Run ID: ERR161149
Sample name:
Date: 2024-04-15T04:03:56.494412
Number of reads: 2987848
Percentage reads mapped: 92.32
Median coverage: 65.0
Strain: lineage4.3.4.2.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.4.2.1 | Euro-American (LAM) | RD174 | 1.0 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 1.0 |
lineage4.3.4.2 | Euro-American (LAM) | RD174 | 0.98 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
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 |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1191 | c.1191T>C | synonymous_variant | 0.14 | isoniazid | |
dnaA | 1215 | c.1215C>T | synonymous_variant | 0.15 | isoniazid | |
dnaA | 1220 | p.Asn407Ser | missense_variant | 0.14 | isoniazid | |
dnaA | 1230 | c.1230A>G | synonymous_variant | 0.15 | isoniazid | |
dnaA | 1242 | c.1242G>C | synonymous_variant | 0.14 | isoniazid | |
dnaA | 1254 | c.1254T>G | synonymous_variant | 0.14 | isoniazid | |
dnaA | 1255 | p.Ala419Thr | missense_variant | 0.86 | isoniazid | Uncertain significance |
gyrB | 6140 | p.Val301Leu | missense_variant | 0.89 | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
nusG | 734475 | c.222T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
nusG | 734481 | c.228C>T | synonymous_variant | 0.12 | rifampicin | |
nusG | 734532 | c.279A>G | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
nusG | 734541 | c.288A>G | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
nusG | 734559 | c.306T>C | synonymous_variant | 0.12 | rifampicin | |
rpoB | 762131 | c.2325C>G | synonymous_variant | 0.14 | rifampicin | |
rpoB | 762143 | c.2337T>C | synonymous_variant | 0.18 | rifampicin | |
rpoB | 762149 | c.2343G>C | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoB | 762176 | c.2370T>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoB | 762185 | c.2379G>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoB | 762197 | c.2391C>T | synonymous_variant | 0.18 | rifampicin | |
rpoB | 762489 | p.Val895Leu | missense_variant | 0.12 | rifampicin | |
rpoC | 764188 | c.819A>G | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 764203 | c.834G>T | synonymous_variant | 0.15 | rifampicin | |
rpoC | 764206 | c.837T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 764213 | p.Arg282Lys | missense_variant | 0.15 | rifampicin | Uncertain significance |
rpoC | 764257 | c.888G>C | synonymous_variant | 0.16 | rifampicin | |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765658 | c.2289C>T | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 765784 | c.2415C>G | synonymous_variant | 0.12 | rifampicin | |
rpoC | 765811 | c.2442T>G | synonymous_variant | 0.15 | rifampicin | |
rpoC | 765826 | c.2457T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 767119 | c.3750A>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 767134 | c.3765C>A | synonymous_variant | 0.13 | rifampicin | |
rpoC | 767158 | c.3789T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 767167 | c.3798C>G | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775639 | p.Ile948Val | 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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 0.18 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rpsA | 1833703 | c.162C>T | synonymous_variant | 0.14 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1833724 | c.183C>G | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1833727 | c.186G>T | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834021 | c.480C>T | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834030 | c.489C>G | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834249 | c.708T>C | synonymous_variant | 0.16 | pyrazinamide | |
rpsA | 1834261 | c.720A>G | synonymous_variant | 0.13 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834264 | c.723G>C | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1834294 | c.753G>C | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834303 | c.762T>C | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834612 | c.1071G>A | synonymous_variant | 0.15 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834618 | c.1077G>T | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834633 | c.1092A>G | synonymous_variant | 0.16 | pyrazinamide | |
rpsA | 1834639 | c.1098T>C | synonymous_variant | 0.16 | pyrazinamide | |
rpsA | 1834654 | c.1113G>A | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834690 | c.1149T>C | synonymous_variant | 0.14 | pyrazinamide | |
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2477c | 2783140 | c.903C>G | synonymous_variant | 0.12 | ethambutol | |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
kanamycin | ||||||
rifampicin | ||||||
amikacin | ||||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.88 | para-aminosalicylic_acid | |
thyA | 3073892 | c.580T>C | synonymous_variant | 0.12 | para-aminosalicylic_acid | |
thyA | 3073917 | c.555C>G | synonymous_variant | 0.14 | para-aminosalicylic_acid | |
thyA | 3073925 | c.547T>C | synonymous_variant | 0.13 | para-aminosalicylic_acid | |
thyA | 3073929 | c.543T>C | synonymous_variant | 0.14 | para-aminosalicylic_acid | |
thyA | 3073953 | c.519T>G | synonymous_variant | 0.17 | para-aminosalicylic_acid | |
thyA | 3073958 | c.514C>T | synonymous_variant | 0.14 | para-aminosalicylic_acid | |
thyA | 3073959 | c.513T>C | synonymous_variant | 0.15 | para-aminosalicylic_acid | |
thyA | 3073977 | c.495A>G | synonymous_variant | 0.15 | para-aminosalicylic_acid | |
thyA | 3073989 | c.483T>C | synonymous_variant | 0.16 | para-aminosalicylic_acid | |
thyA | 3074001 | c.471C>G | synonymous_variant | 0.13 | para-aminosalicylic_acid | |
thyA | 3074004 | c.468T>C | synonymous_variant | 0.12 | para-aminosalicylic_acid | |
thyA | 3074010 | c.462C>G | synonymous_variant | 0.13 | para-aminosalicylic_acid | |
thyA | 3074120 | c.352T>C | synonymous_variant | 0.14 | para-aminosalicylic_acid | |
thyA | 3074121 | c.351T>C | synonymous_variant | 0.13 | para-aminosalicylic_acid | |
thyA | 3074127 | c.345G>C | synonymous_variant | 0.13 | para-aminosalicylic_acid | |
thyA | 3074130 | c.342G>C | synonymous_variant | 0.13 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.98 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3840719 | c.702A>G | synonymous_variant | 1.0 | cycloserine | |
rpoA | 3877920 | c.588G>C | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
rpoA | 3877926 | c.582G>C | synonymous_variant | 0.19 | rifampicin | |
rpoA | 3877962 | c.546G>T | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
ddn | 3986636 | c.-208C>G | upstream_gene_variant | 0.15 | delamanid | |
pretomanid | ||||||
ddn | 3986645 | c.-199G>A | upstream_gene_variant | 0.13 | delamanid | |
pretomanid | ||||||
ddn | 3986648 | c.-196C>G | upstream_gene_variant | 0.13 | delamanid | |
pretomanid | ||||||
ddn | 3986665 | c.-179G>C | upstream_gene_variant | 0.13 | delamanid | |
pretomanid | ||||||
ddn | 3986667 | c.-177_-176delCTinsAC | upstream_gene_variant | 0.13 | delamanid | |
pretomanid | ||||||
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.98 | pyrazinamide | Not assoc w R |
clpC1 | 4039298 | c.1407T>C | synonymous_variant | 0.12 | pyrazinamide | |
clpC1 | 4039577 | c.1128T>C | synonymous_variant | 0.12 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4039610 | c.1095G>C | synonymous_variant | 0.12 | pyrazinamide | |
glpK | 4138535 | c.1221T>C | synonymous_variant | 0.13 | ethambutol | |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
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 | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |