Run ID: SRR12416829
Sample name:
Date: 2024-10-05T02:15:44.716106
Number of reads: 5484039
Percentage reads mapped: 90.49
Median coverage: 133.0
Strain: lineage2.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.99 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 1.0 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.99 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
rpoC | p.Ile491Thr | Uncertain significance | Mutation from literature | |
isoniazid | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Gln127Pro | Uncertain significance | Mutation from literature | |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | c.-11A>G | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.91 | rifampicin | Assoc w R | |
rpoC | 764841 | p.Ile491Thr | missense_variant | 0.86 | rifampicin | Uncertain significance | Mutation from literature |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.93 | streptomycin | Assoc w R | |
inhA | 1673423 | c.-779G>T | upstream_gene_variant | 0.99 | ethionamide | Assoc w R - Interim | Alias fabG1_c.-17G>T |
isoniazid | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155732 | p.Gln127Pro | missense_variant | 0.97 | isoniazid | Uncertain significance | Mutation from literature |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Val | missense_variant | 0.95 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1092 | c.1092T>C | synonymous_variant | 0.14 | isoniazid | Not assoc w R - Interim |
dnaA | 1098 | c.1098A>G | synonymous_variant | 0.14 | isoniazid | |
dnaA | 1104 | c.1104T>C | synonymous_variant | 0.14 | isoniazid | |
dnaA | 1110 | c.1110T>C | synonymous_variant | 0.13 | isoniazid | |
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 | 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 | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.98 | isoniazid | Not assoc w R |
ethionamide | 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 | 0.99 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.99 | ethionamide | Uncertain significance |
rpoB | 760223 | c.417T>C | synonymous_variant | 0.15 | rifampicin | |
rpoB | 760235 | c.429T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 760283 | c.477G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 760298 | c.492G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 760328 | c.522G>C | synonymous_variant | 0.13 | rifampicin | |
rpoB | 761015 | c.1209G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 761021 | c.1215G>C | synonymous_variant | 0.13 | rifampicin | |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 764858 | c.1489T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
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 | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 | bedaquiline | Not assoc w R |
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 |
Rv1129c | 1254242 | p.Glu98Gly | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
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 | |||||
Rv1129c | 1254612 | c.-78G>A | upstream_gene_variant | 0.99 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
fbiC | 1302874 | c.-57G>A | upstream_gene_variant | 0.18 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
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 | 1475599 | n.1942A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | Uncertain significance | |||||
rrl | 1475608 | n.1951T>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475638 | n.1981C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1475657 | n.2000A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | ||||||
rrl | 1475659 | n.2002G>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | ||||||
rrl | 1476214 | n.2557G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
linezolid | ||||||
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rpsA | 1833410 | c.-132G>A | upstream_gene_variant | 1.0 | pyrazinamide | |
rpsA | 1833940 | c.399C>G | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834012 | c.471G>C | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834465 | c.924T>C | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1834468 | c.927A>G | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1834489 | c.948T>C | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1834495 | c.954G>A | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1834499 | c.958C>T | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834528 | c.987T>C | synonymous_variant | 0.13 | pyrazinamide | |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 | capreomycin | Not assoc w R |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | 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 | 2519206 | c.1092C>T | synonymous_variant | 0.13 | isoniazid | |
Rv2681 | 2997439 | p.Trp234Ser | missense_variant | 1.0 | capreomycin | |
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 | |||||
mtrB | 3626972 | c.-359A>G | upstream_gene_variant | 0.16 | rifampicin | |
bedaquiline | ||||||
mtrB | 3626987 | c.-374C>G | upstream_gene_variant | 0.16 | rifampicin | |
bedaquiline | ||||||
mtrB | 3627005 | c.-392G>C | upstream_gene_variant | 0.16 | rifampicin | |
bedaquiline | ||||||
mtrB | 3627008 | c.-395G>C | upstream_gene_variant | 0.17 | rifampicin | |
bedaquiline | ||||||
mtrB | 3627011 | c.-398T>G | upstream_gene_variant | 0.17 | rifampicin | |
bedaquiline | ||||||
alr | 3841614 | c.-194C>G | upstream_gene_variant | 1.0 | cycloserine | |
rpoA | 3878076 | c.432C>T | synonymous_variant | 0.13 | rifampicin | |
rpoA | 3878094 | c.414C>G | synonymous_variant | 0.14 | rifampicin | |
rpoA | 3878103 | c.405A>G | synonymous_variant | 0.15 | rifampicin | |
rpoA | 3878106 | c.402G>C | synonymous_variant | 0.14 | rifampicin | |
rpoA | 3878193 | c.315T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoA | 3878205 | c.303T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoA | 3878217 | c.291A>G | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoA | 3878232 | c.276G>C | synonymous_variant | 0.13 | rifampicin | |
rpoA | 3878247 | c.261G>C | synonymous_variant | 0.15 | rifampicin | |
rpoA | 3878271 | c.237T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoA | 3878276 | c.232C>T | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoA | 3878284 | p.Glu75Ala | missense_variant | 0.13 | rifampicin | |
rpoA | 3878292 | c.216T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoA | 3878304 | c.204G>C | synonymous_variant | 0.16 | rifampicin | |
rpoA | 3878313 | c.195G>T | synonymous_variant | 0.16 | rifampicin | |
rpoA | 3878878 | c.-371T>C | upstream_gene_variant | 0.13 | rifampicin | Uncertain significance |
rpoA | 3878890 | c.-383C>G | upstream_gene_variant | 0.15 | rifampicin | |
rpoA | 3878909 | c.-402A>G | upstream_gene_variant | 0.16 | rifampicin | |
rpoA | 3878914 | c.-407T>C | upstream_gene_variant | 0.14 | rifampicin | Uncertain significance |
rpoA | 3878917 | c.-410G>C | upstream_gene_variant | 0.14 | rifampicin | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
embB | 4248220 | c.1707A>C | synonymous_variant | 0.13 | ethambutol | |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.99 | ethambutol | Not assoc w R |
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 |