Run ID: ERR4797037
Sample name:
Date: 2024-04-15T01:58:43.050540
Number of reads: 2837129
Percentage reads mapped: 91.36
Median coverage: 81.0
Strain: lineage3.1.2
Spoligotype:
Drug-resistance: Pre-XDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage3 | East-African-Indian | RD750 | 0.99 |
| lineage3.1.2 | East-African-Indian | RD750 | 1.0 |
| lineage3.1 | East-African-Indian | RD750 | 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 | embA | c.-16C>T | Uncertain significance | Mutation from literature |
| embB | p.Met306Ile | Assoc w R | ||
| pyrazinamide | pncA | p.Gly108Arg | Assoc w R | |
| streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
| fluoroquinolones | ||||
| moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
| ofloxacin | ||||
| levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Gly | missense_variant | 0.98 | moxifloxacin | Assoc w R | High-level resistance |
| levofloxacin | Assoc w R | ||||||
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.94 | rifampicin | Assoc w R | |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 0.94 | streptomycin | Assoc w R | |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| pncA | 2288920 | p.Gly108Arg | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
| embA | 4243217 | c.-16C>T | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
| embB | 4247431 | p.Met306Ile | missense_variant | 0.98 | ethambutol | 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 | |||||
| gyrA | 9308 | c.2007C>T | synonymous_variant | 0.12 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 9317 | c.2016G>T | synonymous_variant | 0.12 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9323 | c.2022C>G | synonymous_variant | 0.12 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 9335 | c.2034G>C | synonymous_variant | 0.13 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9758 | c.2457C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| Rv0010c | 13605 | c.-47G>T | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 760982 | c.1176G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| rpoB | 760985 | c.1179G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| rpoB | 760988 | c.1182C>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
| rpoB | 760991 | c.1185G>C | synonymous_variant | 0.13 | rifampicin | |
| rpoB | 761006 | c.1200C>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
| rpoB | 761015 | c.1209G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
| rpoB | 761027 | c.1221A>G | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
| rpoB | 762434 | c.2628T>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 764140 | c.771C>T | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
| rpoC | 764266 | c.897T>C | synonymous_variant | 0.12 | rifampicin | |
| rpoC | 764338 | c.969G>A | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
| rpoC | 764353 | c.984G>C | synonymous_variant | 0.22 | rifampicin | |
| rpoC | 764365 | c.996C>T | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoC | 764380 | c.1011G>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
| rpoC | 764554 | c.1185C>T | synonymous_variant | 0.18 | rifampicin | |
| rpoC | 764560 | c.1191T>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoC | 764566 | c.1197C>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoC | 764575 | c.1206T>G | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
| rpoC | 764581 | c.1212T>C | synonymous_variant | 0.16 | rifampicin | |
| rpoC | 764593 | c.1224C>T | synonymous_variant | 0.13 | rifampicin | |
| rpoC | 765982 | c.2613C>G | synonymous_variant | 0.14 | rifampicin | |
| rpoC | 765994 | c.2625A>T | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
| rpoC | 766774 | c.3405T>C | synonymous_variant | 0.14 | rifampicin | |
| rpoC | 766801 | c.3432C>G | synonymous_variant | 0.14 | rifampicin | |
| rpoC | 766804 | c.3435A>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
| rpoC | 766864 | c.3495G>C | synonymous_variant | 0.12 | rifampicin | |
| rpoC | 766972 | c.3603G>C | synonymous_variant | 0.18 | rifampicin | |
| rpoC | 766996 | c.3627C>T | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
| rpoC | 767009 | c.3640_3642delTCGinsAGC | synonymous_variant | 0.18 | rifampicin | |
| rpoC | 767014 | c.3645G>C | synonymous_variant | 0.17 | rifampicin | |
| rpoC | 767033 | c.3664_3666delTCGinsAGT | synonymous_variant | 0.18 | rifampicin | |
| rpoC | 767059 | c.3690T>G | synonymous_variant | 0.18 | rifampicin | Not assoc w R - Interim |
| rpoC | 767062 | c.3693C>A | synonymous_variant | 0.18 | rifampicin | |
| rpoC | 767098 | c.3729T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
| 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 | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| 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 | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1474970 | n.1313G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
| linezolid | ||||||
| rrl | 1475006 | n.1349A>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
| linezolid | ||||||
| rrl | 1475061 | n.1404C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475369 | n.1712G>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
| linezolid | ||||||
| rrl | 1475419 | n.1762C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475436 | n.1779C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
| linezolid | ||||||
| rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
| linezolid | ||||||
| rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.12 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| inhA | 1674102 | c.-100C>A | upstream_gene_variant | 0.99 | ethionamide | Uncertain significance |
| isoniazid | Uncertain significance | |||||
| 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 |
| tlyA | 1918104 | c.165G>A | synonymous_variant | 1.0 | capreomycin | Not assoc w R - Interim |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2168604 | p.Pro670Leu | missense_variant | 0.99 | pyrazinamide | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 | pyrazinamide | |
| ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
| Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.97 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R - Interim | |||||
| levofloxacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| thyA | 3074247 | p.His75Gln | missense_variant | 0.99 | para-aminosalicylic_acid | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| rpoA | 3877949 | p.Thr187Ala | missense_variant | 0.93 | rifampicin | Uncertain significance |
| clpC1 | 4040675 | c.30C>G | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| panD | 4044872 | c.-591C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| glpK | 4138622 | c.1134C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R - Interim | |||||
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4248220 | c.1707A>C | synonymous_variant | 0.14 | ethambutol | |
| embB | 4248304 | c.1791G>C | synonymous_variant | 0.13 | ethambutol | |
| embB | 4248316 | c.1803C>G | synonymous_variant | 0.14 | ethambutol | |
| embB | 4248319 | c.1806A>G | synonymous_variant | 0.14 | ethambutol | |
| ethA | 4327298 | p.Met59Arg | missense_variant | 1.0 | ethionamide | Uncertain significance |
| 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 | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
