Run ID: ERR9119958
Sample name:
Date: 2024-10-04T22:01:43.145264
Number of reads: 5020807
Percentage reads mapped: 98.8
Median coverage: 114.0
Strain: lineage1.2.2.2
Spoligotype:
Drug-resistance: Pre-XDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage1.2.2 | Indo-Oceanic | RD239 | 0.99 |
| lineage1.2.2.2 | Indo-Oceanic | RD239 | 1.0 |
| lineage1 | Indo-Oceanic | RD239 | 0.99 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.His445Leu | Assoc w R | |
| isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| ethambutol | embA | c.-29_-28delCT | Uncertain significance | Mutation from literature |
| embB | p.Gln497Arg | Assoc w R | ||
| pyrazinamide | pncA | c.375_389delCGATGAGGTCGATGT | Assoc w R - Interim | |
| c.375_389delCGATGAGGTCGATGT | Mutation from literature | |||
| streptomycin | rrs | n.517C>T | Assoc w R | |
| fluoroquinolones | ||||
| moxifloxacin | gyrA | p.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
| ofloxacin | ||||
| levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | levofloxacin | Assoc w R | |
| moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
| rpoB | 761140 | p.His445Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
| rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | Assoc w R | |
| katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid | Assoc w R | High-level resistance |
| pncA | 2288852 | c.375_389delCGATGAGGTCGATGT | disruptive_inframe_deletion | 1.0 | pyrazinamide | Assoc w R - Interim | |
| pyrazinamide | Mutation from literature | ||||||
| embA | 4243203 | c.-29_-28delCT | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
| embB | 4248003 | p.Gln497Arg | missense_variant | 1.0 | ethambutol | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7268 | c.-34C>T | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9143 | c.1842T>C | synonymous_variant | 0.99 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 0.99 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13298 | p.Ile87Met | missense_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13482 | p.Ala26Val | missense_variant | 0.99 | isoniazid | Not assoc w R |
| Rv0010c | 13699 | c.-141A>G | upstream_gene_variant | 0.98 | isoniazid | Not assoc w R |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | Not assoc w R - Interim | |||||
| clofazimine | Not assoc w R | |||||
| Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.99 | ethionamide | |
| nusG | 734116 | c.-138T>C | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 0.99 | rifampicin | Not assoc w R |
| rpoC | 763552 | c.183C>T | synonymous_variant | 0.99 | rifampicin | Not assoc w R |
| rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.99 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rplC | 800357 | c.-452C>A | upstream_gene_variant | 1.0 | linezolid | Not assoc w R |
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
| embR | 1417793 | c.-446C>T | upstream_gene_variant | 1.0 | ethambutol | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| tsnR | 1853974 | c.369C>T | synonymous_variant | 1.0 | linezolid | Not assoc w R |
| 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 |
| capreomycin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| ndh | 2102240 | p.Arg268His | missense_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| delamanid | Uncertain significance | |||||
| ethionamide | Uncertain significance | |||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.99 | pyrazinamide | Not assoc w R |
| PPE35 | 2168742 | p.Gly624Asp | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2222098 | p.Thr356Lys | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv1979c | 2223553 | c.-389C>A | upstream_gene_variant | 0.99 | bedaquiline | Uncertain significance |
| clofazimine | Not assoc w R | |||||
| kasA | 2518132 | c.18C>T | synonymous_variant | 0.99 | isoniazid | |
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.99 | isoniazid | |
| thyX | 3068062 | c.-117A>C | upstream_gene_variant | 0.99 | para-aminosalicylic_acid | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.98 | ethionamide | Uncertain significance |
| 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 | |||||
| mtrB | 3626467 | c.147G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| clpC1 | 4040719 | c.-15A>G | upstream_gene_variant | 1.0 | pyrazinamide | Uncertain significance |
| glpK | 4138377 | p.Val460Ala | missense_variant | 0.99 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| ethambutol | Not assoc w R | |||||
| embC | 4240671 | p.Thr270Ile | missense_variant | 0.99 | ethambutol | Not assoc w R |
| embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4245670 | p.Ala813Gly | missense_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4246979 | p.Gly156Cys | missense_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| aftB | 4267960 | p.Val293Met | missense_variant | 0.99 | ethambutol | Uncertain significance |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.98 | ethambutol | Not assoc w R |
| ubiA | 4269606 | c.228T>C | synonymous_variant | 0.97 | ethambutol | Not assoc w R |
| ethA | 4326148 | c.1326G>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 | ethionamide | Uncertain significance |
| whiB6 | 4338203 | p.Arg107Cys | missense_variant | 0.99 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 0.98 | streptomycin | Not assoc w R |
| gid | 4407848 | p.Ala119Thr | missense_variant | 1.0 | streptomycin | Uncertain significance |
| gid | 4407873 | c.330G>T | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
