Run ID: ERR1034902
Sample name:
Date: 2024-10-04T17:33:37.592148
Number of reads: 7509952
Percentage reads mapped: 95.1
Median coverage: 171.0
Strain: lineage4.3.4.2
Spoligotype:
Drug-resistance: Pre-XDR-TB
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 | 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 |
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 | amikacin | Assoc w R | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.99 | 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) | |||||
inhA | 1674782 | p.Ile194Thr | missense_variant | 1.0 | ethionamide | Uncertain significance | Mutation from literature |
isoniazid | 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 |
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 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
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 | 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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
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 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
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 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
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 | 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 | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |