Run ID: 98d3d812-8c16-4b11-a5a1-1be42ac43387
Sample name:
Date: 02-08-2023 04:22:51
Number of reads: 760283
Percentage reads mapped: 99.22
Median coverage: 27
Strain: La3
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| La3 | M.orygis | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| moxifloxacin | ||||
| levofloxacin | ||||
| bedaquiline | ||||
| delamanid | ||||
| pretomanid | ||||
| linezolid | ||||
| streptomycin | ||||
| amikacin | ||||
| kanamycin | ||||
| capreomycin | ||||
| clofazimine | ||||
| ethionamide | ||||
| para-aminosalicylic_acid | ||||
| cycloserine |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5516 | p.Ile93Val | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrB | 6109 | c.870G>A | synonymous_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrB | 6717 | p.Ile493Thr | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrB | 6909 | p.Glu557Gly | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8454 | p.Asn385Asp | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 8930 | c.1629C>T | synonymous_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | fluoroquinolones | |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| ciprofloxacin | ||||||
| ofloxacin | ||||||
| fgd1 | 490661 | c.-122_-121insGCGAGC | upstream_gene_variant | 1.0 | delamanid | |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | delamanid | |
| fgd1 | 491749 | p.Leu323Phe | missense_variant | 1.0 | delamanid | Uncertain significance |
| rpoB | 762352 | c.2557_2562dupGACGAG | conservative_inframe_insertion | 1.0 | rifampicin | Uncertain significance |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 | rifampicin | |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| mmpL5 | 778086 | c.394dupG | frameshift_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | delamanid | Uncertain significance |
| fbiC | 1305454 | p.Arg842Cys | missense_variant | 0.12 | delamanid | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| aminoglycosides | ||||||
| streptomycin | ||||||
| rrl | 1475539 | n.1882A>G | non_coding_transcript_exon_variant | 1.0 | linezolid | Uncertain significance |
| rrl | 1476664 | n.3007T>G | non_coding_transcript_exon_variant | 1.0 | linezolid | Uncertain significance |
| inhA | 1673680 | c.-522C>G | upstream_gene_variant | 1.0 | ethionamide | Uncertain significance |
| isoniazid | Uncertain significance | |||||
| rpsA | 1834363 | c.822G>A | synonymous_variant | 1.0 | pyrazinamide | |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
| katG | 2154707 | p.Val469Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
| katG | 2155503 | c.609C>T | synonymous_variant | 1.0 | isoniazid | |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2169279 | c.1312_1333delAACAATGGTGTCTTTTACCGTG | frameshift_variant | 1.0 | pyrazinamide | |
| PPE35 | 2170669 | c.-57G>A | upstream_gene_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| pncA | 2289978 | c.-737T>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| ahpC | 2726378 | c.186T>A | synonymous_variant | 1.0 | isoniazid | |
| folC | 2746376 | p.Ser408Leu | missense_variant | 0.11 | para-aminosalicylic_acid | |
| folC | 2746391 | p.Val403Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| folC | 2746661 | p.Phe313Ser | missense_variant | 0.12 | para-aminosalicylic_acid | |
| Rv2752c | 3067009 | c.-818A>G | upstream_gene_variant | 1.0 | rifampicin | |
| isoniazid | ||||||
| thyX | 3067812 | p.Gln45Arg | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 | cycloserine | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
| fbiD | 3339049 | c.-69C>T | upstream_gene_variant | 0.12 | delamanid | |
| Rv3083 | 3448783 | p.Val94Ile | missense_variant | 1.0 | ethionamide | Uncertain significance |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| fprA | 3474078 | c.72G>A | synonymous_variant | 0.11 | capreomycin | |
| amikacin | ||||||
| fprA | 3475113 | c.1107G>A | synonymous_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| fprA | 3475323 | c.1317T>C | synonymous_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| whiB7 | 3568470 | p.Ile70Met | missense_variant | 0.12 | streptomycin | |
| kanamycin | ||||||
| amikacin | ||||||
| Rv3236c | 3612694 | c.423T>C | synonymous_variant | 1.0 | pyrazinamide | |
| fbiB | 3641584 | p.Val17Ala | missense_variant | 1.0 | delamanid | Uncertain significance |
| fbiB | 3642797 | c.1266_1315delCGCCATCGCGATCGGATATGCCGACGAGCCGTCCGGGTTGCGCGACCCGG | frameshift_variant | 0.1 | delamanid | |
| rpoA | 3877513 | p.Thr332Ile | missense_variant | 1.0 | rifampicin | Uncertain significance |
| ddn | 3987050 | c.207C>T | synonymous_variant | 1.0 | delamanid | |
| clpC1 | 4038295 | p.Val804Leu | missense_variant | 0.1 | pyrazinamide | |
| clpC1 | 4038561 | p.Asp715Gly | missense_variant | 0.1 | pyrazinamide | |
| clpC1 | 4039853 | c.852G>A | synonymous_variant | 1.0 | pyrazinamide | |
| panD | 4044134 | p.Asp50Asn | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
| embA | 4243585 | p.Phe118Ser | missense_variant | 0.1 | ethambutol | |
| embA | 4244154 | p.Thr308Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | |
| embB | 4246566 | p.Gly18Val | missense_variant | 0.13 | ethambutol | |
| embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | |
| embB | 4247163 | p.Leu217Pro | missense_variant | 0.12 | ethambutol | |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
| aftB | 4268651 | c.186G>A | synonymous_variant | 0.13 | capreomycin | |
| amikacin | ||||||
| aftB | 4269351 | c.-515C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| ubiA | 4269903 | c.-71delG | upstream_gene_variant | 0.1 | ethambutol | |
| ethA | 4327042 | p.Asp144Asn | missense_variant | 1.0 | ethionamide | Uncertain significance |
| ethA | 4328211 | c.-738A>G | upstream_gene_variant | 1.0 | ethionamide | |
| whiB6 | 4338269 | p.Gly85Ser | missense_variant | 1.0 | streptomycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| whiB6 | 4338527 | c.-6T>C | upstream_gene_variant | 0.2 | streptomycin | |
| capreomycin | ||||||
| amikacin | Uncertain significance | |||||
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin |
