Run ID: SRR13861558
Sample name:
Date: 2024-10-04T23:33:20.091495
Number of reads: 2937655
Percentage reads mapped: 73.52
Median coverage: 99.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
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 | ethA | c.905delT | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
ethA | 4326568 | c.905delT | frameshift_variant | 1.0 | ethionamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 8820 | p.Asp507His | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
mshA | 575967 | p.Val207Asp | missense_variant | 1.0 | isoniazid | |
ethionamide | ||||||
rpoB | 759961 | p.Thr52Asn | missense_variant | 1.0 | rifampicin | |
rpoB | 763050 | p.Leu1082Met | missense_variant | 1.0 | rifampicin | |
mmpL5 | 775701 | p.Pro927Gln | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 778828 | c.-348G>A | upstream_gene_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
rplC | 800500 | c.-309A>C | upstream_gene_variant | 1.0 | linezolid | |
rplC | 801353 | p.Val182Ala | missense_variant | 1.0 | linezolid | |
Rv1129c | 1253966 | p.Leu190Trp | missense_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
fbiC | 1304512 | p.Val528Ile | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
embR | 1417704 | c.-357T>C | upstream_gene_variant | 1.0 | ethambutol | |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.17 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rpsA | 1834175 | p.Arg212* | stop_gained | 1.0 | pyrazinamide | Uncertain significance |
katG | 2156840 | c.-729C>T | upstream_gene_variant | 0.99 | isoniazid | |
Rv1979c | 2222085 | c.1080G>C | synonymous_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
ald | 3087218 | p.Met133Ile | missense_variant | 1.0 | cycloserine | |
whiB7 | 3568679 | p.Val1Leu | missense_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
whiB7 | 3568989 | c.-310A>C | upstream_gene_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
mtrB | 3625440 | p.Gly392Arg | missense_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
clpC1 | 4040066 | c.639G>T | synonymous_variant | 1.0 | pyrazinamide | |
embC | 4241259 | c.1397_1398insT | frameshift_variant | 1.0 | ethambutol | |
embA | 4243358 | c.126C>T | synonymous_variant | 0.99 | ethambutol | |
embA | 4243469 | c.237C>T | synonymous_variant | 1.0 | ethambutol | |
embB | 4248436 | c.1923C>T | synonymous_variant | 1.0 | ethambutol | |
ubiA | 4269557 | p.Ala93Pro | missense_variant | 1.0 | ethambutol |