Run ID: ERR13265708
Sample name:
Date: 2025-02-11T13:56:18.808253
Number of reads: 5092320
Percentage reads mapped: 98.62
Median coverage: 154.0
Strain: lineage2.2.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 1.0 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 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 | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7412 | c.111C>G | synonymous_variant | 0.13 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7433 | c.132G>C | synonymous_variant | 0.13 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7442 | c.141G>T | synonymous_variant | 0.12 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7457 | c.156T>C | synonymous_variant | 0.1 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7469 | c.168C>G | synonymous_variant | 0.11 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7511 | c.210C>T | synonymous_variant | 0.13 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7514 | c.213C>G | synonymous_variant | 0.11 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | 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 | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.99 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 801021 | c.213C>T | synonymous_variant | 1.0 | linezolid | Not assoc w R - Interim |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
sigE | 1364958 | c.546G>T | synonymous_variant | 1.0 | pyrazinamide | |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474552 | n.895C>T | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
linezolid | ||||||
rrl | 1474753 | n.1096A>G | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474760 | n.1103A>G | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474794 | n.1137C>A | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474830 | n.1173A>G | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
inhA | 1674542 | p.Ala114Glu | missense_variant | 0.13 | isoniazid | |
ethionamide | ||||||
inhA | 1674546 | c.345T>C | synonymous_variant | 0.13 | isoniazid | |
ethionamide | ||||||
inhA | 1674550 | p.Ser117Ala | missense_variant | 0.13 | isoniazid | |
ethionamide | ||||||
inhA | 1674570 | c.369G>C | synonymous_variant | 0.15 | isoniazid | |
ethionamide | ||||||
inhA | 1674573 | c.372G>A | synonymous_variant | 0.15 | isoniazid | |
ethionamide | ||||||
inhA | 1674576 | c.375T>C | synonymous_variant | 0.14 | isoniazid | |
ethionamide | ||||||
inhA | 1674579 | c.378G>C | synonymous_variant | 0.14 | isoniazid | |
ethionamide | ||||||
inhA | 1674585 | c.384T>C | synonymous_variant | 0.15 | isoniazid | |
ethionamide | ||||||
inhA | 1674589 | p.Met130Leu | missense_variant | 0.16 | isoniazid | |
ethionamide | ||||||
inhA | 1674600 | c.399G>C | synonymous_variant | 0.16 | isoniazid | |
ethionamide | ||||||
inhA | 1674601 | p.Leu134Val | missense_variant | 0.16 | isoniazid | |
ethionamide | ||||||
inhA | 1674624 | c.423A>C | synonymous_variant | 0.15 | isoniazid | |
ethionamide | ||||||
inhA | 1674627 | c.426T>G | synonymous_variant | 0.15 | isoniazid | |
ethionamide | ||||||
inhA | 1674639 | c.438C>T | synonymous_variant | 0.14 | isoniazid | |
ethionamide | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
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 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.99 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2517917 | c.-198G>T | upstream_gene_variant | 0.16 | isoniazid | |
kasA | 2517926 | c.-189G>A | upstream_gene_variant | 0.15 | isoniazid | |
kasA | 2517941 | c.-174C>G | upstream_gene_variant | 0.13 | isoniazid | |
kasA | 2518564 | c.450C>G | synonymous_variant | 0.13 | isoniazid | |
kasA | 2518567 | c.453G>C | synonymous_variant | 0.13 | isoniazid | |
kasA | 2518570 | c.456G>C | synonymous_variant | 0.12 | isoniazid | |
kasA | 2518574 | p.Ile154Val | missense_variant | 0.12 | isoniazid | |
kasA | 2518579 | c.465T>C | synonymous_variant | 0.12 | isoniazid | |
kasA | 2518588 | c.474T>C | synonymous_variant | 0.12 | isoniazid | |
kasA | 2518591 | c.477G>C | synonymous_variant | 0.12 | isoniazid | |
kasA | 2518594 | c.480C>T | synonymous_variant | 0.12 | isoniazid | |
kasA | 2518606 | c.492G>C | synonymous_variant | 0.12 | isoniazid | |
kasA | 2518609 | p.Met165Ile | missense_variant | 0.13 | isoniazid | |
kasA | 2518618 | c.504G>C | synonymous_variant | 0.14 | isoniazid | |
kasA | 2518624 | c.510C>G | synonymous_variant | 0.14 | isoniazid | |
kasA | 2518636 | c.522C>T | synonymous_variant | 0.15 | isoniazid | |
kasA | 2518642 | c.528A>G | synonymous_variant | 0.15 | isoniazid | |
kasA | 2518672 | c.558G>C | synonymous_variant | 0.13 | isoniazid | |
kasA | 2518684 | c.570C>G | synonymous_variant | 0.1 | isoniazid | |
Rv2681 | 2997797 | c.1067_1068delCG | frameshift_variant | 1.0 | capreomycin | Uncertain significance |
thyX | 3067286 | c.660C>T | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4038971 | c.1734T>C | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4038974 | c.1731T>C | synonymous_variant | 0.13 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4038989 | c.1716T>C | synonymous_variant | 0.15 | pyrazinamide | |
clpC1 | 4038997 | c.1708T>C | synonymous_variant | 0.14 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4039001 | p.Asn568Glu | missense_variant | 0.13 | pyrazinamide | |
clpC1 | 4039004 | c.1701C>G | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4039022 | c.1683A>G | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039034 | c.1671C>G | synonymous_variant | 0.16 | pyrazinamide | |
clpC1 | 4039046 | c.1659C>T | synonymous_variant | 0.18 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4039073 | c.1632C>G | synonymous_variant | 0.18 | pyrazinamide | |
clpC1 | 4039085 | c.1620A>G | synonymous_variant | 0.17 | pyrazinamide | |
clpC1 | 4039090 | c.1615C>T | synonymous_variant | 0.19 | pyrazinamide | |
clpC1 | 4039097 | c.1608G>C | synonymous_variant | 0.2 | pyrazinamide | |
clpC1 | 4039106 | c.1599G>C | synonymous_variant | 0.19 | pyrazinamide | |
clpC1 | 4039112 | c.1593C>G | synonymous_variant | 0.18 | pyrazinamide | |
clpC1 | 4039121 | c.1584T>C | synonymous_variant | 0.2 | pyrazinamide | |
clpC1 | 4039139 | c.1566G>A | synonymous_variant | 0.18 | pyrazinamide | |
clpC1 | 4039142 | c.1563A>G | synonymous_variant | 0.18 | pyrazinamide | |
clpC1 | 4039145 | c.1560G>C | synonymous_variant | 0.19 | pyrazinamide | |
clpC1 | 4039169 | p.Glu512Asp | missense_variant | 0.18 | pyrazinamide | |
clpC1 | 4039178 | c.1527G>C | synonymous_variant | 0.17 | pyrazinamide | |
clpC1 | 4039183 | c.1522T>C | synonymous_variant | 0.16 | pyrazinamide | |
glpK | 4138861 | p.Asn299Asp | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326676 | p.Ser266Arg | missense_variant | 1.0 | ethionamide | Uncertain significance |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 | streptomycin | Not assoc w R |