Run ID: SRR4034747
Sample name:
Date: 2024-04-14T15:26:02.965894
Number of reads: 21488552
Percentage reads mapped: 98.52
Median coverage: 355.0
Strain: lineage4.4.1.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.4.1 | Euro-American (S-type) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.4.1.1 | Euro-American | None | 1.0 |
lineage4.4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Asp | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Ile | Assoc w R | |
pyrazinamide | pncA | p.Thr160Arg | Uncertain significance | Mutation from literature |
streptomycin | gid | c.475delA | 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.His445Asp | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288763 | p.Thr160Arg | missense_variant | 1.0 | pyrazinamide | Uncertain significance | Mutation from literature |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R | |
gid | 4407727 | c.475delA | frameshift_variant | 1.0 | streptomycin | Assoc w R |
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 | |||||
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 | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.1 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
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 |
ndh | 2102990 | p.Val18Ala | missense_variant | 1.0 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Not assoc w R | |||||
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2222341 | p.Met275Thr | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
Rv3236c | 3612665 | p.Val151Ala | 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 | |||||
fbiA | 3641010 | c.468C>T | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
clpC1 | 4040711 | c.-7G>T | upstream_gene_variant | 1.0 | pyrazinamide | Uncertain significance |
embC | 4238963 | c.-900C>T | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245512 | c.2280G>C | synonymous_variant | 1.0 | ethambutol | 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 | ||||||
whiB6 | 4338783 | c.-262C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin |