TB-Profiler result

Run: 8c1337c2-b051-444e-8b97-e6f788fe3387
Summary

Run ID: 8c1337c2-b051-444e-8b97-e6f788fe3387

Sample name:

Date: 28-04-2023 10:19:01

Number of reads: 785656

Percentage reads mapped: 96.98

Median coverage: 14

Strain: lineage4.8.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
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: This table reports drug-resistance associated mutations found in known resistance genes
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
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
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
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
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