TB-Profiler result

Run: ERR133938
Summary

Run ID: ERR133938

Sample name:

Date: 2024-10-03T15:10:02.110082

Number of reads: 8938516

Percentage reads mapped: 99.66

Median coverage: 196.0

Strain: lineage4.1;lineage4.8

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.15
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.85
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin eis c.-14C>T Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
capreomycin
kanamycin eis c.-14C>T Assoc w R Can only confer resistance if genetically linked to a functional Eis
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
gyrA 7570 p.Ala90Val missense_variant 0.15 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 0.2 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.14 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.13 isoniazid Assoc w R High-level resistance
eis 2715346 c.-14C>T upstream_gene_variant 0.17 amikacin Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
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 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.82 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.17 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.86 rifampicin Not assoc w R
rpoC 764438 c.1069C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 0.15 rifampicin Not assoc w R
rpoC 765863 p.Ile832Val missense_variant 0.13 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.14 linezolid
rplC 801019 p.Thr71Ala missense_variant 0.18 linezolid
atpE 1461209 c.165C>T synonymous_variant 0.19 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.84 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.18 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.86 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.83 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.19 cycloserine
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.25 ethionamide
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.87 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.13 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627390 c.-41G>A upstream_gene_variant 0.19 rifampicin Uncertain significance
bedaquiline
clpC1 4039729 p.Asp326Asn missense_variant 0.84 pyrazinamide Not assoc w R
embC 4242584 p.Ala908Thr missense_variant 0.14 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.11 ethambutol Not assoc w R
embB 4247296 c.783G>A synonymous_variant 0.17 ethambutol Not assoc w R - Interim
embB 4249408 c.2895G>A synonymous_variant 0.15 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 0.18 kanamycin
capreomycin
amikacin