Run ID: ERR6865775
Sample name:
Date: 2024-10-04T00:10:48.990496
Number of reads: 1652788
Percentage reads mapped: 99.51
Median coverage: 50.0
Strain: lineage4.1.1;lineage4.1.2.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 1.0 |
lineage4.1.2 | Euro-American | None | 0.29 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.27 |
lineage4 | Euro-American | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | None | 0.76 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Phe | 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.Ser315Asn | Assoc w R | High-level resistance | |
ethambutol | embB | p.Gln497Lys | Assoc w R | |
pyrazinamide | pncA | p.Leu4Trp | Assoc w R | |
streptomycin | gid | p.Tyr195* | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Ser91Pro | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrA | p.Ser91Pro | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
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 |
---|---|---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 0.75 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
rpoB | 761155 | p.Ser450Phe | missense_variant | 0.83 | rifampicin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.76 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
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) | |||||
katG | 2155168 | p.Ser315Asn | missense_variant | 0.8 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289231 | p.Leu4Trp | missense_variant | 0.7 | pyrazinamide | Assoc w R | |
embB | 4248002 | p.Gln497Lys | missense_variant | 0.79 | ethambutol | Assoc w R | |
gid | 4407618 | p.Tyr195* | stop_gained | 0.8 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5133 | c.-107A>C | upstream_gene_variant | 0.71 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrB | 6052 | p.Ile271Met | missense_variant | 0.8 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrB | 7221 | p.Ser661Thr | missense_variant | 0.84 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
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 | 0.98 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9620 | c.2319G>A | synonymous_variant | 0.35 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.25 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Not assoc w R | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 0.24 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.17 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765669 | p.His767Pro | missense_variant | 0.77 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781276 | c.-284A>C | upstream_gene_variant | 0.29 | streptomycin | |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800219 | c.-590T>C | upstream_gene_variant | 0.77 | linezolid | |
embR | 1416699 | p.Leu217Val | missense_variant | 0.8 | ethambutol | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
inhA | 1673865 | c.-337C>T | upstream_gene_variant | 0.78 | isoniazid | Uncertain significance |
ethionamide | 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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.23 | isoniazid | |
Rv2752c | 3065797 | p.Gln132Pro | missense_variant | 0.22 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
Rv2752c | 3066898 | c.-707C>T | upstream_gene_variant | 0.75 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3087605 | c.786G>T | synonymous_variant | 0.22 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrA | 3627511 | c.-162C>G | upstream_gene_variant | 0.74 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
panD | 4044944 | c.-663C>T | upstream_gene_variant | 0.37 | pyrazinamide | |
glpK | 4139183 | c.572dupG | frameshift_variant | 0.19 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
embC | 4239298 | c.-565C>T | upstream_gene_variant | 0.29 | 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 |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.73 | ethambutol | Not assoc w R |
ubiA | 4269298 | p.Ile179Thr | missense_variant | 0.67 | ethambutol | Uncertain significance |
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 | 4408159 | p.Arg15Pro | missense_variant | 0.29 | streptomycin | Uncertain significance |