TB-Profiler result

Run: ERR12544262
Summary

Run ID: ERR12544262

Sample name:

Date: 2024-10-04T03:00:02.205169

Number of reads: 2688551

Percentage reads mapped: 99.65

Median coverage: 108.0

Strain: lineage4.2.1.1

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 1.0
lineage4 Euro-American None 1.0
lineage4.2.1.1 Euro-American (TUR) None 1.0
lineage4.2.1 Euro-American (TUR) None 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu449Gln 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
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
rpoB 761152 p.Leu449Gln missense_variant 0.33 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
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
Rv0010c 13824 c.-266A>T upstream_gene_variant 0.24 isoniazid
Rv0010c 13829 c.-271T>A upstream_gene_variant 0.24 isoniazid
Rv0010c 13834 c.-276A>T upstream_gene_variant 0.24 isoniazid
Rv0565c 656592 p.Trp293* stop_gained 1.0 ethionamide Uncertain significance
rpoB 761162 c.1356G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777451 p.Val344Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800179 c.-630G>A upstream_gene_variant 1.0 linezolid
rplC 800204 c.-605T>C upstream_gene_variant 1.0 linezolid
Rv1129c 1254582 c.-48A>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303144 p.Ser72Pro missense_variant 0.12 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.49 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.49 capreomycin
linezolid
rrl 1474438 n.781A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833641 p.Asn34Asp missense_variant 0.13 pyrazinamide
rpsA 1833651 p.Asp37Ala missense_variant 0.12 pyrazinamide
rpsA 1833658 c.117C>T synonymous_variant 0.12 pyrazinamide
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 2063685 c.1044G>A synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170035 p.Val193Ala missense_variant 0.13 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.38 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.4 pyrazinamide
PPE35 2170066 p.Ala183Thr missense_variant 0.12 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518348 c.234A>T synonymous_variant 0.17 isoniazid
Rv2681 2997962 c.1224A>C synonymous_variant 0.15 capreomycin
Rv2681 2997965 c.1227G>T synonymous_variant 0.15 capreomycin
ald 3086742 c.-78A>C upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568845 c.-166G>A upstream_gene_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878567 c.-60C>G upstream_gene_variant 0.61 rifampicin
rpoA 3878578 c.-71C>A upstream_gene_variant 0.32 rifampicin Uncertain significance
rpoA 3878599 c.-92C>G upstream_gene_variant 0.37 rifampicin
rpoA 3878639 c.-132C>G upstream_gene_variant 0.38 rifampicin Uncertain significance
embC 4239281 c.-582C>G upstream_gene_variant 0.16 ethambutol
embC 4239284 c.-579C>G upstream_gene_variant 0.16 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.28 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.32 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.32 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.31 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.33 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.3 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408213 c.-11C>T upstream_gene_variant 1.0 streptomycin Uncertain significance