Run ID: SRR28351652
Sample name:
Date: 2024-05-22T09:49:07.236894
Number of reads: 16113559
Percentage reads mapped: 99.85
Median coverage: 474.0
Strain: La3
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
La3 | M.orygis | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.430_432delGACinsAT | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
ethA | 4327042 | c.430_432delGACinsAT | frameshift_variant&synonymous_variant | 1.0 | ethionamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1501 | p.Ile501Leu | missense_variant | 0.99 | isoniazid | Uncertain significance |
gyrB | 4966 | c.-274C>T | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 5516 | p.Ile93Val | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrB | 5747 | p.Thr170Ala | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrB | 6109 | c.870G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.98 | levofloxacin | Not assoc w R |
moxifloxacin | Uncertain significance | |||||
gyrB | 6717 | p.Ile493Thr | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | 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 | 7775 | c.474C>T | synonymous_variant | 0.99 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 8930 | c.1629C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 9143 | c.1842T>C | synonymous_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 | 13315 | p.Ser82Pro | missense_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13441 | p.Thr40Ala | missense_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
fgd1 | 490661 | c.-122_-121insGCGAGC | upstream_gene_variant | 0.99 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
fgd1 | 491749 | p.Leu323Phe | missense_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
rpoB | 762352 | c.2557_2562dupGACGAG | conservative_inframe_insertion | 0.94 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | 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 | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 778086 | c.394dupG | frameshift_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1253620 | c.915G>T | synonymous_variant | 1.0 | moxifloxacin | Not assoc w R - Interim |
levofloxacin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
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 | |||||
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
sigE | 1364345 | c.-68A>G | upstream_gene_variant | 1.0 | pyrazinamide | |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1475539 | n.1882A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476664 | n.3007T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
inhA | 1673680 | c.-522C>G | upstream_gene_variant | 1.0 | ethionamide | Uncertain significance |
isoniazid | Not assoc w R | |||||
rpsA | 1834363 | c.822G>A | synonymous_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 | 1.0 | capreomycin | Not assoc w R |
bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | streptomycin | Not assoc w R |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
katG | 2154707 | p.Val469Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
katG | 2155503 | c.609C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2169279 | c.1312_1333delAACAATGGTGTCTTTTACCGTG | frameshift_variant | 0.99 | pyrazinamide | Uncertain significance |
PPE35 | 2170669 | c.-57G>A | upstream_gene_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2289978 | c.-737T>G | upstream_gene_variant | 1.0 | pyrazinamide | |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
ahpC | 2726378 | c.186T>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
folC | 2746391 | p.Val403Ala | missense_variant | 0.99 | para-aminosalicylic_acid | |
Rv2681 | 2996910 | p.Ala58Thr | missense_variant | 1.0 | capreomycin | Uncertain significance |
Rv2752c | 3067009 | c.-818A>G | upstream_gene_variant | 1.0 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
thyX | 3067812 | p.Gln45Arg | missense_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3074494 | c.-81_-24delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3074494 | c.-80_-24delCGCTGGGTTTGTTTGGCGGCGAGTCGCTGCGGCGGCTTCGCCGCGCTTGCGATCGCC | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
Rv3083 | 3448783 | p.Val94Ile | missense_variant | 1.0 | ethionamide | Uncertain significance |
Rv3236c | 3612694 | c.423T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
Rv3236c | 3613600 | c.-484G>A | upstream_gene_variant | 1.0 | pyrazinamide | |
lpqB | 3624350 | c.561G>T | synonymous_variant | 0.99 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R | |||||
lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
lpqB | 3624593 | c.318G>A | synonymous_variant | 0.99 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiB | 3641584 | p.Val17Ala | missense_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
clpC1 | 4039853 | c.852G>A | synonymous_variant | 0.99 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4040945 | c.-241G>A | upstream_gene_variant | 1.0 | pyrazinamide | |
glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embC | 4239276 | c.-587_-586insTGGCCGCCGCCATCGGGT | upstream_gene_variant | 0.97 | ethambutol | Uncertain significance |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4244154 | p.Thr308Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4246864 | c.351C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269351 | c.483C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4328211 | c.-738A>G | upstream_gene_variant | 1.0 | ethionamide | |
whiB6 | 4338269 | p.Gly85Ser | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
whiB6 | 4338516 | c.5_6insCTTCCCGCCCCGACAGCCTGGGCCGACCCGTCGGTTAATGCG | disruptive_inframe_insertion | 0.89 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
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 |
gid | 4407800 | p.Val135Met | missense_variant | 1.0 | streptomycin | Uncertain significance |