Run ID: ERR212101
Sample name:
Date: 2024-04-15T01:35:58.765551
Number of reads: 6498577
Percentage reads mapped: 96.8
Median coverage: 137.0
Strain: lineage4.1.1.3
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.2.2.1 | Indo-Oceanic | RD239 | 0.09 |
lineage1.2.2 | Indo-Oceanic | RD239 | 0.05 |
lineage4.1 | Euro-American | None | 0.86 |
lineage4.1.1.3 | Euro-American (X-type) | RD193 | 0.86 |
lineage4 | Euro-American | None | 0.86 |
lineage4.1.1 | Euro-American (X-type) | None | 0.86 |
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 | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8452 | p.Ala384Val | missense_variant | 0.14 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.82 | ethionamide | Uncertain significance |
rpoB | 760898 | c.1092C>T | synonymous_variant | 0.86 | rifampicin | |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.13 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.13 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.86 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.19 | 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 |
rplC | 800219 | c.-590T>C | upstream_gene_variant | 0.92 | linezolid | |
rplC | 800899 | p.Ala31Thr | missense_variant | 0.12 | linezolid | Uncertain significance |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.14 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.12 | ethambutol | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1471842 | n.-4T>G | upstream_gene_variant | 0.14 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476353 | n.2696G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.18 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.11 | 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 | |||||
ahpC | 2726753 | c.561T>G | synonymous_variant | 0.88 | isoniazid | Not assoc w R - Interim |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
rpoA | 3878243 | p.Glu89Gln | missense_variant | 0.84 | rifampicin | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.86 | ethambutol | Not assoc w R |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.96 | 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 | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.13 | streptomycin | Not assoc w R |
gid | 4407989 | p.Ala72Ser | missense_variant | 0.81 | streptomycin |