Run ID: SRR23862091
Sample name:
Date: 12-04-2023 18:08:04
Number of reads: 1678646
Percentage reads mapped: 99.56
Strain: lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Val (1.00) |
Pyrazinamide | R | pncA p.His57Arg (1.00) |
Streptomycin | R | rpsL p.Lys43Arg (1.00) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289072 | p.His57Arg | missense_variant | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.98 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576077 | p.Leu244Val | missense_variant | 0.14 |
mshA | 576093 | p.Pro249Arg | missense_variant | 0.25 |
mshA | 576100 | p.Asp251Glu | missense_variant | 0.15 |
mshA | 576105 | p.Arg253Pro | missense_variant | 0.2 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.2 |
mshA | 576113 | p.Arg256Gly | missense_variant | 0.2 |
mshA | 576116 | p.Ala257Pro | missense_variant | 0.3 |
mshA | 576616 | c.1269G>C | synonymous_variant | 0.14 |
mshA | 576674 | p.Arg443Gly | missense_variant | 0.14 |
ccsA | 620059 | p.Asp57His | missense_variant | 0.15 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.95 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918044 | p.Asp35Glu | missense_variant | 0.14 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pepQ | 2859910 | p.Arg170Pro | missense_variant | 0.14 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fbiD | 3339726 | c.609A>T | synonymous_variant | 0.16 |
fbiD | 3339746 | p.Ala210Gly | missense_variant | 0.16 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568428 | c.252A>C | synonymous_variant | 0.17 |
whiB7 | 3568439 | p.Arg81Gly | missense_variant | 0.2 |
whiB7 | 3568473 | p.Glu69Asp | missense_variant | 0.18 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
rpoA | 3878663 | c.-156A>T | upstream_gene_variant | 0.15 |
rpoA | 3878666 | c.-159C>A | upstream_gene_variant | 0.15 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4246542 | p.Ser10Thr | missense_variant | 0.31 |
embB | 4246552 | p.Asn13Lys | missense_variant | 0.33 |
embB | 4246559 | p.Ile16Phe | missense_variant | 0.33 |
embB | 4246574 | p.Ala21Ser | missense_variant | 0.29 |
embB | 4246974 | p.His154Leu | missense_variant | 0.13 |
embB | 4246993 | p.Asn160Lys | missense_variant | 0.14 |
embB | 4246996 | p.Phe161Leu | missense_variant | 0.21 |
embB | 4246999 | c.486C>G | synonymous_variant | 0.15 |
embB | 4248329 | p.Met606Leu | missense_variant | 0.15 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethR | 4328045 | p.Leu166Gln | missense_variant | 0.16 |
ethR | 4328055 | p.His169Gln | missense_variant | 0.14 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |