Run ID: SRR13838016
Sample name:
Date: 2024-10-04T05:49:48.559015
Number of reads: 2980782
Percentage reads mapped: 96.38
Median coverage: 103.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
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 | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1427 | p.Ala476Gly | missense_variant | 0.99 | isoniazid | |
gyrA | 7346 | p.Ile15Met | missense_variant | 0.99 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 8335 | p.Met345Arg | missense_variant | 0.98 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 9639 | p.Gly780Arg | missense_variant | 0.97 | levofloxacin | |
moxifloxacin | ||||||
fgd1 | 491505 | c.723G>A | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
mshA | 576310 | p.Ile321Met | missense_variant | 1.0 | isoniazid | |
ethionamide | ||||||
Rv0565c | 657451 | p.Ala7Val | missense_variant | 1.0 | ethionamide | |
rpoC | 766765 | c.3396A>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 766774 | c.3405T>C | synonymous_variant | 0.12 | rifampicin | |
mmpL5 | 775981 | p.Leu834Val | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 776732 | c.1749C>T | synonymous_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 777942 | p.Pro180Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
rplC | 800343 | c.-466G>C | upstream_gene_variant | 1.0 | linezolid | |
fbiC | 1303422 | c.492A>G | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
Rv1258c | 1406592 | p.Tyr250Cys | missense_variant | 1.0 | streptomycin | |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embR | 1416737 | p.Arg204Gln | missense_variant | 1.0 | ethambutol | |
rrl | 1475277 | n.1620G>C | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rpsA | 1833940 | c.399C>G | synonymous_variant | 0.12 | pyrazinamide | |
rpsA | 1834091 | p.Val184Met | missense_variant | 0.96 | pyrazinamide | |
tlyA | 1918473 | c.534T>A | synonymous_variant | 0.99 | capreomycin | |
Rv1979c | 2221849 | p.Leu439Gln | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2222231 | p.Met312Leu | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2222710 | p.Asn152Ile | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2223809 | c.-646_-645insT | upstream_gene_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
eis | 2714723 | p.Cys204Gly | missense_variant | 1.0 | kanamycin | |
amikacin | ||||||
folC | 2746975 | p.Asp208Glu | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv2477c | 2782420 | c.1623T>A | synonymous_variant | 1.0 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2784310 | c.-268T>A | upstream_gene_variant | 0.99 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
pepQ | 2860233 | c.186T>G | synonymous_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
thyA | 3073781 | p.Leu231Ile | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv3083 | 3448420 | c.-84_-83insT | upstream_gene_variant | 1.0 | ethionamide | |
whiB7 | 3568689 | c.-11delT | upstream_gene_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
embC | 4240494 | p.Gly211Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
embC | 4241732 | p.Ala624Pro | missense_variant | 1.0 | ethambutol | |
embA | 4245672 | p.Gly814Arg | missense_variant | 0.98 | ethambutol | |
embB | 4247458 | p.Tyr315* | stop_gained | 0.96 | ethambutol | |
aftB | 4268265 | p.Leu191Gln | missense_variant | 1.0 | ethambutol |