Run ID: ERR1035101
Sample name:
Date: 2024-10-05T00:17:35.903727
Number of reads: 5469608
Percentage reads mapped: 99.15
Median coverage: 104.0
Strain: lineage1.1.1.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.1 | Indo-Oceanic | RD239 | 1.0 |
lineage1 | Indo-Oceanic | RD239 | 1.0 |
lineage1.1.1 | Indo-Oceanic | RD239 | 1.0 |
lineage1.1.1.1 | Indo-Oceanic | RD239 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Arg | Assoc w R | |
isoniazid | inhA | c.-770T>A | Assoc w R - Interim | Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | c.93_105dupCAGCGACTACCTG | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Asp461Asn | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrB | p.Asp461Asn | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-770T>A | Assoc w R - Interim | Alias fabG1_c.-8T>A |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6620 | p.Asp461Asn | missense_variant | 1.0 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
rpoB | 761140 | p.His445Arg | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
inhA | 1673432 | c.-770T>A | upstream_gene_variant | 1.0 | ethionamide | Assoc w R - Interim | Alias fabG1_c.-8T>A |
isoniazid | Assoc w R - Interim | Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289136 | c.93_105dupCAGCGACTACCTG | frameshift_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 685 | p.Phe229Val | missense_variant | 1.0 | isoniazid | |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 | 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 | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_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 | 13275 | p.Tyr95Cys | missense_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13298 | p.Ile87Met | missense_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13482 | p.Ala26Val | missense_variant | 1.0 | isoniazid | Not assoc w R |
fgd1 | 490972 | p.Arg64Ser | missense_variant | 1.0 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
rpoB | 762418 | p.Arg871His | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | 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 | 765171 | p.Pro601Leu | missense_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 | |||||
mmpL5 | 777581 | p.Tyr300* | stop_gained | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 1.0 | linezolid | Not assoc w R |
Rv1129c | 1254543 | c.-9T>G | upstream_gene_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
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 | 1364297 | c.-116A>G | upstream_gene_variant | 1.0 | pyrazinamide | |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.99 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473211 | n.1366G>T | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474709 | n.1052G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rpsA | 1834319 | p.Val260Ile | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
tsnR | 1853974 | c.369C>T | synonymous_variant | 1.0 | linezolid | Not assoc w R |
tsnR | 1854045 | p.Tyr147Cys | missense_variant | 1.0 | linezolid | Not assoc w R |
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 |
bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2063106 | c.1623G>A | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
katG | 2156250 | c.-139G>C | upstream_gene_variant | 1.0 | isoniazid | |
katG | 2156389 | c.-278G>C | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | 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 | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.99 | isoniazid | |
Rv2680 | 2995804 | c.-301G>A | upstream_gene_variant | 1.0 | capreomycin | |
Rv2681 | 2997736 | c.1009_1011delCCG | conservative_inframe_deletion | 1.0 | capreomycin | Uncertain significance |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 | ethionamide | Uncertain significance |
lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
rpoA | 3878630 | c.-124delC | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
glpK | 4139074 | p.Leu228Val | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4244096 | c.864C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326917 | p.Thr186Arg | missense_variant | 1.0 | ethionamide | |
whiB6 | 4338242 | p.Gln94Glu | missense_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | 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 | 4338603 | c.-82C>T | 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 | 4407873 | c.330G>T | synonymous_variant | 1.0 | streptomycin | Not assoc w R |