Run ID: SRR13861601
Sample name:
Date: 2024-04-16T05:50:07.148451
Number of reads: 1657754
Percentage reads mapped: 33.19
Median coverage: 55.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| 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 | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 8827 | p.Asp509Gly | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| nusG | 734793 | c.540C>G | synonymous_variant | 1.0 | rifampicin | |
| mmpR5 | 779201 | p.Ala71Val | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rplC | 800119 | c.-690G>C | upstream_gene_variant | 1.0 | linezolid | |
| rplC | 800522 | c.-287C>A | upstream_gene_variant | 1.0 | linezolid | |
| Rv1129c | 1253232 | p.Asp435His | missense_variant | 0.98 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv1129c | 1253562 | p.Gln325Lys | missense_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv1129c | 1254726 | c.-192C>T | upstream_gene_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| fbiC | 1305062 | p.Gly711Glu | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| sigE | 1364621 | p.Ala70Val | missense_variant | 1.0 | pyrazinamide | |
| rrs | 1472361 | n.516C>G | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472936 | n.1091C>T | non_coding_transcript_exon_variant | 0.17 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472956 | n.1111T>C | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472957 | n.1112C>T | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472958 | n.1113A>T | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472959 | n.1114T>A | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472963 | n.1118G>A | non_coding_transcript_exon_variant | 0.17 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472971 | n.1126G>C | non_coding_transcript_exon_variant | 0.15 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472973 | n.1128_1130delAATinsCG | non_coding_transcript_exon_variant | 0.14 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472982 | n.1137G>C | non_coding_transcript_exon_variant | 0.15 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472987 | n.1142G>T | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472988 | n.1143T>A | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472989 | n.1144G>A | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.16 | 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 | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473004 | n.1159T>A | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473009 | n.1164T>C | non_coding_transcript_exon_variant | 0.16 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.2 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.14 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.14 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1475981 | n.2324G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.34 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.42 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.42 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.43 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.43 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.49 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.49 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.49 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.47 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.46 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.22 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rpsA | 1834620 | p.Leu360Ser | missense_variant | 1.0 | pyrazinamide | |
| tlyA | 1918366 | p.Ala143Pro | missense_variant | 1.0 | capreomycin | |
| bacA | 2064408 | c.321C>T | synonymous_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| ndh | 2101701 | c.1341delG | frameshift_variant | 1.0 | ethionamide | Uncertain significance |
| delamanid | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| ndh | 2103327 | c.-285C>A | upstream_gene_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| PPE35 | 2170109 | c.504C>T | synonymous_variant | 0.98 | pyrazinamide | Not assoc w R - Interim |
| kasA | 2518676 | p.Gly188Cys | missense_variant | 1.0 | isoniazid | |
| eis | 2714749 | p.Val195Ala | missense_variant | 1.0 | amikacin | |
| kanamycin | ||||||
| eis | 2715045 | c.288G>A | synonymous_variant | 1.0 | amikacin | |
| kanamycin | ||||||
| Rv2752c | 3067080 | c.-889G>C | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| lpqB | 3624325 | p.Thr196Pro | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| mtrB | 3625849 | p.His255Gln | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| clpC1 | 4039055 | p.Ile550Met | missense_variant | 1.0 | pyrazinamide | |
| embC | 4242797 | p.Asp979His | missense_variant | 1.0 | ethambutol | |
| embB | 4247936 | p.Thr475Ala | missense_variant | 1.0 | ethambutol |
