Run ID: SAMEA3231528
Sample name:
Date: 2024-10-04T13:16:20.595638
Number of reads: 5498640
Percentage reads mapped: 98.85
Median coverage: 159.0
Strain: lineage4.1.2.1.1
Spoligotype:
Drug-resistance: HR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.1 | Euro-American | None | 0.98 |
| lineage4.1.2 | Euro-American | None | 1.0 |
| lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 1.0 |
| lineage4.1.2.1.1 | Euro-American (Haarlem) | RD182 | 0.99 |
| lineage4 | Euro-American | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | gid | c.329_330delTG | Assoc w R | |
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | fbiC | c.1900delT | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| fbiC | 1304826 | c.1900delT | frameshift_variant | 0.12 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| gid | 4407872 | c.329_330delTG | frameshift_variant | 0.88 | streptomycin | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 1434 | c.1434C>A | synonymous_variant | 0.11 | isoniazid | |
| 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 | 8048 | c.747C>T | synonymous_variant | 0.12 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8203 | p.Asn301Ser | missense_variant | 0.12 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8999 | c.1698G>A | synonymous_variant | 0.11 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9528 | p.Gln743Glu | missense_variant | 0.17 | levofloxacin | |
| moxifloxacin | ||||||
| fgd1 | 490814 | p.Ser11Leu | missense_variant | 0.14 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fgd1 | 491591 | p.Lys270Met | missense_variant | 1.0 | pretomanid | |
| delamanid | Uncertain significance | |||||
| clofazimine | Not assoc w R | |||||
| mshA | 575343 | c.-5C>T | upstream_gene_variant | 0.13 | isoniazid | |
| ethionamide | ||||||
| mshA | 575629 | c.282A>G | synonymous_variant | 0.15 | isoniazid | |
| ethionamide | ||||||
| mshA | 575679 | p.Asn111Ser | missense_variant | 0.95 | isoniazid | Not assoc w R |
| ethionamide | Not assoc w R | |||||
| mshA | 575832 | p.Gly162Asp | missense_variant | 0.3 | isoniazid | |
| ethionamide | ||||||
| mshA | 576581 | p.Pro412Ser | missense_variant | 0.13 | isoniazid | |
| ethionamide | ||||||
| mshA | 576718 | c.1371C>T | synonymous_variant | 0.13 | isoniazid | |
| ethionamide | ||||||
| ccsA | 619693 | c.-198G>A | upstream_gene_variant | 0.29 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| ccsA | 620058 | c.168C>T | synonymous_variant | 0.14 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| ccsA | 620568 | c.678C>T | synonymous_variant | 0.12 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
| Rv0565c | 657457 | p.Pro5Arg | missense_variant | 0.1 | ethionamide | |
| Rv0565c | 657618 | c.-148T>C | upstream_gene_variant | 0.11 | ethionamide | |
| mmaA3 | 737775 | c.375G>A | synonymous_variant | 0.12 | isoniazid | |
| rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 760350 | p.Asp182Asn | missense_variant | 0.13 | rifampicin | |
| rpoB | 760879 | p.Pro358Gln | missense_variant | 0.14 | rifampicin | |
| rpoB | 761953 | p.Ala716Val | missense_variant | 0.14 | rifampicin | |
| rpoC | 762443 | c.-927G>A | upstream_gene_variant | 0.12 | rifampicin | |
| rpoB | 762630 | p.Ala942Thr | missense_variant | 0.14 | rifampicin | Uncertain significance |
| rpoC | 763669 | c.300C>A | synonymous_variant | 0.12 | rifampicin | |
| rpoC | 764712 | p.Ala448Gly | missense_variant | 0.17 | rifampicin | |
| rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 777793 | p.Ala230Thr | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| mmpL5 | 779209 | c.-729G>A | upstream_gene_variant | 0.18 | bedaquiline | |
| clofazimine | ||||||
| rpsL | 781193 | c.-367T>C | upstream_gene_variant | 0.11 | streptomycin | |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rplC | 800387 | c.-422C>T | upstream_gene_variant | 0.14 | linezolid | |
| rplC | 800651 | c.-158G>C | upstream_gene_variant | 0.13 | linezolid | |
| rplC | 800658 | c.-151T>A | upstream_gene_variant | 0.12 | linezolid | |
| Rv1129c | 1253351 | p.Ala395Val | missense_variant | 0.12 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| Rv1129c | 1253418 | p.Ala373Thr | missense_variant | 0.12 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| Rv1129c | 1253718 | p.Ala273Thr | missense_variant | 0.12 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| fbiC | 1302873 | c.-58A>T | upstream_gene_variant | 0.12 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiC | 1303084 | p.Gly52Ser | missense_variant | 0.11 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiC | 1304655 | c.1725C>T | synonymous_variant | 0.14 | pretomanid | |
| delamanid | Not assoc w R - Interim | |||||
| clofazimine | Not assoc w R - Interim | |||||
| Rv1258c | 1406159 | c.1182G>A | synonymous_variant | 0.12 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| Rv1258c | 1406539 | p.Ala268Thr | missense_variant | 0.12 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| Rv1258c | 1407159 | p.Val61Ala | missense_variant | 0.14 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| embR | 1416651 | p.Thr233Ala | missense_variant | 0.12 | ethambutol | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472894 | n.1049G>A | non_coding_transcript_exon_variant | 0.17 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472906 | n.1061T>C | non_coding_transcript_exon_variant | 0.13 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1474309 | n.652G>A | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
