Run ID: SRR3743200
Sample name:
Date: 2024-04-15T17:34:43.969742
Number of reads: 5874728
Percentage reads mapped: 99.59
Median coverage: 99.0
Strain: lineage4.4.1.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.4.1 | Euro-American (S-type) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.4.1.1 | Euro-American | None | 0.99 |
lineage4.4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Asp435Gly | Assoc w R - Interim | |
p.His445Asn | Assoc w R | |||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Ile | Assoc w R | |
p.Gly406Asp | Assoc w R | |||
pyrazinamide | pncA | p.Gly97Cys | Assoc w R | |
streptomycin | gid | p.Ser136* | 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 | rrs | n.1401A>G | Assoc w R | |
capreomycin | rrs | n.1401A>G | Assoc w R | |
kanamycin | rrs | n.1401A>G | Assoc w R | |
cycloserine | alr | p.Leu113Arg | Mutation from literature | |
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761110 | p.Asp435Gly | missense_variant | 1.0 | rifampicin | Assoc w R - Interim | |
rpoB | 761139 | p.His445Asn | missense_variant | 1.0 | rifampicin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin | Assoc w R | |
amikacin | Assoc w R | ||||||
capreomycin | Assoc w R | ||||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288953 | p.Gly97Cys | missense_variant | 0.99 | pyrazinamide | Assoc w R | |
alr | 3841083 | p.Leu113Arg | missense_variant | 1.0 | cycloserine | Mutation from literature | |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R | |
embB | 4247730 | p.Gly406Asp | missense_variant | 1.0 | ethambutol | Assoc w R | |
gid | 4407796 | p.Ser136* | stop_gained | 1.0 | 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 | |||||
ccsA | 619785 | c.-106G>C | upstream_gene_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
mmpL5 | 775626 | p.Trp952Leu | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
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 | 1365056 | p.Gly215Ala | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472769 | n.924C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | 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 |
ndh | 2102990 | p.Val18Ala | missense_variant | 1.0 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Not assoc w R | |||||
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 0.98 | pyrazinamide | Not assoc w R |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.2 | pyrazinamide | |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.19 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.98 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3841608 | c.-188A>G | upstream_gene_variant | 0.99 | cycloserine | |
clpC1 | 4040522 | c.183T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
embC | 4238963 | c.-900C>T | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.14 | ethambutol | Uncertain significance |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.15 | ethambutol | Uncertain significance |
embB | 4246555 | c.42G>C | synonymous_variant | 0.16 | ethambutol | |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.16 | ethambutol | Uncertain significance |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.14 | ethambutol | Uncertain significance |
embB | 4246567 | c.54G>T | synonymous_variant | 0.16 | ethambutol | Not assoc w R - Interim |
aftB | 4268041 | c.796C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
ethA | 4326019 | c.1455C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
ethA | 4326267 | p.Cys403Arg | 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 |