Run ID: SRR1146325
Sample name:
Date: 2024-04-16T07:58:02.015736
Number of reads: 4024434
Percentage reads mapped: 98.89
Median coverage: 92.0
Strain: lineage1.1.1.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.1 | Indo-Oceanic | RD239 | 0.89 |
lineage1 | Indo-Oceanic | RD239 | 0.87 |
lineage1.1.1 | Indo-Oceanic | RD239 | 0.96 |
lineage1.1.1.1 | Indo-Oceanic | RD239 | 0.96 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | pncA | p.His137Arg | Not assoc w R - Interim | Mutation from literature |
streptomycin | rrs | n.905C>G | Uncertain significance | Mutation from literature |
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 |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rrs | 1472750 | n.905C>G | non_coding_transcript_exon_variant | 0.95 | streptomycin | Uncertain significance | Mutation from literature |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288832 | p.His137Arg | missense_variant | 0.95 | pyrazinamide | Not assoc w R - Interim | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6016 | c.777C>T | synonymous_variant | 0.42 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6112 | p.Met291Ile | missense_variant | 0.98 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
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 | 0.96 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.95 | 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 | 13275 | p.Tyr95Cys | missense_variant | 0.98 | isoniazid | Not assoc w R |
Rv0010c | 13298 | p.Ile87Met | missense_variant | 0.97 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.92 | isoniazid | Not assoc w R |
Rv0010c | 13482 | p.Ala26Val | missense_variant | 0.9 | isoniazid | Not assoc w R |
fgd1 | 490972 | p.Arg64Ser | missense_variant | 0.93 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.99 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 574653 | c.-695C>T | upstream_gene_variant | 1.0 | ethionamide | |
isoniazid | ||||||
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.98 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.95 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.99 | rifampicin | Not assoc w R |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 764817 | p.Val483Ala | missense_variant | 0.95 | rifampicin | Uncertain significance |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.95 | 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 | 1.0 | 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 | 800357 | c.-452C>A | upstream_gene_variant | 0.96 | linezolid | Not assoc w R |
Rv1129c | 1254543 | c.-9T>G | upstream_gene_variant | 0.92 | moxifloxacin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.99 | 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 | 0.95 | ethambutol | Not assoc w R |
embR | 1417473 | c.-126G>A | upstream_gene_variant | 0.95 | ethambutol | |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.97 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.94 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474709 | n.1052G>T | non_coding_transcript_exon_variant | 0.96 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rpsA | 1834319 | p.Val260Ile | missense_variant | 0.93 | pyrazinamide | Uncertain significance |
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.96 | linezolid | Not assoc w R |
tsnR | 1854045 | p.Tyr147Cys | missense_variant | 0.95 | linezolid | Not assoc w R |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.93 | linezolid | Not assoc w R |
bacA | 2062922 | p.Ile603Val | missense_variant | 0.99 | streptomycin | Not assoc w R |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2063106 | c.1623G>A | synonymous_variant | 0.99 | streptomycin | Not assoc w R - Interim |
kanamycin | Not assoc w R - Interim | |||||
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.99 | pyrazinamide | Not assoc w R |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.95 | pyrazinamide | Uncertain significance |
Rv1979c | 2221786 | p.Pro460Leu | missense_variant | 0.95 | clofazimine | |
bedaquiline | ||||||
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.95 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv1979c | 2222842 | c.322delG | frameshift_variant | 0.95 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.98 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.97 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.98 | isoniazid | |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.93 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.96 | ethionamide | Uncertain significance |
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.93 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3640394 | c.-149_-148insT | upstream_gene_variant | 0.93 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
rpoA | 3878630 | c.-124delC | upstream_gene_variant | 0.97 | rifampicin | Not assoc w R |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.92 | pyrazinamide | Not assoc w R - Interim |
glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
glpK | 4139602 | p.Arg52Trp | missense_variant | 0.92 | ethambutol | Uncertain significance |
moxifloxacin | ||||||
streptomycin | Uncertain significance | |||||
levofloxacin | ||||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embC | 4239652 | c.-211T>G | upstream_gene_variant | 0.97 | ethambutol | Uncertain significance |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.96 | ethambutol | Not assoc w R |
embA | 4244096 | c.864C>T | synonymous_variant | 0.94 | ethambutol | Not assoc w R |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.96 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.92 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.98 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.96 | ethambutol | Not assoc w R |
whiB6 | 4338242 | p.Gln94Glu | missense_variant | 0.94 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
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 | 4338603 | c.-82C>T | upstream_gene_variant | 0.98 | 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 | 0.99 | streptomycin | Not assoc w R |
gid | 4407873 | c.330G>T | synonymous_variant | 0.98 | streptomycin | Not assoc w R |
gid | 4407966 | p.Leu79Phe | missense_variant | 0.98 | streptomycin | Uncertain significance |