Run ID: SRR6046253
Sample name:
Date: 2024-04-15T12:56:25.981415
Number of reads: 55965
Percentage reads mapped: 3.2
Median coverage: 0.0
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 |
---|---|---|---|---|---|---|
nusG | 734472 | c.219T>C | synonymous_variant | 0.9 | rifampicin | |
nusG | 734475 | c.222T>C | synonymous_variant | 0.9 | rifampicin | Not assoc w R - Interim |
nusG | 734502 | c.249G>A | synonymous_variant | 0.9 | rifampicin | |
rpoB | 761282 | c.1476C>A | synonymous_variant | 1.0 | rifampicin | |
rpoB | 761300 | c.1494G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 761969 | c.2163G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 761972 | c.2166C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 762006 | c.2200_2202delCGCinsAG | frameshift_variant&missense_variant | 1.0 | rifampicin | |
rpoB | 762024 | p.Val740Thr | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoB | 762029 | c.2223C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 763115 | c.3309T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 763127 | c.3321G>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoB | 763136 | c.3330C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 763142 | c.-228C>G | upstream_gene_variant | 1.0 | rifampicin | |
rpoC | 763148 | c.-222G>C | upstream_gene_variant | 1.0 | rifampicin | |
rpoC | 763169 | c.-201A>G | upstream_gene_variant | 1.0 | rifampicin | |
rpoC | 763193 | c.-177C>T | upstream_gene_variant | 1.0 | rifampicin | |
rpoC | 763594 | c.225C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 764650 | c.1281G>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 764656 | c.1287C>G | synonymous_variant | 1.0 | rifampicin | |
rpoC | 764668 | c.1299C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 764746 | c.1377G>A | synonymous_variant | 1.0 | rifampicin | |
rpoC | 764752 | c.1383G>T | synonymous_variant | 1.0 | rifampicin | |
rpoC | 764764 | c.1395T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 765611 | p.His748Ser | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 765904 | c.2535C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 765908 | c.2539C>T | synonymous_variant | 1.0 | rifampicin | |
rpoC | 765937 | c.2568T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rrs | 1471986 | n.141C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472019 | n.174G>A | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472683 | n.838_839insTA | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1473123 | n.1278A>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1473876 | n.219G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473887 | n.230delTinsAA | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474174 | n.517A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474181 | n.524C>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475775 | n.2118G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475916 | n.2259C>T | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475975 | n.2318C>T | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475977 | n.2320A>G | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475995 | n.2338G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475997 | n.2340A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476044 | n.2387T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476045 | n.2388G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476049 | n.2392C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476086 | n.2429G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476088 | n.2431A>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476095 | n.2438C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476103 | n.2446C>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476108 | n.2451T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476110 | n.2453G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476115 | n.2458T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476131 | n.2474C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476529 | n.2872A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476665 | n.3008T>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476674 | n.3017T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
kasA | 2518684 | c.570C>G | synonymous_variant | 1.0 | isoniazid | |
kasA | 2518688 | p.Val192Phe | missense_variant | 1.0 | isoniazid | |
kasA | 2518693 | c.579C>G | synonymous_variant | 1.0 | isoniazid | |
kasA | 2518726 | c.612G>A | synonymous_variant | 1.0 | isoniazid | |
kasA | 2518732 | c.618C>G | synonymous_variant | 1.0 | isoniazid | |
kasA | 2518747 | c.633C>G | synonymous_variant | 1.0 | isoniazid | |
kasA | 2518756 | c.642G>C | synonymous_variant | 1.0 | isoniazid | |
clpC1 | 4039865 | c.840T>C | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4039871 | c.834C>T | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4039898 | c.807C>G | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4040522 | c.183T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4040644 | c.61A>C | synonymous_variant | 1.0 | pyrazinamide |