TB-Profiler result

Run: ERR11466062
Summary

Run ID: ERR11466062

Sample name:

Date: 2025-03-09T01:26:09.794209

Number of reads: 2697756

Percentage reads mapped: 99.67

Median coverage: 54.0

Strain: lineage4.9.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.9.1 Euro-American (H37Rv-like) None 0.98
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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
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
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 7745 c.444G>A synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7748 c.447A>G synonymous_variant 0.2 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7758 p.Ile153Val missense_variant 0.2 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7763 c.462T>G synonymous_variant 0.24 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8378 c.1077C>T synonymous_variant 0.14 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8382 p.Leu361Met missense_variant 0.16 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8978 c.1677C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
nusG 734502 c.249G>A synonymous_variant 0.12 rifampicin Uncertain significance
rpoB 760283 c.477G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>T synonymous_variant 0.16 rifampicin Uncertain significance
rpoB 762212 c.2406G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762470 c.2664G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764948 c.1579T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765946 c.2577C>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766381 c.3012C>T synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 766384 c.3015A>G synonymous_variant 0.19 rifampicin Uncertain significance
rpoC 766390 c.3021C>T synonymous_variant 0.24 rifampicin Uncertain significance
rpoC 766408 c.3039C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 766843 c.3474T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766846 c.3477C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766996 c.3627C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767002 c.3633G>C synonymous_variant 0.15 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1303323 c.393T>C synonymous_variant 0.11 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1303512 c.582T>G synonymous_variant 0.12 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1303575 c.645G>C synonymous_variant 0.17 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304567 p.Phe546Tyr missense_variant 0.15 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304580 c.1650T>C synonymous_variant 0.14 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.23 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.18 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.18 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.13 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674690 c.489C>G synonymous_variant 0.13 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1833547 c.6G>A synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834105 c.564C>T synonymous_variant 0.24 pyrazinamide Uncertain significance
rpsA 1834189 c.648G>C synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834432 c.891G>C synonymous_variant 0.15 pyrazinamide Uncertain significance
tsnR 1853444 c.-162C>T upstream_gene_variant 0.19 linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289138 p.Leu35Arg missense_variant 1.0 pyrazinamide Not assoc w R - Interim
fbiD 3339385 p.Asp90Asn missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rpoA 3877818 c.690A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
clpC1 4038941 c.1764G>A synonymous_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039517 c.1188C>G synonymous_variant 0.17 pyrazinamide Uncertain significance
clpC1 4040057 c.648C>T synonymous_variant 0.19 pyrazinamide Uncertain significance
embC 4241185 c.1323G>C synonymous_variant 0.11 ethambutol Uncertain significance
embC 4241188 c.1326C>G synonymous_variant 0.11 ethambutol Uncertain significance
embC 4241194 c.1332C>G synonymous_variant 0.12 ethambutol Uncertain significance
embA 4246062 p.Tyr944Asn missense_variant 0.17 ethambutol Uncertain significance
ethA 4327425 p.Val17Ile missense_variant 0.14 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R