TB-Profiler result

Run: ERR1035296
Summary

Run ID: ERR1035296

Sample name:

Date: 2024-10-05T05:42:19.498988

Number of reads: 10411934

Percentage reads mapped: 99.7

Median coverage: 187.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
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 katG c.316dupG Assoc w R High-level resistance
ahpC c.-81C>T Uncertain significance Mutation from literature
ethambutol
pyrazinamide pncA p.Ala171Val Uncertain significance Mutation from literature
c.246delT Assoc w R
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
katG 2155795 c.316dupG frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288730 p.Ala171Val missense_variant 0.53 pyrazinamide Uncertain significance Mutation from literature
pncA 2288995 c.246delT frameshift_variant 0.38 pyrazinamide Assoc w R
ahpC 2726112 c.-81C>T upstream_gene_variant 0.99 isoniazid Uncertain significance Mutation from literature
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
Rv0565c 656195 p.Gly426Cys missense_variant 1.0 ethionamide
fbiC 1303257 c.327C>T synonymous_variant 1.0 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.27 capreomycin
linezolid Uncertain significance
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid Uncertain significance
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1473981 n.324delGinsAT non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474291 n.634_649delTTTCCTCTCCGGAGGAinsC non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474374 n.717T>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475289 n.1632G>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475297 n.1640C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475315 n.1658A>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.1 capreomycin
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
glpK 4138415 c.1341G>T synonymous_variant 0.99 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
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