Run ID: ERR4798936
Sample name:
Date: 20-10-2023 03:17:54
Number of reads: 4696889
Percentage reads mapped: 99.3
Strain: lineage1.2.2.2
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (0.98) |
| Isoniazid | R | fabG1 c.-15C>T (0.99) |
| Ethambutol | R | embA c.-12C>T (0.98), embB p.Ser347Ile (0.99) |
| Pyrazinamide | R | pncA c.500_515delCCACCGTCGCCGCGCT (0.99) |
| Streptomycin | ||
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | R | rrs n.1401A>G (0.98) |
| Amikacin | R | rrs n.1401A>G (0.98) |
| Capreomycin | R | rrs n.1401A>G (0.98) |
| Kanamycin | R | rrs n.1401A>G (0.98) |
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-15C>T (0.99) |
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage1 | Indo-Oceanic | EAI | RD239 | 0.99 |
| lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 0.99 |
| lineage1.2.2.2 | Indo-Oceanic | NA | RD239 | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.98 | rifampicin |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.98 | kanamycin, capreomycin, aminoglycosides, amikacin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.99 | isoniazid, ethionamide |
| pncA | 2288726 | c.500_515delCCACCGTCGCCGCGCT | frameshift_variant | 0.99 | pyrazinamide |
| embA | 4243221 | c.-12C>T | upstream_gene_variant | 0.98 | ethambutol |
| embB | 4247553 | p.Ser347Ile | missense_variant | 0.99 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 5075 | c.-165C>T | upstream_gene_variant | 0.99 |
| gyrB | 6112 | p.Met291Ile | missense_variant | 0.98 |
| gyrA | 7268 | c.-34C>T | upstream_gene_variant | 0.99 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 8452 | p.Ala384Val | missense_variant | 0.99 |
| gyrA | 9143 | c.1842T>C | synonymous_variant | 0.99 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 0.99 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.99 |
| rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
| rpoC | 763886 | c.517C>A | synonymous_variant | 0.99 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
| mmpS5 | 779625 | c.-720G>A | upstream_gene_variant | 0.99 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.99 |
| embR | 1417019 | p.Cys110Tyr | missense_variant | 0.99 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| inhA | 1674686 | p.Thr162Met | missense_variant | 0.97 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| ndh | 2102240 | p.Arg268His | missense_variant | 0.98 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 0.98 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| PPE35 | 2168742 | p.Gly624Asp | missense_variant | 0.99 |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.99 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| kasA | 2518132 | c.18C>T | synonymous_variant | 0.96 |
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.99 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.99 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fprA | 3474597 | c.591C>A | synonymous_variant | 0.97 |
| fprA | 3475159 | p.Asn385Asp | missense_variant | 0.99 |
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.99 |
| clpC1 | 4040719 | c.-15A>G | upstream_gene_variant | 0.99 |
| embC | 4240671 | p.Thr270Ile | missense_variant | 0.99 |
| embC | 4241042 | p.Asn394Asp | missense_variant | 0.98 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
| embB | 4247646 | p.Glu378Ala | missense_variant | 0.98 |
| aftB | 4267960 | p.Val293Met | missense_variant | 0.97 |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.99 |
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.99 |
| ethA | 4326148 | c.1326G>T | synonymous_variant | 1.0 |
| ethA | 4326439 | p.Asn345Lys | missense_variant | 0.96 |
| whiB6 | 4338203 | p.Arg107Cys | missense_variant | 0.99 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.98 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
| gid | 4407848 | p.Ala119Thr | missense_variant | 1.0 |
| gid | 4407868 | p.Val112Gly | missense_variant | 0.99 |
| gid | 4407873 | c.330G>T | synonymous_variant | 0.99 |
