Run ID: ERR181315
Sample name:
Date: 21-10-2023 06:01:48
Number of reads: 3968055
Percentage reads mapped: 97.73
Strain: lineage9
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Thr427Ile (1.00), rpoB p.His445Asn (1.00) |
| Isoniazid | R | katG c.1650delC (1.00) |
| Ethambutol | R | embB p.Met306Ile (1.00) |
| Pyrazinamide | ||
| Streptomycin | R | gid c.102delG (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 |
|---|---|---|---|---|
| lineage9 | Lineage 9 | None | None | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761086 | p.Thr427Ile | missense_variant | 1.0 | rifampicin |
| rpoB | 761139 | p.His445Asn | missense_variant | 1.0 | rifampicin |
| katG | 2154461 | c.1650delC | frameshift_variant | 1.0 | isoniazid |
| embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
| gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 7914 | p.Leu205Met | missense_variant | 1.0 |
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 0.97 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| rpoB | 759923 | c.117C>T | 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 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 |
| atpE | 1461251 | c.207G>T | synonymous_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrs | 1471970 | n.125G>A | non_coding_transcript_exon_variant | 1.0 |
| rrs | 1473109 | n.1264T>C | non_coding_transcript_exon_variant | 1.0 |
| rrl | 1475017 | n.1360G>A | non_coding_transcript_exon_variant | 0.99 |
| inhA | 1674434 | p.Val78Ala | missense_variant | 0.98 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| ndh | 2102072 | p.Ala324Val | missense_variant | 1.0 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| katG | 2155503 | c.609C>T | synonymous_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2288955 | p.Lys96Met | missense_variant | 1.0 |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
| folC | 2746425 | p.Ala392Thr | missense_variant | 1.0 |
| pepQ | 2860561 | c.-143C>A | upstream_gene_variant | 0.99 |
| Rv2752c | 3066099 | p.Met31Ile | missense_variant | 1.0 |
| ald | 3086728 | c.-92C>T | upstream_gene_variant | 0.99 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 |
| ald | 3087782 | c.963G>T | synonymous_variant | 1.0 |
| Rv3083 | 3449623 | p.Lys374Glu | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
| clpC1 | 4040883 | c.-179G>A | upstream_gene_variant | 1.0 |
| embC | 4241489 | p.Ala543Thr | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 |
| embB | 4246864 | c.351C>T | synonymous_variant | 1.0 |
| aftB | 4269351 | c.-515C>T | upstream_gene_variant | 1.0 |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.99 |
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
| gid | 4407876 | c.327C>T | synonymous_variant | 1.0 |
| gid | 4408457 | c.-255A>G | upstream_gene_variant | 1.0 |
