Run ID: ERR4799460
Sample name:
Date: 20-10-2023 03:48:28
Number of reads: 5322885
Percentage reads mapped: 99.62
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ala286Val (0.98), rpoB p.Ser450Leu (1.00) |
| Isoniazid | R | katG p.Ser315Thr (0.99) |
| Ethambutol | R | embB p.Met306Val (0.99) |
| Pyrazinamide | ||
| Streptomycin | R | rpsL p.Lys43Arg (1.00) |
| Fluoroquinolones | R | gyrA p.Ala90Val (0.98) |
| Moxifloxacin | R | gyrA p.Ala90Val (0.98) |
| Ofloxacin | R | gyrA p.Ala90Val (0.98) |
| Levofloxacin | R | gyrA p.Ala90Val (0.98) |
| Ciprofloxacin | R | gyrA p.Ala90Val (0.98) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage2 | East-Asian | Beijing | RD105 | 0.99 |
| lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.99 |
| lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7570 | p.Ala90Val | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 760663 | p.Ala286Val | missense_variant | 0.98 | rifampicin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid |
| embB | 4247429 | p.Met306Val | missense_variant | 0.99 | 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 | 1.0 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| mshA | 575907 | p.Ala187Val | missense_variant | 0.98 |
| ccsA | 620625 | p.Ile245Met | missense_variant | 0.99 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
| rpoC | 764844 | p.Ala492Val | missense_variant | 0.99 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
| mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.99 |
| mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.97 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.99 |
| rrs | 1471647 | n.-199G>C | upstream_gene_variant | 0.99 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.99 |
| rpsA | 1834177 | c.636A>C | synonymous_variant | 0.98 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| 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 |
| pncA | 2288772 | p.Val157Gly | missense_variant | 0.97 |
| ald | 3086765 | c.-55G>T | upstream_gene_variant | 0.47 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4243460 | c.228C>T | synonymous_variant | 0.99 |
| aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
| ubiA | 4269658 | p.Phe59Ser | missense_variant | 0.99 |
| ethA | 4327060 | p.Ser138Arg | missense_variant | 0.98 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
| gid | 4407927 | p.Glu92Asp | missense_variant | 0.98 |
