Run ID: SRR13837600
Sample name:
Date: 2024-10-04T11:43:16.241582
Number of reads: 2938966
Percentage reads mapped: 95.03
Median coverage: 99.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: HR-TB
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 | katG | c.926_927insA | Assoc w R | High-level resistance |
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 |
---|---|---|---|---|---|---|---|
katG | 2155185 | c.926_927insA | frameshift_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 8396 | p.Tyr365* | stop_gained | 1.0 | levofloxacin | |
moxifloxacin | ||||||
Rv0010c | 13610 | c.-52A>C | upstream_gene_variant | 1.0 | isoniazid | |
fgd1 | 490821 | p.Glu13Asp | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
mshA | 575959 | p.Gln204His | missense_variant | 1.0 | isoniazid | |
ethionamide | ||||||
rpoC | 766364 | p.Ala999Ser | missense_variant | 1.0 | rifampicin | |
mmpL5 | 775945 | p.Val846Leu | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 778345 | p.Leu46Ile | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 778992 | c.-512C>T | upstream_gene_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpR5 | 779231 | p.Glu81Val | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
rplC | 800526 | c.-283G>T | upstream_gene_variant | 1.0 | linezolid | |
fbiC | 1303186 | p.Tyr86His | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.19 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
bacA | 2063272 | c.1456delC | frameshift_variant | 0.99 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
ndh | 2101749 | p.Thr432Ser | missense_variant | 0.99 | isoniazid | |
delamanid | ||||||
ethionamide | ||||||
katG | 2155982 | p.Asn44His | missense_variant | 1.0 | isoniazid | |
PPE35 | 2168042 | c.2571G>C | synonymous_variant | 1.0 | pyrazinamide | |
PPE35 | 2169365 | c.1248C>T | synonymous_variant | 1.0 | pyrazinamide | |
Rv2477c | 2784596 | c.-554A>T | upstream_gene_variant | 1.0 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
thyX | 3067878 | p.Val23Gly | missense_variant | 1.0 | para-aminosalicylic_acid | |
fbiD | 3339188 | p.Thr24Ser | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
whiB7 | 3568496 | p.Pro62Ser | missense_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
Rv3236c | 3612323 | p.Pro265Gln | missense_variant | 1.0 | pyrazinamide | |
fbiA | 3641121 | c.579C>A | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | Not assoc w R - Interim | |||||
clpC1 | 4038346 | p.Glu787* | stop_gained | 1.0 | pyrazinamide | |
glpK | 4139375 | p.Asp127Glu | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
glpK | 4139545 | p.Leu71Val | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
embC | 4238896 | c.-967C>A | upstream_gene_variant | 1.0 | ethambutol | |
embC | 4239894 | p.Ala11Gly | missense_variant | 1.0 | ethambutol | |
ethA | 4327073 | p.Leu134Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |