Run ID: SRR13861599
Sample name:
Date: 2024-04-15T10:14:52.507779
Number of reads: 856492
Percentage reads mapped: 17.15
Median coverage: 29.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ethA | c.905delT | Assoc w R | |
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| ethA | 4326568 | c.905delT | frameshift_variant | 1.0 | ethionamide | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 8820 | p.Asp507His | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| mshA | 575967 | p.Val207Asp | missense_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| rpoB | 759961 | p.Thr52Asn | missense_variant | 1.0 | rifampicin | |
| rpoB | 763050 | p.Leu1082Met | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 775701 | p.Pro927Gln | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpL5 | 778828 | c.-348G>A | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rplC | 800500 | c.-309A>C | upstream_gene_variant | 1.0 | linezolid | |
| rplC | 801353 | p.Val182Ala | missense_variant | 1.0 | linezolid | |
| Rv1129c | 1253966 | p.Leu190Trp | missense_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| fbiC | 1304512 | p.Val528Ile | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| embR | 1417704 | c.-357T>C | upstream_gene_variant | 1.0 | ethambutol | |
| rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.29 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.27 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.26 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.27 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.28 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.29 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.28 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472973 | n.1128_1130delAATinsCG | non_coding_transcript_exon_variant | 0.29 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.27 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.26 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.27 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.27 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.27 | streptomycin | Uncertain significance |
| kanamycin | Not assoc w R | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1473002 | n.1157G>T | non_coding_transcript_exon_variant | 0.28 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.27 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.27 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.27 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.26 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.56 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.63 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.63 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.63 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.63 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.68 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.68 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.68 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.68 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.68 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.69 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.68 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.69 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.69 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.7 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.7 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.69 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.67 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.28 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rpsA | 1834175 | p.Arg212* | stop_gained | 1.0 | pyrazinamide | Uncertain significance |
| katG | 2156840 | c.-729C>T | upstream_gene_variant | 1.0 | isoniazid | |
| Rv1979c | 2222085 | c.1080G>C | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| ald | 3087218 | p.Met133Ile | missense_variant | 1.0 | cycloserine | |
| whiB7 | 3568679 | p.Val1Leu | missense_variant | 1.0 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| whiB7 | 3568989 | c.-310A>C | upstream_gene_variant | 1.0 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| mtrB | 3625440 | p.Gly392Arg | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| clpC1 | 4040066 | c.639G>T | synonymous_variant | 1.0 | pyrazinamide | |
| embC | 4241259 | c.1397_1398insT | frameshift_variant | 1.0 | ethambutol | |
| embA | 4243358 | c.126C>T | synonymous_variant | 1.0 | ethambutol | |
| embA | 4243469 | c.237C>T | synonymous_variant | 1.0 | ethambutol | |
| embB | 4248436 | c.1923C>T | synonymous_variant | 1.0 | ethambutol | |
| ubiA | 4269557 | p.Ala93Pro | missense_variant | 1.0 | ethambutol |
