Run ID: ERR4872048
Sample name:
Date: 2024-10-03T22:12:25.821860
Number of reads: 4268615
Percentage reads mapped: 99.78
Median coverage: 137.0
Strain: lineage4.7
Spoligotype:
Drug-resistance: XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.7 | Euro-American (mainly T) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Phe424Val | Uncertain significance | Mutation from literature |
p.Leu430Pro | Assoc w R | |||
p.Asp435Gly | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB | ||
isoniazid | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>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.Gly406Ala | Assoc w R | |
pyrazinamide | pncA | p.Thr76Pro | Assoc w R | |
streptomycin | gid | c.102delG | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1401A>G | Assoc w R | |
capreomycin | rrs | n.1401A>G | Assoc w R | |
tlyA | c.351dupG | Assoc w R | ||
kanamycin | rrs | n.1401A>G | Assoc w R | |
cycloserine | ||||
ethionamide | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T |
ethA | c.89delA | Assoc w R | ||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid | rplC | p.Cys154Arg | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761076 | p.Phe424Val | missense_variant | 1.0 | rifampicin | Uncertain significance | Mutation from literature |
rpoB | 761095 | p.Leu430Pro | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpoB | 761110 | p.Asp435Gly | missense_variant | 1.0 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
rplC | 801268 | p.Cys154Arg | missense_variant | 0.99 | linezolid | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.98 | amikacin | Assoc w R | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
inhA | 1673423 | c.-779G>T | upstream_gene_variant | 0.99 | ethionamide | Assoc w R - Interim | Alias fabG1_c.-17G>T |
isoniazid | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
tlyA | 1918289 | c.351dupG | frameshift_variant | 1.0 | capreomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289016 | p.Thr76Pro | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247730 | p.Gly406Ala | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4327384 | c.89delA | frameshift_variant | 1.0 | ethionamide | Assoc w R | |
gid | 4408100 | c.102delG | 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 | |||||
Rv0565c | 656579 | p.Cys298Arg | missense_variant | 1.0 | ethionamide | Uncertain significance |
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 |
Rv1129c | 1253535 | p.Phe334Leu | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474294 | n.637C>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
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 | |||||
ribD | 2986827 | c.-12G>A | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
Rv2680 | 2996053 | c.-52_-51insCA | upstream_gene_variant | 0.28 | capreomycin | |
Rv2680 | 2996059 | c.-46C>T | upstream_gene_variant | 0.31 | capreomycin | |
Rv2680 | 2996060 | c.-45T>A | upstream_gene_variant | 0.33 | capreomycin | |
Rv2680 | 2996104 | c.-1_1insCA | frameshift_variant&start_lost | 0.3 | capreomycin | Uncertain significance |
Rv2681 | 2996110 | c.-629C>T | upstream_gene_variant | 0.26 | capreomycin | |
Rv2680 | 2996111 | p.Ser3Thr | missense_variant | 0.26 | capreomycin | |
ald | 3086896 | c.79dupA | frameshift_variant | 1.0 | cycloserine | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243190 | c.-43G>C | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4249732 | c.3219C>G | 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 | |||||
gid | 4408406 | c.-204A>C | upstream_gene_variant | 0.99 | streptomycin |