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.76 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.88 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 4241042 p.Asn394Asp missense_variant 0.16 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.84 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 0.21 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.3 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.26 ethambutol Not assoc w R
aftB 4268540 p.Met99Ile missense_variant 0.23 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.23 ethambutol 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 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 4407733 p.Gly157Glu missense_variant 0.8 streptomycin Uncertain significance