Run ID: ERR10869162
Sample name:
Date: 2024-03-26T15:11:23.642987
Number of reads: 3202469
Percentage reads mapped: 99.77
Median coverage: 156.0
Strain: lineage4.3.3
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.3 | Euro-American (LAM) | RD115 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Gln497Arg | Assoc w R | |
pyrazinamide | pncA | p.Asp63Gly | Assoc w R - Interim | |
streptomycin | rrs | n.514A>C | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | tlyA | p.Leu74Pro | Uncertain significance | Mutation from literature |
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | fbiC | c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT | Assoc w R - Interim | Confers DLM-PMD cross-resistance | ||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin | Assoc w R | |
fbiC | 1305494 | c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | frameshift_variant&stop_lost&splice_region_variant | 1.0 | pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
fbiC | 1305494 | c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT | frameshift_variant&stop_lost&splice_region_variant | 0.37 | pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 1.0 | isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethionamide | Assoc w R | Alias fabG1_c.-15C>T | |||||
tlyA | 1918160 | p.Leu74Pro | missense_variant | 1.0 | capreomycin | Uncertain significance | Mutation from literature |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289054 | p.Asp63Gly | missense_variant | 1.0 | pyrazinamide | Assoc w R - Interim | |
embB | 4248003 | p.Gln497Arg | missense_variant | 1.0 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 698 | p.Arg233Gln | missense_variant | 1.0 | isoniazid | Uncertain significance |
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 | 8040 | p.Gly247Ser | missense_variant | 0.99 | 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 | |||||
rpoC | 764931 | p.Ala521Asp | 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 |
fbiC | 1303095 | c.165G>A | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
fbiC | 1304962 | p.Trp678Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.99 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474425 | n.768A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | ||||||
rrl | 1474428 | n.771C>T | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | ||||||
rpsA | 1834836 | p.Met432Thr | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 | capreomycin | Not assoc w R |
katG | 2156196 | c.-85C>T | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.27 | pyrazinamide | |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.26 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 | isoniazid | |
folC | 2746340 | p.Ala420Val | missense_variant | 0.99 | para-aminosalicylic_acid | |
ribD | 2986827 | c.-12G>A | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | 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 | 3878567 | c.-60C>G | upstream_gene_variant | 0.19 | rifampicin | |
rpoA | 3878599 | c.-92C>G | upstream_gene_variant | 0.15 | rifampicin | |
rpoA | 3878639 | c.-132C>G | upstream_gene_variant | 0.12 | rifampicin | Uncertain significance |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
clpC1 | 4038968 | c.1737G>A | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243222 | c.-11C>T | upstream_gene_variant | 0.99 | ethambutol | Uncertain significance |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.27 | ethambutol | Uncertain significance |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.32 | ethambutol | Uncertain significance |
embB | 4246555 | c.42G>C | synonymous_variant | 0.33 | ethambutol | |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.33 | ethambutol | Uncertain significance |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.33 | ethambutol | Uncertain significance |
embB | 4246567 | c.54G>T | synonymous_variant | 0.33 | ethambutol | Not assoc w R - Interim |
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 | 1.0 | streptomycin | Not assoc w R |