Run ID: SRR2024949
Sample name:
Date: 2024-10-03T18:47:37.116966
Number of reads: 9929956
Percentage reads mapped: 95.94
Median coverage: 203.0
Strain: lineage4.4.2
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.4 | Euro-American | None | 1.0 |
lineage4.4.2 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Leu430Pro | Assoc w R | |
p.Asp435Gly | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB | ||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embA | c.-12C>T | Uncertain significance | Mutation from literature |
embB | p.Met306Val | Assoc w R | ||
pyrazinamide | pncA | c.-11A>G | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
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 | ||||
clofazimine | ||||
para-aminosalicylic_acid | thyX | c.-16C>T | Mutation from literature | |
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | 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 | 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 |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | amikacin | Assoc w R | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 1.0 | pyrazinamide | Assoc w R | |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | Mutation from literature | |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 0.99 | ethambutol | 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 |
---|---|---|---|---|---|---|
gyrB | 6184 | c.945C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | 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 | 7739 | c.438C>T | synonymous_variant | 1.0 | levofloxacin | |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13663 | c.-105C>G | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
rpoB | 761981 | c.2175C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 778325 | p.Gln52His | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
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 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 | 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 | |||||
Rv2752c | 3066099 | p.Met31Ile | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
thyA | 3073954 | p.Gly173Asp | missense_variant | 1.0 | para-aminosalicylic_acid | |
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 | |||||
mtrA | 3627455 | c.-106A>G | upstream_gene_variant | 1.0 | rifampicin | Uncertain significance |
bedaquiline | ||||||
clpC1 | 4040102 | p.Met201Ile | missense_variant | 1.0 | pyrazinamide | |
embC | 4238963 | c.-900C>T | upstream_gene_variant | 0.99 | ethambutol | Not assoc w R |
embC | 4242550 | c.2688C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245406 | p.Ala725Val | missense_variant | 1.0 | ethambutol | Uncertain significance |
embA | 4246508 | c.3276G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4268928 | c.906C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
ubiA | 4269375 | c.459G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326041 | p.Leu478Arg | missense_variant | 1.0 | ethionamide | 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 | 4407956 | p.Arg83Gly | missense_variant | 1.0 | streptomycin | Uncertain significance |