Run ID: SRR7535079
Sample name:
Date: 2024-10-04T12:03:34.068184
Number of reads: 432404
Percentage reads mapped: 3.47
Median coverage: 8.0
Strain: lineage4.6.1.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6 | Euro-American | None | 0.97 |
lineage4 | Euro-American | None | 1.0 |
lineage4.6.1.1 | Euro-American | RD724 | 1.0 |
lineage4.6.1 | Euro-American (Uganda) | RD724 | 0.98 |
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 | 762894 | c.3088C>T | synonymous_variant | 0.71 | rifampicin | Not assoc w R - Interim |
rpoB | 762911 | p.Ile1035Met | missense_variant | 0.79 | rifampicin | |
rpoB | 762923 | c.3117C>G | synonymous_variant | 0.77 | rifampicin | Not assoc w R - Interim |
rpoB | 762929 | c.3123G>T | synonymous_variant | 0.73 | rifampicin | Not assoc w R - Interim |
rpoC | 762932 | c.-438G>T | upstream_gene_variant | 0.73 | rifampicin | |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.71 | rifampicin | |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.71 | rifampicin | Uncertain significance |
rpoC | 762947 | c.-423C>G | upstream_gene_variant | 0.73 | rifampicin | |
rpoB | 762962 | c.3156C>T | synonymous_variant | 0.76 | rifampicin | Not assoc w R - Interim |
rpoB | 762989 | c.3183G>T | synonymous_variant | 0.64 | rifampicin | Not assoc w R - Interim |
rpoC | 764893 | c.1524T>C | synonymous_variant | 0.59 | rifampicin | |
rpoC | 764905 | c.1536C>T | synonymous_variant | 0.66 | rifampicin | |
rpoC | 764911 | c.1542A>C | synonymous_variant | 0.66 | rifampicin | |
rpoC | 764914 | p.Met515Ile | missense_variant | 0.63 | rifampicin | Uncertain significance |
rpoC | 764918 | p.Val517Ile | missense_variant | 0.63 | rifampicin | |
rpoC | 764939 | c.1570C>T | synonymous_variant | 0.61 | rifampicin | |
rpoC | 764947 | c.1578G>C | synonymous_variant | 0.54 | rifampicin | |
rpoC | 764948 | c.1579_1581delTTGinsCTC | synonymous_variant | 0.54 | rifampicin | Not assoc w R - Interim |
rpoC | 764953 | c.1584G>T | synonymous_variant | 0.52 | rifampicin | |
rpoC | 764956 | c.1587T>C | synonymous_variant | 0.5 | rifampicin | |
rpoC | 764958 | p.Glu530Ala | missense_variant | 0.56 | rifampicin | |
rpoC | 764962 | c.1593G>C | synonymous_variant | 0.56 | rifampicin | Not assoc w R - Interim |
rpoC | 764968 | c.1599T>C | synonymous_variant | 0.58 | rifampicin | Not assoc w R - Interim |
fbiC | 1303622 | p.Tyr231Cys | missense_variant | 0.92 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.95 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472210 | n.365A>T | non_coding_transcript_exon_variant | 0.98 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.98 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.97 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.97 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.97 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472251 | n.406G>C | non_coding_transcript_exon_variant | 0.96 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472252 | n.407G>A | non_coding_transcript_exon_variant | 0.96 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.95 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.48 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.47 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.47 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.47 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.92 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.96 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472785 | n.940G>T | non_coding_transcript_exon_variant | 0.93 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472786 | n.941C>G | non_coding_transcript_exon_variant | 0.93 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.96 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472814 | n.969G>A | non_coding_transcript_exon_variant | 0.92 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472887 | n.1042G>C | non_coding_transcript_exon_variant | 0.33 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473147 | n.1302G>C | non_coding_transcript_exon_variant | 0.79 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.83 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.9 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473164 | n.1319C>G | non_coding_transcript_exon_variant | 0.9 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.92 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.92 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473198 | n.1354delC | non_coding_transcript_exon_variant | 0.93 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.92 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473204 | n.1359C>T | non_coding_transcript_exon_variant | 0.92 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.92 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473226 | n.1381C>T | non_coding_transcript_exon_variant | 0.9 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1475783 | n.2126T>G | non_coding_transcript_exon_variant | 0.37 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475787 | n.2130C>T | non_coding_transcript_exon_variant | 0.44 | capreomycin | |
linezolid | ||||||
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.47 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.48 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.55 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.56 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.96 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.96 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.96 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.98 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.98 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>T | non_coding_transcript_exon_variant | 0.98 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>A | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.97 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476483 | n.2826G>A | non_coding_transcript_exon_variant | 0.96 | capreomycin | |
linezolid | ||||||
rrl | 1476501 | n.2844C>T | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.85 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin |