Run ID: ERR1034907
Sample name:
Date: 2024-04-15T06:20:49.861758
Number of reads: 7066858
Percentage reads mapped: 98.08
Median coverage: 156.0
Strain: lineage4.3.4.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.3 | Euro-American (LAM) | None | 1.0 |
| lineage4.3.4.1 | Euro-American (LAM) | RD174 | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.3.4 | Euro-American (LAM) | RD174 | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
| isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| ethambutol | embB | p.Met306Ile | Assoc w R | |
| pyrazinamide | pncA | p.Pro69Leu | Assoc w R | |
| streptomycin | gid | p.Arg102* | Assoc w R | |
| fluoroquinolones | ||||
| moxifloxacin | gyrB | p.Ala504Val | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
| ofloxacin | ||||
| levofloxacin | gyrB | p.Ala504Val | Assoc w R - Interim | |
| 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 |
|---|---|---|---|---|---|---|---|
| gyrB | 6750 | p.Ala504Val | missense_variant | 0.92 | moxifloxacin | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
| levofloxacin | Assoc w R - Interim | ||||||
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin | Assoc w R | |
| capreomycin | Assoc w R | ||||||
| amikacin | Assoc w R | ||||||
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| pncA | 2289036 | p.Pro69Leu | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
| embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R | |
| gid | 4407899 | p.Arg102* | stop_gained | 0.99 | streptomycin | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13483 | p.Ala26Thr | missense_variant | 0.99 | isoniazid | Uncertain significance |
| rpoB | 761998 | p.Leu731Pro | missense_variant | 1.0 | rifampicin | Uncertain significance |
| rpoC | 764995 | c.1626C>G | synonymous_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 | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| sigE | 1364434 | p.Arg8Trp | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1473752 | n.95G>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1473815 | n.158T>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1473836 | n.179A>G | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | Uncertain significance | |||||
| rrl | 1473995 | n.338G>T | non_coding_transcript_exon_variant | 0.1 | capreomycin | |
| linezolid | ||||||
| rrl | 1474034 | n.377G>A | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
| linezolid | ||||||
| rrl | 1474040 | n.383G>A | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
| linezolid | ||||||
| rrl | 1474111 | n.454T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
| linezolid | ||||||
| rrl | 1474716 | n.1059A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
| linezolid | ||||||
| rrl | 1474760 | n.1103A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1474794 | n.1137C>A | non_coding_transcript_exon_variant | 0.1 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475202 | n.1545G>C | non_coding_transcript_exon_variant | 0.1 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475402 | n.1745C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
| linezolid | ||||||
| rrl | 1475419 | n.1762C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475429 | n.1772G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1475446 | n.1789G>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1475608 | n.1951T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475638 | n.1981C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
| linezolid | ||||||
| rrl | 1475657 | n.2000A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
| linezolid | ||||||
| rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
| linezolid | ||||||
| rrl | 1476115 | n.2458T>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476117 | n.2460G>C | non_coding_transcript_exon_variant | 0.11 | capreomycin | |
| linezolid | ||||||
| rrl | 1476214 | n.2557G>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
| linezolid | ||||||
| rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476628 | n.2971T>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476629 | n.2972C>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| 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 |
| Rv1979c | 2222854 | p.Ile104Thr | 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 | |||||
| eis | 2714504 | p.His277Tyr | missense_variant | 0.99 | amikacin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| clpC1 | 4039991 | c.714G>A | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| embC | 4242159 | p.Leu766Pro | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| 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 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| gid | 4408156 | p.Leu16Arg | missense_variant | 0.99 | streptomycin | Not assoc w R |
