Run ID: SRR13861296
Sample name:
Date: 2024-04-15T02:58:35.745696
Number of reads: 2335408
Percentage reads mapped: 77.92
Median coverage: 80.0
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 | 377 | p.Thr126Asn | missense_variant | 1.0 | isoniazid | |
dnaA | 1519 | p.Arg507Ser | missense_variant | 1.0 | isoniazid | |
gyrB | 5709 | p.Gly157Val | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 9028 | p.Val576Ala | missense_variant | 0.94 | levofloxacin | |
moxifloxacin | ||||||
fgd1 | 491212 | p.Ser144Arg | missense_variant | 0.15 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fgd1 | 491217 | c.435T>C | synonymous_variant | 0.14 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fgd1 | 491232 | c.450T>C | synonymous_variant | 0.15 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fgd1 | 491241 | p.Asp153Glu | missense_variant | 0.15 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fgd1 | 491244 | c.462T>C | synonymous_variant | 0.13 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
Rv0565c | 657669 | c.-199C>A | upstream_gene_variant | 0.97 | ethionamide | |
nusG | 734472 | c.219T>C | synonymous_variant | 0.13 | rifampicin | |
nusG | 734475 | c.222T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
nusG | 734481 | c.228C>G | synonymous_variant | 0.13 | rifampicin | |
nusG | 734499 | c.246G>C | synonymous_variant | 0.15 | rifampicin | |
nusG | 734559 | c.306T>C | synonymous_variant | 0.14 | rifampicin | |
nusG | 734610 | c.357C>G | synonymous_variant | 0.14 | rifampicin | |
rpoB | 762011 | c.2205G>C | synonymous_variant | 0.91 | rifampicin | Not assoc w R - Interim |
rpoB | 762279 | c.2474delA | frameshift_variant | 0.95 | rifampicin | |
rpoC | 764752 | c.1383G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 764764 | c.1395T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 764791 | c.1422C>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 764809 | c.1440C>T | synonymous_variant | 0.13 | rifampicin | Not assoc w R |
rpoC | 764824 | c.1455T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 764830 | c.1461C>G | synonymous_variant | 0.13 | rifampicin | |
rpoC | 764858 | c.1489T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 764872 | c.1503A>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 764893 | c.1524T>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 764911 | c.1542A>G | synonymous_variant | 0.16 | rifampicin | |
rpoC | 764923 | c.1554A>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoC | 764932 | c.1563C>A | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoC | 764968 | c.1599T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R |
rpoC | 765007 | c.1638T>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
mmpS5 | 778823 | p.Ile28Thr | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
rplC | 800279 | c.-530A>C | upstream_gene_variant | 1.0 | linezolid | |
fbiC | 1304640 | c.1710A>C | synonymous_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
Rv1258c | 1406376 | p.Gly322Val | missense_variant | 1.0 | streptomycin | |
isoniazid | ||||||
pyrazinamide | ||||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
tsnR | 1853370 | c.-236_-234delGCAinsTG | upstream_gene_variant | 0.13 | linezolid | |
tsnR | 1853384 | c.-222G>C | upstream_gene_variant | 0.13 | linezolid | |
tsnR | 1853394 | c.-212_-211delCTinsGC | upstream_gene_variant | 0.14 | linezolid | |
tsnR | 1853420 | c.-186T>G | upstream_gene_variant | 0.14 | linezolid | |
tsnR | 1853429 | c.-177G>C | upstream_gene_variant | 0.13 | linezolid | |
tsnR | 1853432 | c.-174G>C | upstream_gene_variant | 0.13 | linezolid | |
PPE35 | 2169882 | p.Ser244Ile | missense_variant | 1.0 | pyrazinamide | |
eis | 2714940 | c.392delA | frameshift_variant | 1.0 | amikacin | Uncertain significance |
kanamycin | Uncertain significance | |||||
Rv2477c | 2782900 | c.1143C>G | synonymous_variant | 0.99 | ethambutol | |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
kanamycin | ||||||
rifampicin | ||||||
amikacin | ||||||
ald | 3087311 | c.492C>G | synonymous_variant | 0.99 | cycloserine | |
Rv3236c | 3613629 | c.-513C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
mtrB | 3625750 | c.864G>A | synonymous_variant | 0.13 | bedaquiline | |
rifampicin | Not assoc w R - Interim | |||||
mtrB | 3625755 | p.Ala287Thr | missense_variant | 0.13 | bedaquiline | |
rifampicin | Uncertain significance | |||||
fbiB | 3642465 | p.Asp311His | missense_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
alr | 3840300 | p.Pro374His | missense_variant | 0.99 | cycloserine | |
rpoA | 3878288 | p.Thr74Pro | missense_variant | 0.91 | rifampicin | |
clpC1 | 4038671 | c.2034T>C | synonymous_variant | 0.12 | pyrazinamide | |
clpC1 | 4038740 | c.1965G>C | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4038748 | p.Arg653Cys | missense_variant | 0.14 | pyrazinamide | |
clpC1 | 4039415 | c.1289dupA | frameshift_variant | 0.96 | pyrazinamide | |
clpC1 | 4039524 | p.Phe394Tyr | missense_variant | 0.12 | pyrazinamide | |
clpC1 | 4039576 | p.Ala377Ser | missense_variant | 0.13 | pyrazinamide | |
clpC1 | 4039577 | c.1128T>C | synonymous_variant | 0.13 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4039610 | c.1095G>C | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039616 | c.1089G>C | synonymous_variant | 0.15 | pyrazinamide | |
clpC1 | 4039622 | c.1083C>G | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039685 | c.1020C>T | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4040354 | c.351A>G | synonymous_variant | 0.16 | pyrazinamide | |
clpC1 | 4040363 | c.342A>C | synonymous_variant | 0.16 | pyrazinamide | |
clpC1 | 4040369 | c.336C>G | synonymous_variant | 0.17 | pyrazinamide | |
clpC1 | 4040380 | c.325T>C | synonymous_variant | 0.16 | pyrazinamide | |
clpC1 | 4040381 | c.324T>C | synonymous_variant | 0.16 | pyrazinamide | |
clpC1 | 4040387 | c.318A>G | synonymous_variant | 0.16 | pyrazinamide | |
clpC1 | 4040393 | c.312G>C | synonymous_variant | 0.14 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4040792 | c.-88A>T | upstream_gene_variant | 1.0 | pyrazinamide | |
embA | 4243235 | c.3G>T | synonymous_variant | 1.0 | ethambutol |