Run ID: SRR19573671
Sample name:
Date: 2024-03-26T12:33:08.733859
Number of reads: 15116906
Percentage reads mapped: 98.05
Median coverage: 172.0
Strain: lineage1.2.2.2
Spoligotype:
Drug-resistance: Other
| 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 | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | embB | p.Gln497Arg | Assoc w R | |
| 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 |
|---|---|---|---|---|---|---|---|
| embB | 4248003 | p.Gln497Arg | missense_variant | 0.33 | 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 | 5078 | c.-162_-161insG | 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 | 0.99 | 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 | 13460 | c.99T>C | synonymous_variant | 0.99 | isoniazid | Not assoc w R |
| Rv0010c | 13482 | p.Ala26Val | missense_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13548 | p.Thr4Ile | missense_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13699 | c.-141A>G | upstream_gene_variant | 0.82 | 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 | |||||
| mshA | 575092 | c.-256C>A | upstream_gene_variant | 0.17 | ethionamide | |
| isoniazid | ||||||
| mshA | 575121 | c.-227G>C | upstream_gene_variant | 0.2 | ethionamide | |
| isoniazid | ||||||
| mshA | 575265 | c.-83C>A | upstream_gene_variant | 0.27 | ethionamide | |
| isoniazid | ||||||
| mshA | 576337 | c.990G>A | synonymous_variant | 0.27 | ethionamide | Not assoc w R - Interim |
| isoniazid | Not assoc w R - Interim | |||||
| Rv0565c | 656322 | c.1149C>T | synonymous_variant | 0.5 | ethionamide | |
| Rv0565c | 656991 | c.480G>A | synonymous_variant | 0.24 | ethionamide | |
| 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 | 759670 | c.-137C>T | upstream_gene_variant | 0.15 | rifampicin | Uncertain significance |
| rpoB | 761012 | p.Asp402Glu | missense_variant | 0.22 | rifampicin | |
| rpoB | 761748 | p.Ser648Thr | missense_variant | 0.32 | rifampicin | |
| rpoB | 761786 | c.1980C>T | synonymous_variant | 0.99 | rifampicin | Not assoc w R - Interim |
| rpoB | 761863 | p.Ala686Val | missense_variant | 0.99 | rifampicin | |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 763321 | p.Ala1172Val | missense_variant | 0.69 | rifampicin | |
| 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 | 764002 | c.633C>T | synonymous_variant | 0.96 | rifampicin | |
| 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 | 778483 | c.-3C>T | upstream_gene_variant | 0.12 | clofazimine | |
| bedaquiline | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.99 | streptomycin | Not assoc w R |
| rplC | 800815 | p.Arg3* | stop_gained | 0.27 | linezolid | |
| rplC | 800838 | p.Lys10Asn | missense_variant | 0.17 | linezolid | |
| Rv1129c | 1253587 | c.948C>T | synonymous_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| 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 | |||||
| Rv1129c | 1254747 | c.-213C>A | upstream_gene_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| fbiC | 1304750 | p.Pro607Leu | missense_variant | 0.72 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| embR | 1417019 | p.Cys110Tyr | missense_variant | 0.73 | ethambutol | Not assoc w R |
| embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
| embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.89 | ethambutol | |
| embR | 1417933 | c.-587_-586insT | upstream_gene_variant | 0.26 | ethambutol | |
| embR | 1417933 | c.-586G>T | upstream_gene_variant | 0.64 | ethambutol | |
| embR | 1417933 | c.-587_-586insT | upstream_gene_variant | 0.26 | ethambutol | |
| embR | 1417933 | c.-586G>T | upstream_gene_variant | 0.64 | ethambutol | |
| atpE | 1460975 | c.-70G>A | upstream_gene_variant | 0.2 | bedaquiline | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.11 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1474625 | n.968T>G | non_coding_transcript_exon_variant | 0.37 | capreomycin | |
| linezolid | ||||||
| rrl | 1474711 | n.1054_1055insC | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
| linezolid | ||||||
| rrl | 1475601 | n.1944C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| tsnR | 1853763 | p.Ala53Val | missense_variant | 0.57 | linezolid | Uncertain significance |
| tsnR | 1853974 | c.369C>T | synonymous_variant | 1.0 | linezolid | Not assoc w R |
| tsnR | 1854038 | p.Asp145Asn | missense_variant | 0.44 | linezolid | |
| tsnR | 1854144 | p.Ala180Val | missense_variant | 0.29 | linezolid | |
| 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 | 2102078 | p.Asp322Val | missense_variant | 0.22 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| ndh | 2102242 | c.801G>A | synonymous_variant | 0.71 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| katG | 2155668 | c.444G>A | synonymous_variant | 0.57 | isoniazid | |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2168742 | p.Gly624Asp | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv1979c | 2222519 | p.Gly216Ser | missense_variant | 0.85 | clofazimine | |
| bedaquiline | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv1979c | 2223553 | c.-389C>A | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| eis | 2715261 | c.72C>T | synonymous_variant | 0.23 | amikacin | |
| kanamycin | ||||||
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 | isoniazid | |
| ahpC | 2726693 | c.501C>T | synonymous_variant | 0.36 | isoniazid | |
| folC | 2746509 | p.Gln364* | stop_gained | 0.45 | para-aminosalicylic_acid | |
| folC | 2747542 | c.57C>T | synonymous_variant | 0.89 | para-aminosalicylic_acid | |
| Rv2477c | 2783487 | p.Pro186Ala | missense_variant | 0.21 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| pepQ | 2859323 | p.Pro366Ser | missense_variant | 0.25 | clofazimine | |
| bedaquiline | ||||||
| Rv2681 | 2997883 | p.Cys382Tyr | missense_variant | 0.75 | capreomycin | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| ald | 3086953 | p.Ile45Thr | missense_variant | 0.35 | cycloserine | |
| Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.96 | ethionamide | Uncertain significance |
| whiB7 | 3568821 | c.-142A>C | upstream_gene_variant | 0.2 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| lpqB | 3623551 | p.Arg454Cys | missense_variant | 0.36 | bedaquiline | |
| rifampicin | ||||||
| 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 | |||||
| lpqB | 3625492 | c.-582C>T | upstream_gene_variant | 0.2 | bedaquiline | |
| rifampicin | ||||||
| lpqB | 3625587 | c.-677C>T | upstream_gene_variant | 0.46 | bedaquiline | |
| rifampicin | ||||||
| mtrB | 3626467 | c.147G>A | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| rifampicin | Not assoc w R | |||||
| rpoA | 3878817 | c.-310T>A | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| 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 | |||||
| embC | 4240276 | c.414G>A | synonymous_variant | 0.78 | ethambutol | |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | 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 | 4245969 | p.Pro913Ser | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4246312 | p.Gly1027Ala | missense_variant | 0.21 | ethambutol | |
| embA | 4246314 | p.Gly1028Arg | missense_variant | 0.38 | ethambutol | |
| embA | 4246359 | p.Ala1043Thr | missense_variant | 0.21 | ethambutol | |
| embB | 4247512 | c.999T>C | synonymous_variant | 0.24 | ethambutol | |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4247889 | p.Gly459Asp | missense_variant | 0.28 | ethambutol | |
| aftB | 4267055 | c.1782C>T | synonymous_variant | 0.62 | ethambutol | |
| aftB | 4267472 | c.1365C>G | synonymous_variant | 0.19 | ethambutol | |
| aftB | 4268560 | p.Leu93Met | missense_variant | 0.48 | ethambutol | |
| ubiA | 4269606 | c.228T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4326019 | c.1455C>T | synonymous_variant | 0.32 | ethionamide | Not assoc w R - Interim |
| 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 |
| ethR | 4327828 | p.Pro94Ser | missense_variant | 0.79 | ethionamide | Uncertain significance |
| whiB6 | 4338203 | p.Arg107Cys | missense_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 | 0.96 | streptomycin | Not assoc w R |
| gid | 4408013 | p.Arg64Trp | missense_variant | 0.93 | streptomycin | Uncertain significance |
