Run ID: SRR10500312
Sample name:
Date: 2024-04-15T09:56:59.743823
Number of reads: 2476660
Percentage reads mapped: 99.21
Median coverage: 70.0
Strain: lineage1.1.2
Spoligotype:
Drug-resistance: Pre-XDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage1.1.2 | Indo-Oceanic | RD239 | 1.0 |
| lineage1.1 | Indo-Oceanic | RD239 | 1.0 |
| lineage1 | Indo-Oceanic | RD239 | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.Ser450Trp | Assoc w R | |
| isoniazid | katG | p.Asn138Ser | Uncertain significance | Mutation from literature |
| ethambutol | embB | p.Gly406Cys | Assoc w R | |
| pyrazinamide | pncA | p.Val139Leu | Assoc w R - Interim | |
| streptomycin | ||||
| 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 | rrs | n.1401A>G | Assoc w R | |
| capreomycin | rrs | n.1401A>G | Assoc w R | |
| kanamycin | rrs | n.1401A>G | Assoc w R | |
| 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 | 761155 | p.Ser450Trp | missense_variant | 1.0 | rifampicin | Assoc w R | |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin | Assoc w R | |
| amikacin | Assoc w R | ||||||
| capreomycin | Assoc w R | ||||||
| katG | 2155699 | p.Asn138Ser | missense_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
| pncA | 2288827 | p.Val139Leu | missense_variant | 1.0 | pyrazinamide | Assoc w R - Interim | |
| embB | 4247729 | p.Gly406Cys | missense_variant | 1.0 | ethambutol | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrB | 6124 | c.885C>T | synonymous_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 | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13298 | p.Ile87Met | missense_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13304 | c.255G>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| 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 | |
| nusG | 734116 | c.-138T>C | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 759546 | c.-261A>G | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 760490 | c.684C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | 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 |
| rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| 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 | |||||
| mmpL5 | 776395 | p.Phe696Leu | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| mmpL5 | 779346 | c.-866G>A | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| 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 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| fbiC | 1303051 | p.Val41Met | missense_variant | 1.0 | clofazimine | Uncertain significance |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| 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 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.2 | ethionamide | |
| isoniazid | ||||||
| tsnR | 1853974 | c.369C>T | synonymous_variant | 1.0 | linezolid | Not assoc w R |
| tsnR | 1854045 | p.Tyr147Cys | missense_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 | streptomycin | Not assoc w R |
| kanamycin | Not assoc w R | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| ndh | 2101913 | c.1129delT | frameshift_variant | 1.0 | ethionamide | Uncertain significance |
| delamanid | Uncertain significance | |||||
| isoniazid | 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 |
| PPE35 | 2167983 | p.Gly877Asp | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2168969 | p.Ile548Met | missense_variant | 1.0 | pyrazinamide | |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.45 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.47 | pyrazinamide | |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv1979c | 2223136 | p.Ala10Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 | isoniazid | |
| Rv2681 | 2996912 | c.174C>T | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| ald | 3086961 | p.Ala48Ser | missense_variant | 1.0 | cycloserine | |
| ald | 3087135 | p.Ala106Pro | missense_variant | 1.0 | cycloserine | |
| Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 | ethionamide | Uncertain significance |
| whiB7 | 3569101 | c.-422C>T | upstream_gene_variant | 1.0 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| mtrB | 3626467 | c.147G>A | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| rifampicin | Not assoc w R | |||||
| alr | 3841068 | p.Ile118Thr | missense_variant | 1.0 | cycloserine | |
| alr | 3841125 | p.Ala99Gly | missense_variant | 1.0 | cycloserine | |
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| panD | 4044740 | c.-459C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| glpK | 4139183 | c.572dupG | frameshift_variant | 0.98 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| embC | 4239593 | c.-270G>A | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4241042 | p.Asn394Asp | missense_variant | 0.98 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243848 | p.Val206Met | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244167 | p.Ala312Val | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 | ethambutol | Not assoc w R |
| 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 | 4326432 | p.Leu348Phe | missense_variant | 1.0 | ethionamide | Uncertain significance |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
| gid | 4407873 | c.330G>T | synonymous_variant | 0.99 | streptomycin | Not assoc w R |
