Run ID: 69abd25c-0f3f-48c0-8a5e-ae8854be384d
Sample name:
Date: 24-07-2023 18:42:06
Number of reads: 785656
Percentage reads mapped: 96.98
Median coverage: 14
Strain: lineage4.8.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.99 |
lineage4.8.1 | Euro-American (mainly T) | RD219 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Asp435Val | Assoc w R | |
isoniazid | katG | p.Glu588* | Assoc w R - interim | |
p.Ser315Thr | Assoc w R | |||
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | p.Leu151Ser | Assoc w R | |
moxifloxacin | ||||
levofloxacin | ||||
bedaquiline | ||||
delamanid | ||||
pretomanid | ||||
linezolid | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
gid | p.Gln87* | Assoc w R - interim | ||
amikacin | ||||
kanamycin | ||||
capreomycin | ||||
clofazimine | ||||
ethionamide | ethA | p.Gln206* | Assoc w R - interim | |
para-aminosalicylic_acid | ||||
cycloserine |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761110 | p.Asp435Val | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2154350 | p.Glu588* | stop_gained | 0.18 | isoniazid | Assoc w R - interim | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | |
pncA | 2288790 | p.Leu151Ser | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4326858 | p.Gln206* | stop_gained | 1.0 | ethionamide | Assoc w R - interim | |
gid | 4407944 | p.Gln87* | stop_gained | 0.14 | streptomycin | Assoc w R - interim |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5759 | c.523dupG | frameshift_variant | 0.17 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrB | 6144 | p.His302Leu | missense_variant | 0.1 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 6730 | c.-572A>G | upstream_gene_variant | 0.17 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 7914 | c.613C>T | synonymous_variant | 0.18 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 7918 | p.Glu206Val | missense_variant | 0.2 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 8921 | c.1620C>T | synonymous_variant | 0.1 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
ccsA | 620278 | p.Arg130Cys | missense_variant | 0.15 | capreomycin | |
amikacin | ||||||
ccsA | 620307 | c.419delT | frameshift_variant | 0.14 | capreomycin | |
amikacin | ||||||
ccsA | 620437 | p.Ser183Thr | missense_variant | 0.11 | capreomycin | |
amikacin | ||||||
ccsA | 620825 | p.Leu312Gln | missense_variant | 0.11 | capreomycin | |
amikacin | ||||||
rpoB | 760469 | c.663C>T | synonymous_variant | 0.13 | rifampicin | |
rpoB | 760719 | p.Val305Ile | missense_variant | 0.17 | rifampicin | Uncertain significance |
rpoB | 761062 | p.Ala419Val | missense_variant | 0.12 | rifampicin | |
rpoB | 761814 | p.Ala670Ser | missense_variant | 0.12 | rifampicin | |
rpoB | 762348 | c.2545dupC | frameshift_variant | 0.12 | rifampicin | |
rpoC | 765234 | p.Ala622Val | missense_variant | 0.14 | rifampicin | |
rpoC | 765533 | p.Tyr722His | missense_variant | 0.2 | rifampicin | |
rpoC | 765571 | c.2202C>T | synonymous_variant | 0.18 | rifampicin | |
rpoC | 765695 | p.Glu776Gln | missense_variant | 0.14 | rifampicin | |
rpoC | 766003 | c.2634G>T | synonymous_variant | 0.1 | rifampicin | |
rpoC | 766866 | p.Thr1166Ile | missense_variant | 0.12 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpL5 | 775656 | p.Val942Asp | missense_variant | 0.14 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 777835 | p.Ile216Phe | missense_variant | 0.11 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 777972 | p.Lys170Met | missense_variant | 0.12 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 778438 | c.38_42dupTCCCG | frameshift_variant | 0.15 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 779407 | c.-927G>T | upstream_gene_variant | 0.17 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
fbiC | 1304758 | p.Pro610Ser | missense_variant | 0.18 | delamanid | |
embR | 1416378 | p.Asn324Tyr | missense_variant | 0.14 | ethambutol | |
embR | 1417009 | c.339G>C | synonymous_variant | 0.2 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
rrs | 1471984 | n.139T>C | non_coding_transcript_exon_variant | 0.15 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
rrs | 1472823 | n.978C>A | non_coding_transcript_exon_variant | 0.17 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
