TB-Profiler result

Run: ERR1034902
Summary

Run ID: ERR1034902

Sample name:

Date: 2024-03-27T02:54:19.434954

Number of reads: 7509952

Percentage reads mapped: 95.1

Median coverage: 169.0

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 1.0
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 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.Ile194Thr Uncertain significance Mutation from literature
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
p.Met423Thr Uncertain significance Mutation from literature
pyrazinamide pncA p.Val125Gly Assoc w R
streptomycin gid p.Ala80Pro Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ile194Thr Uncertain significance Mutation from literature
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 7582 p.Asp94Ala missense_variant 1.0 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 1.0 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.99 kanamycin Assoc w R
capreomycin Assoc w R
amikacin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.99 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
ethionamide Uncertain significance Mutation from literature
pncA 2288868 p.Val125Gly missense_variant 1.0 pyrazinamide Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol Assoc w R
embB 4247781 p.Met423Thr missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
gid 4407965 p.Ala80Pro missense_variant 0.99 streptomycin 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
gyrB 6140 p.Val301Leu missense_variant 1.0 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 490655 c.-128T>C upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
rpoB 761998 p.Leu731Pro missense_variant 1.0 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid Uncertain significance
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid Uncertain significance
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.1 capreomycin
linezolid
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.1 capreomycin
linezolid
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.18 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476032 n.2375C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1476035 n.2378G>A non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.1 capreomycin
linezolid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethR 4328127 c.579G>C synonymous_variant 1.0 ethionamide Not assoc w R - Interim
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 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R