Run ID: SRR3675513
Sample name:
Date: 2024-04-14T19:55:28.748536
Number of reads: 868174
Percentage reads mapped: 85.79
Median coverage: 28.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rrs | n.799C>T | Uncertain significance | Mutation from literature |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
capreomycin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
kanamycin | rrs | n.1402C>A | Uncertain significance | Mutation from literature |
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rrs | 1472644 | n.799C>T | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance | Mutation from literature |
rrs | 1473247 | n.1402C>A | non_coding_transcript_exon_variant | 0.8 | kanamycin | Uncertain significance | Mutation from literature |
capreomycin | Uncertain significance | Mutation from literature | |||||
amikacin | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7379 | c.78C>G | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
Rv0565c | 656265 | c.1204_1205delAC | frameshift_variant | 1.0 | ethionamide | Uncertain significance |
nusG | 734141 | c.-113G>A | upstream_gene_variant | 1.0 | rifampicin | Uncertain significance |
nusG | 734658 | c.405A>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
fbiC | 1302875 | c.-56C>T | upstream_gene_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
rrs | 1472558 | n.713G>A | non_coding_transcript_exon_variant | 0.73 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472569 | n.724G>A | non_coding_transcript_exon_variant | 0.62 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.85 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472597 | n.752G>A | non_coding_transcript_exon_variant | 0.56 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472607 | n.762G>A | non_coding_transcript_exon_variant | 0.53 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.33 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.47 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.43 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.43 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472670 | n.825G>T | non_coding_transcript_exon_variant | 0.4 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472673 | n.828T>G | non_coding_transcript_exon_variant | 0.85 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472675 | n.830T>C | non_coding_transcript_exon_variant | 0.5 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472677 | n.832C>T | non_coding_transcript_exon_variant | 0.5 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472682 | n.837_842delTTGGGAinsGGGAC | non_coding_transcript_exon_variant | 0.5 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472690 | n.845C>A | non_coding_transcript_exon_variant | 0.5 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.62 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473066 | n.1221A>G | non_coding_transcript_exon_variant | 0.56 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473088 | n.1243A>G | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473100 | n.1255G>A | non_coding_transcript_exon_variant | 0.46 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473102 | n.1257C>T | non_coding_transcript_exon_variant | 0.46 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.46 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 0.46 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 0.46 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473115 | n.1270G>T | non_coding_transcript_exon_variant | 0.5 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 0.55 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.64 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.58 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.8 | streptomycin | Uncertain significance |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.8 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473270 | n.1425G>A | non_coding_transcript_exon_variant | 0.8 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473276 | n.1431A>G | non_coding_transcript_exon_variant | 0.8 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1475869 | n.2212C>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1475883 | n.2226A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475898 | n.2241A>G | non_coding_transcript_exon_variant | 0.92 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475899 | n.2242G>A | non_coding_transcript_exon_variant | 0.92 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475916 | n.2259C>G | non_coding_transcript_exon_variant | 0.92 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475937 | n.2280A>T | non_coding_transcript_exon_variant | 0.91 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475952 | n.2295A>G | non_coding_transcript_exon_variant | 0.82 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476337 | n.2680C>T | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.4 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.83 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.74 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.87 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 1.0 | capreomycin | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
Rv3236c | 3613636 | c.-520A>G | upstream_gene_variant | 1.0 | pyrazinamide | Not assoc w R |
rpoA | 3878158 | p.Thr117Ile | missense_variant | 1.0 | rifampicin | Uncertain significance |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R |