Run ID: SRR13837897
Sample name:
Date: 2024-10-05T03:36:32.203676
Number of reads: 2938311
Percentage reads mapped: 98.01
Median coverage: 100.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | fbiC | c.170dupA | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
c.1116delC | Assoc w R - Interim | Confers DLM-PMD cross-resistance | ||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
fbiC | 1303099 | c.170dupA | frameshift_variant | 1.0 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
fbiC | 1304043 | c.1116delC | frameshift_variant | 1.0 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 9490 | p.Gly730Asp | missense_variant | 0.99 | levofloxacin | |
moxifloxacin | ||||||
Rv0010c | 13883 | c.-325T>A | upstream_gene_variant | 0.99 | isoniazid | |
fgd1 | 491231 | p.Phe150Tyr | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
Rv0565c | 656020 | p.Gly484Val | missense_variant | 1.0 | ethionamide | |
rpoC | 766128 | p.Ala920Gly | missense_variant | 1.0 | rifampicin | |
rpsL | 781503 | c.-57T>C | upstream_gene_variant | 1.0 | streptomycin | |
rplC | 800381 | c.-428A>G | upstream_gene_variant | 1.0 | linezolid | Uncertain significance |
sigE | 1364655 | p.Met81Ile | missense_variant | 1.0 | pyrazinamide | |
Rv1258c | 1406861 | p.Ile160Met | missense_variant | 1.0 | streptomycin | |
pyrazinamide | ||||||
isoniazid | ||||||
Rv1258c | 1407463 | c.-123G>C | upstream_gene_variant | 1.0 | streptomycin | |
pyrazinamide | ||||||
isoniazid | ||||||
rrs | 1472303 | n.458G>A | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474235 | n.578G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475139 | n.1482C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476248 | n.2591G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476576 | n.2919C>G | non_coding_transcript_exon_variant | 0.99 | capreomycin | |
linezolid | ||||||
bacA | 2063299 | p.Trp477Leu | missense_variant | 0.99 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
kasA | 2518209 | p.Thr32Arg | missense_variant | 1.0 | isoniazid | |
folC | 2746788 | p.Ala271Pro | missense_variant | 1.0 | para-aminosalicylic_acid | |
thyX | 3067214 | p.Ser244Arg | missense_variant | 1.0 | para-aminosalicylic_acid | |
fbiD | 3339396 | c.279C>T | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
mtrA | 3627293 | p.Glu19Asp | missense_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
rpoA | 3878048 | p.Ala154Ser | missense_variant | 1.0 | rifampicin | |
panD | 4044922 | c.-641G>T | upstream_gene_variant | 1.0 | pyrazinamide | |
glpK | 4139628 | p.Gln43Leu | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
embB | 4248368 | p.Leu619Val | missense_variant | 1.0 | ethambutol | |
ethA | 4327082 | p.Cys131Ser | missense_variant | 1.0 | ethionamide | |
ethA | 4327097 | p.Leu126His | missense_variant | 1.0 | ethionamide | |
gid | 4407792 | c.411G>C | synonymous_variant | 1.0 | streptomycin |