Run ID: SRR28393374
Sample name:
Date: 2024-05-22T12:53:18.559886
Number of reads: 5042643
Percentage reads mapped: 99.58
Median coverage: 148.0
Strain: lineage4.1.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 0.76 |
lineage4.1.2 | Euro-American | None | 0.74 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.76 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>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 | |
ahpC | c.-54C>T | Uncertain significance | Mutation from literature | |
ethambutol | embB | p.Met306Ile | Assoc w R | |
pyrazinamide | pncA | c.335delA | Assoc w R | |
p.Ile5Thr | Uncertain significance | Mutation from literature | ||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T |
ethA | p.Asp58Ala | Uncertain significance | Mutation from literature | |
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 | |
inhA | 1673423 | c.-779G>T | upstream_gene_variant | 0.16 | ethionamide | Assoc w R - Interim | Alias fabG1_c.-17G>T |
isoniazid | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.81 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288906 | c.335delA | frameshift_variant | 0.18 | pyrazinamide | Assoc w R | |
pncA | 2289228 | p.Ile5Thr | missense_variant | 0.73 | pyrazinamide | Uncertain significance | Mutation from literature |
ahpC | 2726139 | c.-54C>T | upstream_gene_variant | 0.8 | isoniazid | Uncertain significance | Mutation from literature |
embB | 4247431 | p.Met306Ile | missense_variant | 0.77 | ethambutol | Assoc w R | |
ethA | 4327301 | p.Asp58Ala | missense_variant | 0.72 | ethionamide | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.81 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 0.78 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.71 | ethionamide | Uncertain significance |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.71 | rifampicin | Not assoc w R |
rpoB | 761407 | p.Val534Gly | missense_variant | 0.32 | rifampicin | Uncertain significance |
rpoB | 761889 | p.Val695Leu | missense_variant | 0.17 | rifampicin | Uncertain significance |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.74 | rifampicin | Not assoc w R |
rpoC | 765617 | p.Glu750Gln | missense_variant | 0.75 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781276 | c.-284A>C | upstream_gene_variant | 0.75 | streptomycin | |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 801009 | c.201A>G | synonymous_variant | 0.29 | linezolid | Not assoc w R - Interim |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
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 |
katG | 2153911 | p.Leu734Arg | missense_variant | 0.21 | isoniazid | Uncertain significance |
Rv1979c | 2223214 | c.-50A>C | upstream_gene_variant | 0.21 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.76 | isoniazid | |
Rv2680 | 2996034 | c.-71G>A | upstream_gene_variant | 0.6 | capreomycin | Uncertain significance |
Rv2680 | 2996085 | c.-20G>A | upstream_gene_variant | 0.18 | capreomycin | Uncertain significance |
Rv2680 | 2996136 | p.Ser11Asn | missense_variant | 0.16 | capreomycin | |
Rv2752c | 3065517 | c.675C>T | synonymous_variant | 0.26 | ethambutol | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.75 | cycloserine | |
Rv3083 | 3448439 | c.-64delA | upstream_gene_variant | 0.23 | ethionamide | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.75 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
embC | 4239298 | c.-565C>T | upstream_gene_variant | 0.79 | 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 | 0.8 | ethambutol | Not assoc w R |
ethA | 4328317 | c.-844C>T | upstream_gene_variant | 0.28 | ethionamide | |
whiB6 | 4338440 | p.Glu28* | stop_gained | 0.74 | 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 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4408064 | p.Arg47Gly | missense_variant | 0.73 | streptomycin |