Run ID: SRR7131120
Sample name:
Date: 2024-04-14T08:57:20.094822
Number of reads: 1834098
Percentage reads mapped: 99.99
Median coverage: 62.0
Strain: lineage4.1.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 1.0 |
lineage4.1.2 | Euro-American | None | 1.0 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 1.0 |
lineage4 | Euro-American | None | 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) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Met306Ile | Assoc w R | |
pyrazinamide | pncA | c.419_420dupGC | Assoc w R | |
streptomycin | rpsL | p.Lys88Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
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 |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Assoc w R | |
kanamycin | Assoc w R | ||||||
amikacin | Assoc w R | ||||||
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 1.0 | 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 | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288821 | c.419_420dupGC | frameshift_variant | 0.94 | pyrazinamide | Assoc w R | |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | 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 | |||||
fgd1 | 491591 | p.Lys270Met | missense_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 1.0 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 766487 | p.Pro1040Ser | missense_variant | 1.0 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781276 | c.-284A>C | upstream_gene_variant | 1.0 | streptomycin | |
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 | ||||||
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 | |||||
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 | isoniazid | |
Rv2680 | 2996034 | c.-71G>A | upstream_gene_variant | 0.2 | capreomycin | Uncertain significance |
Rv2680 | 2996085 | c.-20G>A | upstream_gene_variant | 0.13 | capreomycin | Uncertain significance |
Rv2680 | 2996136 | p.Ser11Asn | missense_variant | 0.21 | capreomycin | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
embC | 4239298 | c.-565C>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 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 | ethambutol | Not assoc w R |
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 |