Run ID: SRR28393588
Sample name:
Date: 2024-05-22T18:56:58.258768
Number of reads: 5232674
Percentage reads mapped: 99.61
Median coverage: 147.0
Strain: lineage4.1.2.1;lineage4.8
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 0.68 |
lineage4.1.2 | Euro-American | None | 0.7 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.7 |
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.29 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Gln497Arg | Assoc w R | |
pyrazinamide | pncA | p.Thr135Pro | Assoc w R | |
streptomycin | rpsL | p.Lys88Thr | Uncertain significance | Mutation from literature |
gid | c.351delG | 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 | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781822 | p.Lys88Thr | missense_variant | 0.62 | streptomycin | Uncertain significance | Mutation from literature |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.34 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288839 | p.Thr135Pro | missense_variant | 0.35 | pyrazinamide | Assoc w R | |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.29 | ethambutol | Assoc w R | |
gid | 4407851 | c.351delG | frameshift_variant | 0.43 | 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 | 0.72 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.67 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.69 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 0.7 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.62 | ethionamide | Uncertain significance |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.65 | rifampicin | Not assoc w R |
rpoB | 760555 | p.Glu250Gly | missense_variant | 0.74 | rifampicin | Not assoc w R - Interim |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.7 | 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 |
fbiC | 1302920 | c.-11G>A | upstream_gene_variant | 0.66 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.24 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.69 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
bacA | 2063078 | c.1650dupG | frameshift_variant | 0.34 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
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 | 0.56 | isoniazid | |
folC | 2746277 | p.Asp441Gly | missense_variant | 0.75 | para-aminosalicylic_acid | |
Rv2680 | 2996085 | c.-20G>A | upstream_gene_variant | 0.17 | capreomycin | Uncertain significance |
Rv2680 | 2996136 | p.Ser11Asn | missense_variant | 0.16 | capreomycin | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.7 | cycloserine | |
ald | 3087095 | c.276C>T | synonymous_variant | 0.3 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.76 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
glpK | 4139183 | c.572dupG | frameshift_variant | 0.37 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embC | 4239298 | c.-565C>T | upstream_gene_variant | 0.72 | 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 | 0.69 | ethambutol | Not assoc w R |
ubiA | 4269015 | p.Glu273Asp | missense_variant | 0.24 | ethambutol | Uncertain significance |
ethA | 4326908 | p.Thr189Lys | missense_variant | 0.33 | ethionamide | Uncertain significance |
ethA | 4327761 | c.-288C>T | upstream_gene_variant | 0.68 | ethionamide | |
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 | 0.72 | capreomycin | |
amikacin | ||||||
kanamycin |