Run ID: SAMN02360560
Sample name:
Date: 2024-04-15T07:37:09.989854
Number of reads: 14179619
Percentage reads mapped: 93.73
Median coverage: 298.0
Strain: lineage2.2.2
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 1.0 |
lineage2.2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.98 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ahpC | c.-48G>A | Uncertain significance | Mutation from literature | |
ethambutol | embB | p.Tyr319Ser | Assoc w R | |
pyrazinamide | pncA | c.282delC | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Thr500Asn | Uncertain significance | Mutation from literature |
gyrA | p.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |
ofloxacin | ||||
levofloxacin | gyrB | p.Thr500Asn | Uncertain significance | Mutation from literature |
gyrA | p.Ala90Val | Assoc w R | ||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1401A>G | Assoc w R | |
capreomycin | rrs | n.1401A>G | Assoc w R | |
kanamycin | rrs | n.1401A>G | Assoc w R | |
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | folC | p.Ile43Ser | Mutation from literature | |
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6738 | p.Thr500Asn | missense_variant | 1.0 | levofloxacin | Uncertain significance | Mutation from literature |
moxifloxacin | Uncertain significance | Mutation from literature | |||||
gyrA | 7570 | p.Ala90Val | missense_variant | 0.99 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | amikacin | Assoc w R | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 1.0 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
pncA | 2288959 | c.282delC | frameshift_variant | 0.99 | pyrazinamide | Assoc w R | |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
folC | 2747471 | p.Ile43Ser | missense_variant | 1.0 | para-aminosalicylic_acid | Mutation from literature | |
embB | 4247469 | p.Tyr319Ser | missense_variant | 1.0 | ethambutol | Assoc w R |
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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13638 | c.-80A>G | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 1.0 | ethionamide | Uncertain significance |
hadA | 731693 | c.-237C>T | upstream_gene_variant | 1.0 | isoniazid | |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 766479 | c.3112_3126dupCGGGTACCGCGTGGC | conservative_inframe_insertion | 1.0 | rifampicin | |
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 | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1253247 | p.Thr430Pro | missense_variant | 0.12 | moxifloxacin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
Rv1129c | 1254056 | p.Asp160Ala | missense_variant | 0.86 | moxifloxacin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472127 | n.282C>T | non_coding_transcript_exon_variant | 0.13 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472129 | n.284G>C | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472137 | n.292G>A | non_coding_transcript_exon_variant | 0.18 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.2 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 0.2 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.22 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472203 | n.358G>A | non_coding_transcript_exon_variant | 0.17 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472210 | n.365A>C | non_coding_transcript_exon_variant | 0.15 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472213 | n.368G>C | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.11 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Uncertain significance | |||||
rrs | 1472570 | n.725G>A | non_coding_transcript_exon_variant | 0.13 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.13 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472573 | n.728C>A | non_coding_transcript_exon_variant | 0.13 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.13 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472591 | n.746G>A | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.12 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.11 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.15 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.17 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.15 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.12 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrl | 1474896 | n.1239A>G | non_coding_transcript_exon_variant | 0.1 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.1 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.21 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
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 | 1.0 | isoniazid | Not assoc w R |
katG | 2155563 | p.Phe183Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
katG | 2155742 | p.Gly124Ser | missense_variant | 0.99 | isoniazid | |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | 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 | |||||
Rv2752c | 3064757 | p.Val479Ile | missense_variant | 0.82 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086856 | p.Glu13Lys | missense_variant | 1.0 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.99 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3640362 | c.-181_-180insCGCGAAATGACACTGATGTG | upstream_gene_variant | 0.98 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
clpC1 | 4040976 | c.-272T>G | upstream_gene_variant | 1.0 | pyrazinamide | |
glpK | 4139183 | c.572dupG | frameshift_variant | 0.91 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
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 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4327501 | c.-28C>A | upstream_gene_variant | 1.0 | ethionamide | |
ethR | 4327894 | p.Ser116Pro | missense_variant | 1.0 | ethionamide | |
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 | 1.0 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 | streptomycin | Not assoc w R |