Run ID: ERR4821747
Sample name:
Date: 2024-10-04T21:52:46.254759
Number of reads: 189973
Percentage reads mapped: 4.15
Median coverage: 1.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.96 |
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 |
---|---|---|---|---|---|---|
rpoB | 760244 | c.438G>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 760253 | c.447T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 760263 | p.Met153Leu | missense_variant | 1.0 | rifampicin | |
rpoB | 760266 | p.Met154Gln | missense_variant | 1.0 | rifampicin | |
rpoB | 760274 | p.Glu156Asp | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoB | 762879 | p.Met1025Leu | missense_variant | 0.89 | rifampicin | Uncertain significance |
rpoC | 762896 | c.-474G>C | upstream_gene_variant | 0.94 | rifampicin | |
rpoB | 762917 | c.3111C>G | synonymous_variant | 0.98 | rifampicin | Not assoc w R - Interim |
rpoB | 762929 | c.3123G>T | synonymous_variant | 0.94 | rifampicin | Not assoc w R - Interim |
rpoC | 762947 | c.-423C>G | upstream_gene_variant | 0.95 | rifampicin | |
rpoB | 762962 | c.3156C>T | synonymous_variant | 0.95 | rifampicin | Not assoc w R - Interim |
rpoC | 762980 | c.-390T>C | upstream_gene_variant | 0.93 | rifampicin | |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.9 | rifampicin | |
rpoB | 762995 | c.3189G>T | synonymous_variant | 0.88 | rifampicin | Not assoc w R - Interim |
rpoB | 763028 | c.3222T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoB | 763038 | p.Thr1078Ala | missense_variant | 1.0 | rifampicin | |
rpoC | 763052 | c.-318G>C | upstream_gene_variant | 1.0 | rifampicin | |
rpoC | 763053 | c.-317_-315delTTGinsCTC | upstream_gene_variant | 1.0 | rifampicin | |
rpoC | 763058 | c.-312C>G | upstream_gene_variant | 1.0 | rifampicin | |
rpoB | 763070 | c.3264T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 763075 | p.Thr1090Ile | missense_variant | 1.0 | rifampicin | |
rpoB | 763077 | p.Val1091Leu | missense_variant | 1.0 | rifampicin | |
rpoB | 763115 | c.3309T>C | synonymous_variant | 0.97 | rifampicin | Not assoc w R - Interim |
rpoB | 763126 | p.Pro1107Gln | missense_variant | 0.96 | rifampicin | |
rpoC | 763133 | c.-237G>C | upstream_gene_variant | 0.95 | rifampicin | |
rpoB | 763136 | c.3330C>T | synonymous_variant | 0.95 | rifampicin | Not assoc w R - Interim |
rpoC | 763148 | c.-222G>C | upstream_gene_variant | 0.93 | rifampicin | |
rpoC | 763462 | c.93G>C | synonymous_variant | 1.0 | rifampicin | |
rpoC | 763483 | c.114G>C | synonymous_variant | 1.0 | rifampicin | |
rpoC | 763486 | c.117T>G | synonymous_variant | 0.95 | rifampicin | |
rpoC | 763492 | c.123G>C | synonymous_variant | 0.95 | rifampicin | Not assoc w R - Interim |
rpoC | 763504 | c.135C>T | synonymous_variant | 0.96 | rifampicin | |
rpoC | 763511 | p.Cys48Gly | missense_variant | 0.95 | rifampicin | |
rpoC | 763517 | p.Lys50Gln | missense_variant | 0.96 | rifampicin | |
rpoC | 763528 | c.159G>A | synonymous_variant | 0.96 | rifampicin | Not assoc w R - Interim |
rpoC | 763531 | c.162G>C | synonymous_variant | 0.96 | rifampicin | Not assoc w R |
