Run ID: ERR2704686
Sample name:
Date: 21-10-2023 05:08:59
Number of reads: 4203279
Percentage reads mapped: 99.26
Strain: lineage5.1.1
Drug-resistance: Sensitive
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | ||
| Isoniazid | ||
| Ethambutol | ||
| Pyrazinamide | ||
| Streptomycin | ||
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage5 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 1.0 |
| lineage5.1 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 0.9 |
| lineage5.1.1 | West-Africa 1 | AFRI_2;AFRI_3 | RD711 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 6446 | p.Ala403Ser | missense_variant | 0.99 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| gyrA | 9566 | c.2265C>T | synonymous_variant | 1.0 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
| rpoC | 763280 | c.-90C>T | 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 |
| Rv1258c | 1406511 | p.Gly277Val | missense_variant | 1.0 |
| Rv1258c | 1407273 | p.Asp23Val | missense_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrl | 1474289 | n.632C>G | non_coding_transcript_exon_variant | 1.0 |
| inhA | 1673338 | c.-864G>A | upstream_gene_variant | 0.97 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| ndh | 2101921 | c.1122G>A | synonymous_variant | 1.0 |
| ndh | 2103112 | c.-70G>T | upstream_gene_variant | 1.0 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2290062 | c.-821G>A | upstream_gene_variant | 1.0 |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 |
| ald | 3087184 | c.368_373delCCGACG | disruptive_inframe_deletion | 1.0 |
| Rv3083 | 3449644 | p.Ala381Thr | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
| alr | 3840932 | c.489C>T | synonymous_variant | 1.0 |
| rpoA | 3878493 | c.15G>A | synonymous_variant | 1.0 |
| ddn | 3986987 | c.144G>T | synonymous_variant | 1.0 |
| ddn | 3987180 | p.Asp113Asn | missense_variant | 1.0 |
| clpC1 | 4040824 | c.-120C>T | upstream_gene_variant | 1.0 |
| embC | 4239843 | c.-20A>C | upstream_gene_variant | 0.99 |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 |
| embA | 4244635 | p.Val468Ala | missense_variant | 1.0 |
| embA | 4245147 | p.Pro639Ser | 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 |
| ethR | 4326928 | c.-621G>A | upstream_gene_variant | 1.0 |
| ethA | 4327103 | p.Gly124Asp | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
