TB-Profiler result

Run: ERR9786507
Summary

Run ID: ERR9786507

Sample name:

Date: 2024-04-15T12:05:43.121139

Number of reads: 1878336

Percentage reads mapped: 92.03

Median coverage: 79.0

Strain: lineage4.7

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.7 Euro-American (mainly T) None 1.0
lineage4 Euro-American None 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 c.1327_1329delTTGinsCC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fgd1 c.301_303delGTTinsAC Assoc w R - Interim Confers DLM-PMD cross-resistance
bedaquiline
linezolid
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
fgd1 491083 c.301_303delGTTinsAC frameshift_variant&missense_variant 0.15 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
rpoB 761133 c.1327_1329delTTGinsCC frameshift_variant&missense_variant 0.14 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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 6798 p.Gly520Ala missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491007 c.225G>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fgd1 491013 c.231C>G synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fgd1 491022 c.240C>G synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491043 c.261T>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fgd1 491049 c.267T>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fgd1 491058 c.276C>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fgd1 491064 c.282A>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fgd1 491082 c.300T>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fgd1 491091 c.309T>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fgd1 491097 c.315G>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
mshA 575578 c.231G>C synonymous_variant 0.99 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rpoB 760520 c.714C>G synonymous_variant 0.13 rifampicin
rpoB 760522 p.Ser239Asn missense_variant 0.13 rifampicin Uncertain significance
rpoB 761006 c.1200C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.13 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761084 c.1278C>G synonymous_variant 0.15 rifampicin
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.15 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.15 rifampicin
rpoB 761129 c.1323G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763891 c.522G>C synonymous_variant 0.13 rifampicin
rpoC 763894 c.525A>G synonymous_variant 0.14 rifampicin
rpoC 764344 c.975C>G synonymous_variant 0.15 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.14 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765562 c.2193G>C synonymous_variant 0.14 rifampicin
rpoC 765613 p.His748Gln missense_variant 0.15 rifampicin
rpoC 765625 c.2256C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765628 c.2259G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765631 p.Asp754Glu missense_variant 0.15 rifampicin
rpoC 765658 c.2289C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765700 c.2331T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.14 rifampicin
rpoC 765751 c.2382C>G synonymous_variant 0.13 rifampicin
rpoC 765753 p.Asp795Ala missense_variant 0.13 rifampicin Uncertain significance
rpoC 766573 c.3204T>C synonymous_variant 0.15 rifampicin
rpoC 766583 c.3214_3216delGGTinsAC frameshift_variant&missense_variant 0.14 rifampicin
rpoC 766591 c.3222A>G synonymous_variant 0.15 rifampicin
rpoC 766594 c.3225G>C synonymous_variant 0.15 rifampicin
rpoC 766597 c.3228C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766607 p.Ile1080Leu missense_variant 0.16 rifampicin
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
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474054 n.397T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
inhA 1674732 c.531C>T synonymous_variant 0.15 ethionamide
isoniazid
inhA 1674738 c.537C>G synonymous_variant 0.15 ethionamide
isoniazid
inhA 1674746 p.Tyr182Phe missense_variant 0.13 ethionamide
isoniazid
inhA 1674756 c.555T>A synonymous_variant 0.13 ethionamide
isoniazid
inhA 1674771 c.570C>G synonymous_variant 0.13 ethionamide
isoniazid
inhA 1674774 c.573A>G synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674786 c.585G>A synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674789 c.588G>C synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674795 c.594G>C synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674801 c.600T>C synonymous_variant 0.15 ethionamide
isoniazid
inhA 1674804 c.603G>C synonymous_variant 0.14 ethionamide Not assoc w R - Interim
isoniazid
inhA 1674816 c.615T>G synonymous_variant 0.15 ethionamide
isoniazid
rpsA 1833703 c.162C>T synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1833724 c.183C>G synonymous_variant 0.17 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833760 c.219C>T synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
rpsA 1833793 c.252C>T synonymous_variant 0.15 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833835 c.294C>T synonymous_variant 0.16 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.16 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.14 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
thyX 3067349 c.597G>C synonymous_variant 0.14 para-aminosalicylic_acid
thyX 3067355 c.591A>C synonymous_variant 0.14 para-aminosalicylic_acid
thyX 3067367 c.579G>C synonymous_variant 0.15 para-aminosalicylic_acid
thyX 3067394 c.552G>C synonymous_variant 0.14 para-aminosalicylic_acid
embC 4240726 c.864G>C synonymous_variant 0.13 ethambutol Not assoc w R - Interim
embC 4240780 c.918T>C synonymous_variant 0.15 ethambutol
embC 4240783 c.921G>C synonymous_variant 0.15 ethambutol
embC 4240897 c.1035C>G synonymous_variant 0.13 ethambutol Not assoc w R
embC 4240900 c.1038A>G synonymous_variant 0.16 ethambutol
embC 4240921 c.1059C>G synonymous_variant 0.16 ethambutol
embC 4240924 c.1062C>G synonymous_variant 0.15 ethambutol
embC 4240936 c.1074A>G synonymous_variant 0.14 ethambutol
embC 4240945 c.1083T>C synonymous_variant 0.14 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267992 p.Thr282Met missense_variant 1.0 ethambutol 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