| linezolid | ||||||
| rrl | 1475181 | n.1524A>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | |
| linezolid | ||||||
| rrl | 1476264 | n.2607A>G | non_coding_transcript_exon_variant | 0.1 | capreomycin | |
| linezolid | ||||||
| rpsA | 1833426 | c.-116T>C | upstream_gene_variant | 0.11 | pyrazinamide | |
| tsnR | 1853857 | c.252G>A | synonymous_variant | 0.14 | linezolid | |
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tsnR | 1854373 | c.768G>A | synonymous_variant | 0.12 | linezolid | |
| tlyA | 1917919 | c.-21C>T | upstream_gene_variant | 0.13 | capreomycin | |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| tlyA | 1918095 | c.156G>A | synonymous_variant | 0.12 | capreomycin | |
| tlyA | 1918182 | c.243G>A | synonymous_variant | 0.15 | capreomycin | |
| ndh | 2102394 | p.Ala217Thr | missense_variant | 0.17 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| PPE35 | 2168436 | p.Leu726Pro | missense_variant | 0.11 | pyrazinamide | |
| PPE35 | 2169558 | p.Phe352Tyr | missense_variant | 0.13 | pyrazinamide | |
| Rv1979c | 2222204 | p.Phe321Leu | missense_variant | 0.12 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2222656 | p.Lys170Thr | missense_variant | 0.1 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| pncA | 2289637 | c.-396G>A | upstream_gene_variant | 0.12 | pyrazinamide | |
| kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 | isoniazid | |
| eis | 2714543 | c.790C>A | synonymous_variant | 0.17 | kanamycin | |
| amikacin | ||||||
| eis | 2715209 | p.Thr42Ala | missense_variant | 0.11 | kanamycin | |
| amikacin | ||||||
| folC | 2746609 | c.990T>C | synonymous_variant | 0.1 | para-aminosalicylic_acid | |
| Rv2477c | 2782753 | c.1290G>A | synonymous_variant | 0.14 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2784200 | c.-158T>C | upstream_gene_variant | 0.15 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2784232 | c.-190C>T | upstream_gene_variant | 0.14 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| ribD | 2987048 | c.212delT | frameshift_variant | 0.17 | para-aminosalicylic_acid | |
| Rv2680 | 2996085 | c.-20G>A | upstream_gene_variant | 0.17 | capreomycin | Uncertain significance |
| Rv2680 | 2996136 | p.Ser11Asn | missense_variant | 0.32 | capreomycin | |
| Rv2680 | 2996523 | p.Arg140Met | missense_variant | 0.14 | capreomycin | |
| Rv2752c | 3064901 | p.Leu431Met | missense_variant | 0.14 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| Rv2752c | 3065396 | p.Met266Val | missense_variant | 0.1 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| Rv2752c | 3066989 | c.-798T>C | upstream_gene_variant | 0.15 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| thyA | 3074466 | c.6G>A | synonymous_variant | 0.13 | para-aminosalicylic_acid | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| fbiD | 3339029 | c.-89C>T | upstream_gene_variant | 0.18 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv3236c | 3612718 | c.399C>T | synonymous_variant | 0.25 | pyrazinamide | |
| Rv3236c | 3612759 | p.Gly120Arg | missense_variant | 0.5 | pyrazinamide | |
| Rv3236c | 3613106 | p.Ser4Leu | missense_variant | 0.11 | pyrazinamide | |
| Rv3236c | 3613301 | c.-185G>A | upstream_gene_variant | 0.22 | pyrazinamide | |
| Rv3236c | 3613674 | c.-558G>A | upstream_gene_variant | 0.95 | pyrazinamide | |
| Rv3236c | 3613781 | c.-665C>T | upstream_gene_variant | 0.33 | pyrazinamide | |
| lpqB | 3623693 | c.1218G>T | synonymous_variant | 0.15 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| mtrB | 3625136 | p.Arg493Gln | missense_variant | 0.12 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3625188 | p.Arg476Cys | missense_variant | 0.12 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3625703 | p.Ser304Ile | missense_variant | 0.12 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3626240 | p.Gly125Asp | missense_variant | 0.12 | rifampicin | |
| bedaquiline | ||||||
| mtrA | 3627699 | c.-350G>T | upstream_gene_variant | 0.2 | rifampicin | |
| bedaquiline | ||||||
| fbiB | 3642114 | p.Val194Ile | missense_variant | 0.22 | pretomanid | |
| delamanid | ||||||
| clofazimine | Uncertain significance | |||||
| alr | 3840663 | p.Pro253Arg | missense_variant | 0.13 | cycloserine | |
| glpK | 4138575 | p.Ala394Glu | missense_variant | 0.11 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| glpK | 4139601 | c.154delC | frameshift_variant | 0.15 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| embC | 4239298 | c.-565C>T | upstream_gene_variant | 0.96 | ethambutol | Not assoc w R |
| embC | 4242642 | p.Arg927His | missense_variant | 0.17 | ethambutol | Uncertain significance |
| embC | 4242803 | p.Val981Leu | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244329 | p.Ala366Val | missense_variant | 0.13 | ethambutol | |
| embA | 4244364 | p.Gly378Ser | missense_variant | 0.12 | ethambutol | Uncertain significance |
| embA | 4245114 | p.Gly628Ser | missense_variant | 0.13 | ethambutol | |
| embA | 4245213 | p.Ala661Thr | missense_variant | 0.29 | ethambutol | |
| embA | 4245907 | p.Leu892Pro | missense_variant | 0.12 | ethambutol | |
| embA | 4246195 | p.Pro988His | missense_variant | 0.14 | ethambutol | |
| embB | 4247079 | p.Phe189Ser | missense_variant | 0.12 | ethambutol | |
| aftB | 4267622 | c.1215G>A | synonymous_variant | 0.14 | ethambutol | |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin |
