Run ID: SRR16149126
Sample name:
Date: 2024-10-03T20:38:42.653701
Number of reads: 1798718
Percentage reads mapped: 76.91
Median coverage: 43.0
Strain: lineage4.2.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.2.2.1 | Euro-American | None | 1.0 |
lineage4.2.2 | Euro-American (Ural) | None | 0.99 |
lineage4.2 | Euro-American | None | 0.99 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Tyr | 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) |
p.Ile194Thr | Uncertain significance | Mutation from literature | ||
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
p.Ile194Thr | Uncertain significance | Mutation from literature | ||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761139 | p.His445Tyr | missense_variant | 0.92 | rifampicin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 1.0 | 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) | |||||
inhA | 1674782 | p.Ile194Thr | missense_variant | 1.0 | ethionamide | Uncertain significance | Mutation from literature |
isoniazid | Uncertain significance | Mutation from literature | |||||
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1131 | c.1131C>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
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 | |||||
mshA | 576077 | c.730C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R - Interim | |||||
Rv0565c | 656226 | c.1245C>G | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
rpoC | 763537 | c.168C>G | synonymous_variant | 0.12 | rifampicin | |
rpoC | 763546 | c.177A>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 764365 | c.996C>T | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 764377 | c.1008C>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 764380 | c.1011G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 764387 | c.1018_1020delTTGinsCTC | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.19 | rifampicin | Not assoc w R - Interim |
rpoC | 764662 | c.1293G>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 764706 | p.Leu446Gln | missense_variant | 0.15 | rifampicin | Uncertain significance |
rpoC | 764752 | c.1383G>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 765764 | p.Ile799Leu | missense_variant | 1.0 | rifampicin | |
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 |
rplC | 800204 | c.-605T>C | upstream_gene_variant | 1.0 | linezolid | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.16 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472558 | n.713G>A | non_coding_transcript_exon_variant | 0.11 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472597 | n.752G>A | non_coding_transcript_exon_variant | 0.11 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472607 | n.762G>A | non_coding_transcript_exon_variant | 0.13 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472790 | n.945T>C | non_coding_transcript_exon_variant | 0.11 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.16 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrl | 1474488 | n.831G>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474516 | n.859C>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474537 | n.880G>A | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475883 | n.2226A>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476529 | n.2872A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | ||||||
rpsA | 1834294 | c.753G>C | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834306 | c.765T>C | synonymous_variant | 0.15 | pyrazinamide | |
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 |
bacA | 2063685 | c.1044G>A | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R | |||||
bacA | 2063911 | p.Ile273Thr | missense_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
ndh | 2102726 | p.His106Arg | missense_variant | 1.0 | isoniazid | Uncertain significance |
delamanid | Uncertain significance | |||||
ethionamide | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
ald | 3086742 | c.-78A>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
embC | 4239334 | c.-529T>C | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | 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 | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4408009 | p.Val65Ala | missense_variant | 1.0 | streptomycin | Uncertain significance |