Run ID: SRR5709792
Sample name:
Date: 20-10-2023 16:49:50
Number of reads: 1761441
Percentage reads mapped: 99.36
Strain: lineage1.1
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.His445Asp (1.00) |
| Isoniazid | ||
| Ethambutol | R | embB p.Met306Val (1.00) |
| Pyrazinamide | R | pncA c.391dupG (0.95), pncA c.391dupG (0.95) |
| Streptomycin | R | rrs n.514A>C (1.00) |
| Fluoroquinolones | R | gyrA p.Asp94Gly (1.00) |
| Moxifloxacin | R | gyrA p.Asp94Gly (1.00) |
| Ofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Levofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Ciprofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | R | folC p.Arg49Trp (1.00) |
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
| lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761139 | p.His445Asp | missense_variant | 1.0 | rifampicin |
| rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 1.0 | streptomycin |
| pncA | 2288850 | c.391dupG | frameshift_variant | 0.95 | pyrazinamide, pyrazinamide |
| folC | 2747454 | p.Arg49Trp | missense_variant | 1.0 | para-aminosalicylic_acid |
| embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 5047 | c.-193C>T | upstream_gene_variant | 1.0 |
| gyrB | 5984 | p.Arg249Cys | missense_variant | 0.97 |
| gyrB | 6112 | p.Met291Ile | missense_variant | 0.97 |
| 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 | 8993 | c.1692C>T | synonymous_variant | 1.0 |
| gyrA | 9143 | c.1842T>C | synonymous_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 |
| rpoC | 763067 | c.-303C>A | upstream_gene_variant | 1.0 |
| rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
| rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
| rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
| rpoC | 766009 | c.2640G>C | synonymous_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776041 | p.Ala814Thr | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrs | 1472029 | n.184C>A | non_coding_transcript_exon_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 |
| PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2290000 | c.-759C>T | upstream_gene_variant | 1.0 |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
| Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fbiD | 3339101 | c.-17G>A | 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 |
| Rv3236c | 3612739 | c.378C>T | synonymous_variant | 1.0 |
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
| embC | 4240040 | p.Asn60His | missense_variant | 1.0 |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
| embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4243848 | p.Val206Met | missense_variant | 1.0 |
| embA | 4244695 | p.Lys488Met | missense_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 |
| whiB6 | 4338412 | p.Asp37Gly | missense_variant | 0.98 |
| 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 | 4407758 | p.Ser149Arg | missense_variant | 1.0 |
| gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
