Run ID: ERR1140794
Sample name:
Date: 2024-05-17T14:12:08.949180
Number of reads: 13537021
Percentage reads mapped: 98.33
Median coverage: 131.5
Strain: lineage5.1.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage5.1.1 | West-Africa 1 | RD711 | 1.0 |
| lineage5 | West-Africa 1 | RD711 | 1.0 |
| lineage5.1 | West-Africa 1 | RD711 | 0.93 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 1088 | p.Ser363Asn | missense_variant | 1.0 | isoniazid | Uncertain significance |
| gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 | moxifloxacin | Uncertain significance |
| levofloxacin | Not assoc w R | |||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| gyrA | 9143 | c.1842T>C | synonymous_variant | 0.99 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| gyrA | 9566 | c.2265C>T | synonymous_variant | 0.98 | moxifloxacin | Not assoc w R - Interim |
| levofloxacin | Not assoc w R - Interim | |||||
| Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13579 | c.-21G>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
| hadA | 731750 | c.-180G>C | upstream_gene_variant | 0.99 | isoniazid | |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 0.99 | rifampicin | Not assoc w R |
| rpoB | 763280 | c.3474C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| Rv1258c | 1406511 | p.Gly277Val | missense_variant | 1.0 | streptomycin | |
| isoniazid | ||||||
| pyrazinamide | ||||||
| Rv1258c | 1407273 | p.Asp23Val | missense_variant | 1.0 | streptomycin | Uncertain significance |
| isoniazid | Uncertain significance | |||||
| pyrazinamide | Uncertain significance | |||||
| embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| capreomycin | ||||||
| rrs | 1472349 | n.504A>C | non_coding_transcript_exon_variant | 0.12 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| capreomycin | ||||||
| rrs | 1472374 | n.529T>G | non_coding_transcript_exon_variant | 0.13 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| capreomycin | ||||||
| rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
| amikacin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.13 | kanamycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.13 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| capreomycin | ||||||
| rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.13 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| capreomycin | ||||||
| rrl | 1474289 | n.632C>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.21 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.21 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.18 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| tsnR | 1853565 | c.-41G>A | upstream_gene_variant | 1.0 | linezolid | Uncertain significance |
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | kanamycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| capreomycin | Not assoc w R | |||||
| ndh | 2101921 | c.1122G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| isoniazid | Not assoc w R - Interim | |||||
| delamanid | Not assoc w R - Interim | |||||
| ndh | 2103112 | c.-70G>T | upstream_gene_variant | 1.0 | ethionamide | Uncertain significance |
| isoniazid | Not assoc w R - Interim | |||||
| delamanid | Uncertain significance | |||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| pncA | 2290062 | c.-821G>A | upstream_gene_variant | 1.0 | pyrazinamide | |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
| ald | 3087184 | c.368_373delCCGACG | disruptive_inframe_deletion | 0.99 | cycloserine | |
| Rv3083 | 3449644 | p.Ala381Thr | missense_variant | 1.0 | ethionamide | Uncertain significance |
| lpqB | 3624350 | c.561G>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| alr | 3840932 | c.489C>T | synonymous_variant | 1.0 | cycloserine | |
| rpoA | 3878493 | c.15G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| ddn | 3986987 | c.144G>T | synonymous_variant | 1.0 | pretomanid | |
| delamanid | Not assoc w R - Interim | |||||
| ddn | 3987180 | p.Asp113Asn | missense_variant | 1.0 | pretomanid | |
| delamanid | Uncertain significance | |||||
| clpC1 | 4040824 | c.-120C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | isoniazid | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| ethambutol | Not assoc w R | |||||
| levofloxacin | Not assoc w R | |||||
| glpK | 4139131 | p.Glu209Lys | missense_variant | 1.0 | isoniazid | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| rifampicin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| embC | 4239843 | c.-20A>C | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244635 | p.Val468Ala | missense_variant | 0.96 | ethambutol | Not assoc w R - Interim |
| embA | 4245147 | p.Pro639Ser | missense_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269606 | c.228T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4326928 | c.546C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| ethA | 4327103 | p.Gly124Asp | missense_variant | 1.0 | ethionamide | Uncertain significance |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
