Run ID: SRR13861151
Sample name:
Date: 2024-10-04T22:11:19.046610
Number of reads: 739881
Percentage reads mapped: 12.34
Median coverage: 24.0
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 |
---|---|---|---|---|---|---|
gyrA | 9502 | p.Arg734His | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
Rv0010c | 13527 | p.Ser11* | stop_gained | 1.0 | isoniazid | Uncertain significance |
rpoB | 759681 | c.-126C>T | upstream_gene_variant | 0.95 | rifampicin | |
rpoB | 761239 | p.Cys478Tyr | missense_variant | 0.68 | rifampicin | |
rpoC | 764530 | c.1161C>G | synonymous_variant | 0.21 | rifampicin | Not assoc w R - Interim |
mmpL5 | 776185 | p.Lys766Glu | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 779400 | c.-920C>A | upstream_gene_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
embR | 1417986 | c.-639T>A | upstream_gene_variant | 1.0 | ethambutol | |
rrs | 1472865 | n.1020C>G | non_coding_transcript_exon_variant | 0.93 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.38 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.38 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.38 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.4 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472973 | n.1128_1130delAATinsCG | non_coding_transcript_exon_variant | 0.4 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.4 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.39 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.39 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.38 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.37 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.33 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.34 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.33 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.35 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.24 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.21 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1473839 | n.182G>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | |
linezolid | ||||||
rrl | 1474012 | n.355C>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
linezolid | ||||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.78 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.84 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.84 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.84 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.85 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.86 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.84 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.84 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.84 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.82 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.82 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.79 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.79 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.41 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
linezolid | ||||||
tlyA | 1918063 | p.Pro42Ala | missense_variant | 1.0 | capreomycin | |
ndh | 2102985 | p.Ile20Val | missense_variant | 1.0 | isoniazid | |
delamanid | ||||||
ethionamide | ||||||
katG | 2155856 | p.Thr86Ser | missense_variant | 1.0 | isoniazid | |
PPE35 | 2169233 | c.1379delT | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv2477c | 2783395 | c.648T>C | synonymous_variant | 0.28 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2752c | 3065376 | c.815delT | frameshift_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
Rv2752c | 3066351 | c.-160G>T | upstream_gene_variant | 0.94 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
thyX | 3067731 | p.Val72Ala | missense_variant | 0.94 | para-aminosalicylic_acid | |
thyX | 3067825 | p.Arg41Gly | missense_variant | 1.0 | para-aminosalicylic_acid | |
fbiD | 3338949 | c.-169_-168insT | upstream_gene_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
Rv3083 | 3448707 | c.204G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
Rv3083 | 3449768 | p.Thr422Lys | missense_variant | 1.0 | ethionamide | |
lpqB | 3623219 | c.1692A>G | synonymous_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
mtrA | 3627790 | c.-441A>G | upstream_gene_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
fbiB | 3641403 | c.-132C>T | upstream_gene_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
alr | 3841257 | p.His55Leu | missense_variant | 1.0 | cycloserine | |
rpoA | 3877601 | p.Gln303* | stop_gained | 0.96 | rifampicin | |
ddn | 3986668 | c.-176T>C | upstream_gene_variant | 1.0 | pretomanid | |
delamanid | ||||||
embC | 4239401 | c.-462A>C | upstream_gene_variant | 1.0 | ethambutol | |
embC | 4241864 | p.Leu668Met | missense_variant | 1.0 | ethambutol | |
embB | 4245557 | c.-957G>A | upstream_gene_variant | 1.0 | ethambutol | |
ethA | 4327092 | p.Ala128Pro | missense_variant | 1.0 | ethionamide | |
gid | 4408151 | p.Leu18Val | missense_variant | 1.0 | streptomycin |