rrl | 1473574 | n.-84G>T | upstream_gene_variant | 0.17 | linezolid | |
rrl | 1474623 | n.966C>G | non_coding_transcript_exon_variant | 0.17 | linezolid | |
rrl | 1476515 | n.2858C>G | non_coding_transcript_exon_variant | 0.15 | linezolid | |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
ndh | 2102401 | c.642T>G | synonymous_variant | 0.11 | ethionamide | |
isoniazid | ||||||
ndh | 2102556 | p.Asp163Asn | missense_variant | 0.2 | ethionamide | |
isoniazid | ||||||
ndh | 2102686 | c.357G>A | synonymous_variant | 0.11 | ethionamide | |
isoniazid | ||||||
katG | 2155853 | p.Ser87Thr | missense_variant | 0.13 | isoniazid | |
katG | 2156345 | c.-234C>A | upstream_gene_variant | 0.11 | isoniazid | |
PPE35 | 2169097 | c.1515dupG | frameshift_variant | 0.14 | pyrazinamide | |
Rv1979c | 2222555 | p.Pro204Thr | missense_variant | 0.11 | clofazimine | |
bedaquiline | ||||||
Rv1979c | 2223060 | c.105T>C | synonymous_variant | 0.12 | clofazimine | |
bedaquiline | ||||||
Rv1979c | 2223185 | c.-21C>A | upstream_gene_variant | 0.2 | clofazimine | |
bedaquiline | ||||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
pncA | 2289449 | c.-208T>C | upstream_gene_variant | 0.15 | pyrazinamide | |
pncA | 2289578 | c.-337T>G | upstream_gene_variant | 0.11 | pyrazinamide | |
eis | 2714136 | c.1197G>A | synonymous_variant | 0.13 | kanamycin | |
amikacin | ||||||
eis | 2714491 | p.Asp281Gly | missense_variant | 0.11 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
eis | 2715121 | c.211dupG | frameshift_variant | 0.18 | kanamycin | |
amikacin | ||||||
eis | 2715309 | c.24G>T | synonymous_variant | 0.15 | kanamycin | |
amikacin | ||||||
pepQ | 2859726 | c.693C>A | synonymous_variant | 0.17 | clofazimine | |
bedaquiline | ||||||
Rv2752c | 3064578 | c.1614C>A | synonymous_variant | 0.11 | rifampicin | |
isoniazid | ||||||
Rv2752c | 3065956 | c.235_236insGG | frameshift_variant | 0.14 | rifampicin | |
isoniazid | ||||||
Rv2752c | 3067070 | c.-879A>G | upstream_gene_variant | 0.13 | rifampicin | |
isoniazid | ||||||
Rv2752c | 3067116 | c.-925C>T | upstream_gene_variant | 0.12 | rifampicin | |
isoniazid | ||||||
ald | 3087135 | p.Ala106Thr | missense_variant | 0.18 | cycloserine | |
ald | 3087540 | p.Val241Leu | missense_variant | 0.12 | cycloserine | |
fprA | 3474086 | p.Asp27Ala | missense_variant | 0.12 | capreomycin | |
amikacin | ||||||
fprA | 3475118 | p.Asn371Thr | missense_variant | 0.14 | capreomycin | |
amikacin | ||||||
fprA | 3475125 | c.1119G>A | synonymous_variant | 0.14 | capreomycin | |
amikacin | ||||||
fbiA | 3641411 | p.Val290Ala | missense_variant | 0.13 | delamanid | |
fbiB | 3642099 | c.566dupT | frameshift_variant | 0.13 | delamanid | |
fbiB | 3642103 | p.Thr190Ile | missense_variant | 0.12 | delamanid | |
fbiB | 3642874 | p.Leu447Arg | missense_variant | 1.0 | delamanid | Uncertain significance |
alr | 3840514 | p.Arg303Cys | missense_variant | 0.13 | cycloserine | |
alr | 3841325 | c.96T>A | synonymous_variant | 0.14 | cycloserine | |
clpC1 | 4039327 | p.Gln460* | stop_gained | 0.11 | pyrazinamide | |
embC | 4239666 | c.-197C>T | upstream_gene_variant | 0.13 | ethambutol | Uncertain significance |
embC | 4240124 | p.Cys88Arg | missense_variant | 0.15 | ethambutol | |
embC | 4241040 | p.Asp393Gly | missense_variant | 0.12 | ethambutol | |
embC | 4241243 | p.His461Tyr | missense_variant | 0.12 | ethambutol | |
embA | 4242292 | c.-941C>T | upstream_gene_variant | 0.15 | ethambutol | |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
embC | 4242741 | p.Leu960Pro | missense_variant | 0.12 | ethambutol | |
embA | 4244753 | c.1521G>A | synonymous_variant | 0.14 | ethambutol | |
embB | 4246157 | c.-357A>T | upstream_gene_variant | 0.12 | ethambutol | |
embB | 4247315 | c.802C>T | synonymous_variant | 0.2 | ethambutol | |
embB | 4249147 | c.2634C>A | synonymous_variant | 0.2 | ethambutol | |
ubiA | 4269767 | p.Pro23Thr | missense_variant | 0.2 | ethambutol | |
ethR | 4327060 | c.-489G>A | upstream_gene_variant | 0.12 | ethionamide | |
ethR | 4327941 | p.Ser131Arg | missense_variant | 0.11 | ethionamide | Uncertain significance |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
gid | 4408019 | p.Gly62Cys | missense_variant | 0.12 | streptomycin | |
gid | 4408145 | p.Arg20Trp | missense_variant | 0.17 | streptomycin |