Run ID: ERR1035301
Sample name:
Date: 2024-10-04T21:34:41.178411
Number of reads: 9715631
Percentage reads mapped: 96.02
Median coverage: 201.0
Strain: lineage4.3.2
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 1.0 |
lineage4.3.2 | Euro-American (LAM) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Tyr | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761139 | p.His445Tyr | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
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 | 0.99 | streptomycin | Not assoc w R |
Rv1129c | 1254590 | c.-56C>G | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.99 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R | |||||
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.16 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.16 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473815 | n.158T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473836 | n.179A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | Uncertain significance | |||||
rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
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 | 0.11 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474181 | n.524C>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.99 | 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 | 0.99 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2519131 | c.1017G>T | synonymous_variant | 1.0 | isoniazid | |
Rv2477c | 2784613 | c.-571T>C | upstream_gene_variant | 1.0 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2752c | 3065899 | p.Pro98Leu | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.99 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
ddn | 3986910 | p.Arg23Trp | missense_variant | 1.0 | pretomanid | |
delamanid | Uncertain significance | |||||
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 |
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 | 0.99 | streptomycin | Not assoc w R |