Run ID: SRR2100270
Sample name:
Date: 2024-10-05T13:07:38.894483
Number of reads: 14480339
Percentage reads mapped: 99.4
Median coverage: 290.0
Strain: lineage1.2.2.2;lineage4.1.1.3
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.2.2 | Indo-Oceanic | RD239 | 0.26 |
lineage1.2.2.2 | Indo-Oceanic | RD239 | 0.25 |
lineage4.1 | Euro-American | None | 0.73 |
lineage4.1.1.3 | Euro-American (X-type) | RD193 | 0.74 |
lineage4 | Euro-American | None | 0.73 |
lineage4.1.1 | Euro-American (X-type) | None | 0.74 |
lineage1 | Indo-Oceanic | RD239 | 0.25 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | gid | c.102delG | Assoc w R | |
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 |
---|---|---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 0.78 | isoniazid | Assoc w R | High-level resistance |
gid | 4408100 | c.102delG | frameshift_variant | 0.27 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 0.28 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6112 | p.Met291Ile | missense_variant | 0.19 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7268 | c.-34C>T | upstream_gene_variant | 0.29 | 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 | 7532 | c.231T>C | synonymous_variant | 0.3 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8452 | p.Ala384Val | missense_variant | 0.3 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.25 | 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 | |||||
gyrA | 9782 | c.2481C>A | synonymous_variant | 0.24 | levofloxacin | |
moxifloxacin | ||||||
Rv0010c | 13298 | p.Ile87Met | missense_variant | 0.21 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.29 | isoniazid | Not assoc w R |
Rv0010c | 13482 | p.Ala26Val | missense_variant | 0.27 | isoniazid | Not assoc w R |
Rv0010c | 13699 | c.-141A>G | upstream_gene_variant | 0.24 | isoniazid | Not assoc w R |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.25 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
Rv0565c | 656180 | p.Asp431Asn | missense_variant | 0.3 | ethionamide | Uncertain significance |
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.7 | ethionamide | Uncertain significance |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.31 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.18 | rifampicin | Not assoc w R |
rpoB | 760865 | c.1059C>T | synonymous_variant | 0.3 | rifampicin | Not assoc w R - Interim |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.28 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.29 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.78 | 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 | 0.24 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800219 | c.-590T>C | upstream_gene_variant | 0.72 | linezolid | |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 0.31 | linezolid | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.26 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.26 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.28 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.2 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rpsA | 1833684 | p.Arg48Pro | missense_variant | 0.76 | pyrazinamide | |
rpsA | 1834130 | p.Glu197Lys | missense_variant | 0.77 | pyrazinamide | Uncertain significance |
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.33 | 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 | 0.27 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.23 | isoniazid | Not assoc w R |
PPE35 | 2167683 | p.Leu977Arg | missense_variant | 0.28 | pyrazinamide | Uncertain significance |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.23 | pyrazinamide | Not assoc w R |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 0.2 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.25 | 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 | |||||
Rv1979c | 2223553 | c.-389C>A | upstream_gene_variant | 0.23 | bedaquiline | Uncertain significance |
clofazimine | Not assoc w R | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.31 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.14 | isoniazid | |
Rv2681 | 2997949 | p.Arg404His | missense_variant | 0.33 | capreomycin | |
thyX | 3067901 | c.45C>T | synonymous_variant | 0.73 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.34 | ethionamide | Uncertain significance |
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.26 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626467 | c.147G>A | synonymous_variant | 0.28 | rifampicin | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpoA | 3878817 | c.-310T>A | upstream_gene_variant | 0.24 | rifampicin | Not assoc w R |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.25 | pyrazinamide | Not assoc w R - Interim |
glpK | 4138377 | p.Val460Ala | missense_variant | 0.23 | 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 | 0.23 | ethambutol | Not assoc w R |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.32 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.78 | ethambutol | Not assoc w R |
embA | 4243622 | c.390G>A | synonymous_variant | 0.78 | ethambutol | Not assoc w R - Interim |
embA | 4244456 | c.1224C>G | synonymous_variant | 0.26 | ethambutol | Not assoc w R - Interim |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.23 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.25 | ethambutol | Not assoc w R |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.71 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.23 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.36 | ethambutol | Not assoc w R |
ethA | 4326148 | c.1326G>T | synonymous_variant | 0.24 | ethionamide | Not assoc w R - Interim |
ethA | 4326439 | p.Asn345Lys | missense_variant | 0.25 | ethionamide | Uncertain significance |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 0.29 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
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 | 0.26 | 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 | 0.26 | streptomycin | Not assoc w R |
gid | 4407873 | c.330G>T | synonymous_variant | 0.23 | streptomycin | Not assoc w R |