Run ID: SRR13861620
Sample name:
Date: 2024-10-05T06:19:01.272903
Number of reads: 1950026
Percentage reads mapped: 39.04
Median coverage: 66.0
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 |
---|---|---|---|---|---|---|
dnaA | 1427 | p.Ala476Gly | missense_variant | 1.0 | isoniazid | |
gyrA | 7346 | p.Ile15Met | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 8335 | p.Met345Arg | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 9639 | p.Gly780Arg | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
fgd1 | 491505 | c.723G>A | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
mshA | 576310 | p.Ile321Met | missense_variant | 1.0 | isoniazid | |
ethionamide | ||||||
Rv0565c | 657451 | p.Ala7Val | missense_variant | 1.0 | ethionamide | |
mmpL5 | 775981 | p.Leu834Val | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 776732 | c.1749C>T | synonymous_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 777942 | p.Pro180Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
rplC | 800343 | c.-466G>C | upstream_gene_variant | 1.0 | linezolid | |
fbiC | 1303422 | c.492A>G | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
Rv1258c | 1406592 | p.Tyr250Cys | missense_variant | 1.0 | streptomycin | |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embR | 1416737 | p.Arg204Gln | missense_variant | 1.0 | ethambutol | |
rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.12 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.12 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.12 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.12 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.11 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.11 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.11 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1475277 | n.1620G>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.43 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.42 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.42 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.42 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.47 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.46 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.45 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.45 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.45 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.46 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.46 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.46 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.47 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.47 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.47 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.43 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.43 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.43 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.42 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rpsA | 1834091 | p.Val184Met | missense_variant | 1.0 | pyrazinamide | |
tlyA | 1918473 | c.534T>A | synonymous_variant | 1.0 | capreomycin | |
Rv1979c | 2221849 | p.Leu439Gln | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2222231 | p.Met312Leu | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2222710 | p.Asn152Ile | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2223809 | c.-646_-645insT | upstream_gene_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
eis | 2714723 | p.Cys204Gly | missense_variant | 1.0 | kanamycin | |
amikacin | ||||||
folC | 2746975 | p.Asp208Glu | missense_variant | 0.99 | para-aminosalicylic_acid | |
Rv2477c | 2782420 | c.1623T>A | synonymous_variant | 1.0 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
Rv2477c | 2784310 | c.-268T>A | upstream_gene_variant | 1.0 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
pepQ | 2860233 | c.186T>G | synonymous_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
thyA | 3073781 | p.Leu231Ile | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv3083 | 3448420 | c.-84_-83insT | upstream_gene_variant | 1.0 | ethionamide | |
whiB7 | 3568689 | c.-11delT | upstream_gene_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
embC | 4240494 | p.Gly211Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
embC | 4241732 | p.Ala624Pro | missense_variant | 1.0 | ethambutol | |
embA | 4245672 | p.Gly814Arg | missense_variant | 1.0 | ethambutol | |
embB | 4247458 | p.Tyr315* | stop_gained | 1.0 | ethambutol | |
aftB | 4268265 | p.Leu191Gln | missense_variant | 1.0 | ethambutol |