Run ID: ERR4799416
Sample name:
Date: 20-10-2023 03:52:32
Number of reads: 5364156
Percentage reads mapped: 99.04
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00), rpoC p.Ile491Thr (0.99) |
| Isoniazid | R | fabG1 c.-8T>C (0.64), katG p.Ser315Thr (1.00) |
| Ethambutol | R | embA c.-16C>T (1.00) |
| Pyrazinamide | R | pncA p.Ile5Ser (0.99) |
| Streptomycin | R | rpsL p.Lys43Arg (0.98) |
| Fluoroquinolones | R | gyrA p.Asp94Gly (0.98) |
| Moxifloxacin | R | gyrA p.Asp94Gly (0.98) |
| Ofloxacin | R | gyrA p.Asp94Gly (0.98) |
| Levofloxacin | R | gyrA p.Asp94Gly (0.98) |
| Ciprofloxacin | R | gyrA p.Asp94Gly (0.98) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | R | eis c.-12C>T (0.99) |
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-8T>C (0.64), ethA c.1054delG (1.00), ethA c.1054delG (1.00) |
| Clofazimine | ||
| Para-aminosalicylic_acid | R | thyA p.Thr22Ala (1.00) |
| 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 |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Gly | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| rpoC | 764841 | p.Ile491Thr | missense_variant | 0.99 | rifampicin |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 0.98 | streptomycin |
| fabG1 | 1673432 | c.-8T>C | upstream_gene_variant | 0.64 | isoniazid, ethionamide |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2289228 | p.Ile5Ser | missense_variant | 0.99 | pyrazinamide |
| eis | 2715344 | c.-12C>T | upstream_gene_variant | 0.99 | kanamycin |
| thyA | 3074408 | p.Thr22Ala | missense_variant | 1.0 | para-aminosalicylic_acid |
| embA | 4243217 | c.-16C>T | upstream_gene_variant | 1.0 | ethambutol |
| ethA | 4326419 | c.1054delG | frameshift_variant | 1.0 | ethionamide, ethionamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 0.99 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| fgd1 | 491290 | p.Val170Met | missense_variant | 0.98 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
| ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
| rpoC | 763031 | c.-339T>C | upstream_gene_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 | 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 |
| rrl | 1475479 | n.1822C>T | non_coding_transcript_exon_variant | 1.0 |
| rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
| 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 |
| thyX | 3067949 | c.-4C>T | upstream_gene_variant | 0.99 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3448598 | c.97_98dupGC | frameshift_variant | 0.18 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
| embC | 4241022 | p.Ala387Val | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4243460 | c.228C>T | synonymous_variant | 0.99 |
| embB | 4247847 | p.Gln445Arg | missense_variant | 1.0 |
| aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
| whiB6 | 4338292 | p.Ala77Val | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
| gid | 4407620 | p.Tyr195His | missense_variant | 0.99 |
| gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |
