Run ID: ERR10610189
Sample name:
Date: 22-05-2023 22:41:15
Number of reads: 3411965
Percentage reads mapped: 99.15
Strain: lineage1.2.2.1
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.Gln497Arg (0.99) |
| Pyrazinamide | R | pncA p.Ser66Pro (1.00) |
| Streptomycin | ||
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | R | alr p.Met343Thr (0.99) |
| Ethionamide | R | ethA c.825delG (1.00), ethA c.825delG (1.00) |
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
| lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 1.0 |
| lineage1.2.2.1 | Indo-Oceanic | NA | RD239 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2289046 | p.Ser66Pro | missense_variant | 1.0 | pyrazinamide |
| alr | 3840393 | p.Met343Thr | missense_variant | 0.99 | cycloserine |
| embB | 4248003 | p.Gln497Arg | missense_variant | 0.99 | ethambutol |
| ethA | 4326648 | c.825delG | frameshift_variant | 1.0 | ethionamide, ethionamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 |
| gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| fgd1 | 491060 | p.Met93Thr | missense_variant | 1.0 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| ccsA | 620659 | p.Arg257Cys | missense_variant | 1.0 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
| rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
| rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
| rpoC | 765926 | p.Thr853Ala | missense_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 |
| rplC | 800899 | p.Ala31Thr | missense_variant | 1.0 |
| embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrs | 1471842 | n.-4T>G | upstream_gene_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| tlyA | 1918197 | p.Cys86Trp | missense_variant | 1.0 |
| ndh | 2102633 | c.408_409delCG | frameshift_variant | 1.0 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.99 |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
| thyX | 3068115 | c.-170C>T | upstream_gene_variant | 1.0 |
| thyA | 3074034 | c.438T>C | synonymous_variant | 0.99 |
| thyA | 3074290 | p.Trp61Leu | missense_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
| alr | 3841560 | c.-141_-140insA | upstream_gene_variant | 1.0 |
| rpoA | 3878641 | c.-135delG | upstream_gene_variant | 0.17 |
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
| embC | 4240750 | c.888C>T | synonymous_variant | 1.0 |
| embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 |
| ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 |
| ethR | 4327450 | c.-99G>A | upstream_gene_variant | 0.99 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
| gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
| gid | 4407995 | p.Ser70Gly | missense_variant | 1.0 |
