TB-Profiler result

Run: ERR3324330
Summary

Run ID: ERR3324330

Sample name:

Date: 2024-03-25T23:01:47.097091

Number of reads: 2063393

Percentage reads mapped: 99.19

Median coverage: 90.0

Strain: lineage4.8;lineage5.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.92
lineage4.8 Euro-American (mainly T) RD219 0.85
lineage5.1.1 West-Africa 1 RD711 0.08
lineage5 West-Africa 1 RD711 0.1
lineage5.1 West-Africa 1 RD711 0.1
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
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
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 770 p.Ala257Val missense_variant 0.88 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.18 isoniazid Not assoc w R
Rv0010c 13579 c.-21G>A upstream_gene_variant 0.2 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.14 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
hadA 731750 c.-180G>C upstream_gene_variant 0.12 isoniazid
rpoB 763031 c.3225T>C synonymous_variant 0.1 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 0.18 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
Rv1258c 1406402 c.939C>G synonymous_variant 0.88 streptomycin
isoniazid
pyrazinamide
embR 1417554 c.-207C>G upstream_gene_variant 0.18 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.85 capreomycin Not assoc w R
linezolid Not assoc w R
fabG1 1673338 c.-102G>A upstream_gene_variant 0.13 ethionamide
isoniazid
tsnR 1853565 c.-41G>A upstream_gene_variant 0.17 linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.2 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2101840 c.1203G>A synonymous_variant 0.17 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ndh 2101921 c.1122G>A synonymous_variant 0.25 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ndh 2103112 c.-70G>T upstream_gene_variant 0.15 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.18 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.81 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290062 c.-821G>A upstream_gene_variant 0.23 pyrazinamide
Rv2477c 2783769 p.Gly92Arg missense_variant 0.87 ethambutol Uncertain significance
moxifloxacin
streptomycin Uncertain significance
levofloxacin
kanamycin
rifampicin Uncertain significance
amikacin
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.87 capreomycin
Rv3083 3449644 p.Ala381Thr missense_variant 0.79 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.34 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840932 c.489C>T synonymous_variant 0.14 cycloserine
ddn 3986987 c.144G>T synonymous_variant 0.16 delamanid Not assoc w R - Interim
pretomanid
ddn 3987180 p.Asp113Asn missense_variant 0.19 delamanid Uncertain significance
pretomanid
glpK 4138377 p.Val460Ala missense_variant 0.13 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 4139131 p.Glu209Lys missense_variant 0.15 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Uncertain significance
embC 4239843 c.-20A>C upstream_gene_variant 0.1 ethambutol Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 0.18 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.14 ethambutol Not assoc w R
aftB 4268050 p.Pro263Thr missense_variant 0.81 ethambutol
ethA 4326928 c.546C>T synonymous_variant 0.18 ethionamide Not assoc w R - Interim
ethA 4327103 p.Gly124Asp missense_variant 0.18 ethionamide Uncertain significance
whiB6 4338547 c.-26A>G upstream_gene_variant 0.12 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 4338732 c.-211C>T upstream_gene_variant 0.26 capreomycin
amikacin
kanamycin
gid 4407790 p.Ala138Val missense_variant 0.8 streptomycin Uncertain significance