Run ID: SRR21887709
Sample name:
Date: 07-07-2023 05:42:08
Number of reads: 11546285
Percentage reads mapped: 99.67
Strain: lineage2.2.2
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (0.99) |
| Isoniazid | R | katG p.Ser315Thr (0.99) |
| Ethambutol | ||
| Pyrazinamide | R | pncA p.Val7Ala (0.99) |
| Streptomycin | R | rrs n.906A>G (0.98) |
| Fluoroquinolones | R | gyrB p.Asn499Asp (0.26) |
| Moxifloxacin | R | gyrB p.Asn499Asp (0.26) |
| Ofloxacin | R | gyrB p.Asn499Asp (0.26) |
| Levofloxacin | R | gyrB p.Asn499Asp (0.26) |
| Ciprofloxacin | R | gyrB p.Asn499Asp (0.26) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | R | eis c.-37G>T (0.97) |
| 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 |
| lineage2.2.2 | East-Asian (Beijing) | Beijing-RD105/RD207 | RD105;RD207 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrB | 6734 | p.Asn499Asp | missense_variant | 0.26 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin |
| rrs | 1472751 | n.906A>G | non_coding_transcript_exon_variant | 0.98 | streptomycin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid |
| pncA | 2289222 | p.Val7Ala | missense_variant | 0.99 | pyrazinamide |
| eis | 2715369 | c.-37G>T | upstream_gene_variant | 0.97 | kanamycin |
| 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 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
| mmpL5 | 776356 | p.Leu709Ile | 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 | 1406276 | c.1065G>A | synonymous_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrs | 1471786 | n.-60T>G | upstream_gene_variant | 0.16 |
| rrl | 1476750 | n.3093T>G | non_coding_transcript_exon_variant | 0.99 |
| rpsA | 1834177 | c.636A>C | synonymous_variant | 0.99 |
| 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 | 2222418 | p.Asp249Glu | missense_variant | 0.8 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2289469 | c.-228C>G | upstream_gene_variant | 0.99 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fprA | 3474851 | p.Arg282Leu | missense_variant | 0.99 |
| whiB7 | 3568428 | c.252A>C | synonymous_variant | 0.15 |
| Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
| fbiA | 3641137 | p.Ala199Thr | missense_variant | 1.0 |
| alr | 3841437 | c.-17G>T | upstream_gene_variant | 0.14 |
| rpoA | 3878613 | c.-106A>C | upstream_gene_variant | 0.23 |
| rpoA | 3878618 | c.-111A>C | upstream_gene_variant | 0.2 |
| rpoA | 3878653 | c.-146A>C | upstream_gene_variant | 0.13 |
| clpC1 | 4040249 | p.Glu152Asp | missense_variant | 0.13 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4243217 | c.-16C>A | upstream_gene_variant | 1.0 |
| embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
| embB | 4247028 | p.Leu172Arg | missense_variant | 0.26 |
| embB | 4247033 | p.Ser174Arg | missense_variant | 0.17 |
| aftB | 4267647 | p.Asp397Gly | 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 |
| gid | 4407985 | p.Gly73Glu | missense_variant | 0.99 |
| Rv1979c | 2217878 | c.746_*3840del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |
