Run ID: SRR25827614
Sample name:
Date: 2024-10-04T15:50:33.348362
Number of reads: 2297904
Percentage reads mapped: 99.13
Median coverage: 74.0
Strain: lineage1.2.2.2;lineage2.2.1;lineage3;lineage4.9
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.09 |
lineage1.2.2 | Indo-Oceanic | RD239 | 0.3 |
lineage2 | East-Asian | RD105 | 0.39 |
lineage1.2.2.2 | Indo-Oceanic | RD239 | 0.22 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.37 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.38 |
lineage4 | Euro-American | None | 0.19 |
lineage1 | Indo-Oceanic | RD239 | 0.27 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.12 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Val170Phe | Assoc w R | |
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) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | p.Gly132Ala | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
p.Asp94Gly | Assoc w R | High-level resistance | ||
ofloxacin | ||||
levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
p.Asp94Gly | Assoc w R | |||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.28 | 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) | |||||
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.52 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 760314 | p.Val170Phe | missense_variant | 0.34 | rifampicin | Assoc w R | |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.4 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.41 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.14 | 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) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.6 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288847 | p.Gly132Ala | missense_variant | 0.16 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Val | missense_variant | 0.35 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 0.33 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6112 | p.Met291Ile | missense_variant | 0.31 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrB | 6184 | c.945C>T | synonymous_variant | 0.38 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7268 | c.-34C>T | upstream_gene_variant | 0.25 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 0.87 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.84 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7943 | p.Glu214Asp | missense_variant | 0.27 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrA | 8452 | p.Ala384Val | missense_variant | 0.28 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.29 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.76 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13298 | p.Ile87Met | missense_variant | 0.26 | isoniazid | Not assoc w R |
Rv0010c | 13548 | p.Thr4Ile | missense_variant | 0.27 | isoniazid | Not assoc w R |
Rv0010c | 13699 | c.-141A>G | upstream_gene_variant | 0.27 | isoniazid | Not assoc w R |
fgd1 | 491290 | p.Val170Met | missense_variant | 0.17 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.72 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.44 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.34 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.5 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.37 | ethionamide | Uncertain significance |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.34 | ethionamide | |
hadA | 732359 | c.435_439delTGCCG | frameshift_variant | 0.17 | isoniazid | Uncertain significance |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.24 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.79 | rifampicin | Not assoc w R |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.29 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.29 | rifampicin | Not assoc w R |
rpoC | 764840 | p.Ile491Val | missense_variant | 0.13 | rifampicin | Uncertain significance |
rpoC | 765863 | p.Ile832Val | missense_variant | 0.31 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.83 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.9 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.46 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.36 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.83 | streptomycin | Not assoc w R |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 0.23 | linezolid | Not assoc w R |
rplC | 800458 | c.-351_-350insGCTCGAGTGGGAGTGA | upstream_gene_variant | 0.2 | linezolid | |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.82 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
Rv1129c | 1254747 | c.-213C>A | upstream_gene_variant | 0.26 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.46 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.25 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.25 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.18 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.95 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.47 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.22 | linezolid | Not assoc w R |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.86 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.88 | capreomycin | Not assoc w R |
bacA | 2062922 | p.Ile603Val | missense_variant | 0.27 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2063675 | p.Ile352Val | missense_variant | 0.21 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.76 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.88 | pyrazinamide | Not assoc w R |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 0.29 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.35 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.88 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223553 | c.-389C>A | upstream_gene_variant | 0.31 | bedaquiline | Uncertain significance |
clofazimine | Not assoc w R | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.36 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.25 | isoniazid | |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.26 | kanamycin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv2477c | 2783781 | p.Asn88Asp | missense_variant | 0.31 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.86 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.2 | ethionamide | Uncertain significance |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.35 | pyrazinamide | Not assoc w R - Interim |
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.3 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.85 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626467 | c.147G>A | synonymous_variant | 0.23 | rifampicin | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.43 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
rpoA | 3878817 | c.-310T>A | upstream_gene_variant | 0.44 | rifampicin | Not assoc w R |
clpC1 | 4038425 | c.2280C>T | synonymous_variant | 0.32 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.27 | pyrazinamide | Not assoc w R - Interim |
glpK | 4138377 | p.Val460Ala | missense_variant | 0.24 | 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 | |||||
embC | 4240671 | p.Thr270Ile | missense_variant | 0.21 | ethambutol | Not assoc w R |
embC | 4241022 | p.Ala387Val | missense_variant | 0.19 | ethambutol | Uncertain significance |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.25 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 0.89 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.4 | ethambutol | Not assoc w R |
embA | 4244061 | p.Leu277Phe | missense_variant | 0.26 | ethambutol | |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.26 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.28 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.28 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.28 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.28 | ethambutol | Not assoc w R |
ethA | 4326148 | c.1326G>T | synonymous_variant | 0.32 | ethionamide | Not assoc w R - Interim |
ethA | 4326439 | p.Asn345Lys | missense_variant | 0.25 | ethionamide | Uncertain significance |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 0.35 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 0.91 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.32 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 0.89 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.82 | streptomycin | Not assoc w R |
gid | 4407620 | p.Tyr195His | missense_variant | 0.18 | streptomycin | Not assoc w R |
gid | 4407873 | c.330G>T | synonymous_variant | 0.31 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.36 | streptomycin | Not assoc w R |