rpoC | 763532 | p.Thr55Ser | missense_variant | 0.96 | rifampicin | |
rpoC | 763546 | c.177A>G | synonymous_variant | 0.96 | rifampicin | Not assoc w R - Interim |
rpoC | 763550 | p.Tyr61Ala | missense_variant | 0.93 | rifampicin | |
rpoC | 763570 | c.201G>C | synonymous_variant | 0.88 | rifampicin | Not assoc w R - Interim |
rpoC | 763573 | c.204G>C | synonymous_variant | 0.88 | rifampicin | Not assoc w R - Interim |
rpoC | 763589 | p.Ile74Val | missense_variant | 0.94 | rifampicin | |
rpoC | 763609 | c.240C>G | synonymous_variant | 0.88 | rifampicin | |
rpoC | 763660 | c.291T>C | synonymous_variant | 0.92 | rifampicin | Not assoc w R - Interim |
rpoC | 763696 | c.327T>C | synonymous_variant | 0.93 | rifampicin | Not assoc w R - Interim |
rpoC | 763699 | c.330G>C | synonymous_variant | 0.93 | rifampicin | |
rpoC | 763708 | c.339G>C | synonymous_variant | 0.93 | rifampicin | |
rpoC | 763709 | c.340C>T | synonymous_variant | 0.93 | rifampicin | |
rpoC | 763714 | c.345G>C | synonymous_variant | 0.93 | rifampicin | Not assoc w R - Interim |
rpoC | 763717 | c.348T>C | synonymous_variant | 0.93 | rifampicin | Not assoc w R - Interim |
rpoC | 763723 | c.354G>C | synonymous_variant | 0.93 | rifampicin | |
rpoC | 763727 | p.Leu120Met | missense_variant | 0.93 | rifampicin | |
rpoC | 763732 | c.363C>G | synonymous_variant | 0.93 | rifampicin | |
rpoC | 763744 | c.375G>C | synonymous_variant | 0.89 | rifampicin | |
rpoC | 763751 | p.Ile128Val | missense_variant | 0.91 | rifampicin | |
rpoC | 763765 | c.396T>C | synonymous_variant | 0.79 | rifampicin | |
rpoC | 764593 | c.1224C>T | synonymous_variant | 0.95 | rifampicin | |
rpoC | 764602 | c.1233C>T | synonymous_variant | 0.97 | rifampicin | |
rpoC | 764611 | c.1242G>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.98 | rifampicin | Not assoc w R - Interim |
rpoC | 764650 | c.1281G>T | synonymous_variant | 0.99 | rifampicin | Not assoc w R - Interim |
rpoC | 764660 | p.Val431Ile | missense_variant | 0.99 | rifampicin | |
rpoC | 764692 | c.1323C>T | synonymous_variant | 0.96 | rifampicin | Not assoc w R - Interim |
rpoC | 764706 | p.Leu446Gln | missense_variant | 0.95 | rifampicin | Uncertain significance |
rpoC | 764713 | c.1344G>C | synonymous_variant | 0.94 | rifampicin | Not assoc w R - Interim |
rpsL | 781751 | c.192G>C | synonymous_variant | 0.83 | streptomycin | |
rpsL | 781754 | c.195G>C | synonymous_variant | 0.92 | streptomycin | |
rpsL | 781760 | c.201T>C | synonymous_variant | 0.89 | streptomycin | |
rpsL | 781794 | p.Met79Leu | missense_variant | 0.9 | streptomycin | |
rpsL | 781814 | c.255C>T | synonymous_variant | 0.96 | streptomycin | |
rpsL | 781817 | c.258G>T | synonymous_variant | 0.96 | streptomycin | |
rpsL | 781829 | c.270G>C | synonymous_variant | 0.96 | streptomycin | |
rpsL | 781832 | c.273T>C | synonymous_variant | 0.96 | streptomycin | |
rpsL | 781841 | c.282C>T | synonymous_variant | 0.95 | streptomycin | |
rrs | 1472982 | n.1137G>A | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473226 | n.1381C>T | non_coding_transcript_exon_variant | 0.8 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance |