Run ID: 7cebe26f-f63f-40e1-9a40-408496768e52
Sample name:
Date: 13-05-2024 03:19:52
Number of reads: 5436742
Percentage reads mapped: 98.83
Median coverage: 168
Strain: lineage1.2.1.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1 | Indo-Oceanic | RD239 | 1.0 |
lineage1.2.1 | Indo-Oceanic | RD239 | 1.0 |
lineage1.2.1.2 | Indo-Oceanic | RD239 | 1.0 |
lineage1.2.1.2.1 | Indo-Oceanic | RD239 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | |
ethambutol | ||||
pyrazinamide | pncA | p.Pro62Leu | Assoc w R | |
moxifloxacin | ||||
levofloxacin | ||||
bedaquiline | ||||
delamanid | ||||
pretomanid | ||||
linezolid | ||||
streptomycin | ||||
amikacin | ||||
kanamycin | ||||
capreomycin | ||||
clofazimine | ||||
ethionamide | ||||
para-aminosalicylic_acid | ||||
cycloserine |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | |
pncA | 2289057 | p.Pro62Leu | missense_variant | 1.0 | pyrazinamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 9260 | c.1959G>C | synonymous_variant | 1.0 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | delamanid | |
mshA | 575368 | c.21T>C | synonymous_variant | 1.0 | ethionamide | |
isoniazid | ||||||
mshA | 576108 | p.Ala254Gly | missense_variant | 0.23 | ethionamide | Uncertain significance |
isoniazid | ||||||
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 | rifampicin | |
rpoC | 763531 | c.162G>C | synonymous_variant | 1.0 | rifampicin | |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 | rifampicin | |
rpoC | 764809 | c.1440C>T | synonymous_variant | 1.0 | rifampicin | |
rpoC | 764918 | p.Val517Leu | missense_variant | 0.99 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
fbiC | 1302821 | c.-110G>A | upstream_gene_variant | 1.0 | delamanid | Uncertain significance |
Rv1258c | 1406312 | c.1029T>C | synonymous_variant | 1.0 | streptomycin | |
pyrazinamide | ||||||
isoniazid | ||||||
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 | ethambutol | Uncertain significance |
atpE | 1460907 | c.-138T>C | upstream_gene_variant | 1.0 | bedaquiline | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
inhA | 1674162 | c.-40C>T | upstream_gene_variant | 0.99 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
tlyA | 1918189 | p.Arg84Gly | missense_variant | 1.0 | capreomycin | |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
kasA | 2518544 | p.Met144Leu | missense_variant | 1.0 | isoniazid | |
kasA | 2519048 | p.Gly312Ser | missense_variant | 1.0 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.99 | isoniazid | |
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.14 | clofazimine | |
bedaquiline | ||||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
fbiD | 3339417 | c.300A>G | synonymous_variant | 1.0 | delamanid | |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.54 | delamanid | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 | ethionamide | Uncertain significance |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 | capreomycin | |
amikacin | ||||||
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
whiB7 | 3568488 | c.191delG | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
fbiB | 3640557 | c.-978T>C | upstream_gene_variant | 0.99 | delamanid | |
rpoA | 3878641 | c.-134C>G | upstream_gene_variant | 0.26 | rifampicin | |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
embA | 4243580 | c.348G>A | synonymous_variant | 1.0 | ethambutol | |
embA | 4244420 | c.1188G>C | synonymous_variant | 1.0 | ethambutol | |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4247578 | c.1065G>A | synonymous_variant | 1.0 | ethambutol | |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
aftB | 4267493 | c.1344G>A | synonymous_variant | 1.0 | capreomycin | |
amikacin | ||||||
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
ubiA | 4269864 | c.-32delG | upstream_gene_variant | 1.0 | ethambutol | |
whiB6 | 4338361 | p.Arg54Gln | missense_variant | 1.0 | streptomycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | |
gid | 4407790 | p.Ala138Val | missense_variant | 1.0 | streptomycin | Uncertain significance |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 | streptomycin |