TB-Profiler result

Run: ERR11465830
Summary

Run ID: ERR11465830

Sample name:

Date: 2024-10-03T14:31:29.271091

Number of reads: 1656433

Percentage reads mapped: 99.62

Median coverage: 34.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
lineage4.9 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
mshA 575761 c.414C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
Rv0565c 657192 p.Met93Ile missense_variant 1.0 ethionamide Uncertain significance
mmaA3 737358 c.792A>C synonymous_variant 0.17 isoniazid
rpoB 759814 p.Asp3Gly missense_variant 1.0 rifampicin Uncertain significance
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.19 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.19 rifampicin
rpoB 761579 c.1773G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763483 c.114G>C synonymous_variant 0.17 rifampicin
rpoC 763486 c.117T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763495 c.126G>A synonymous_variant 0.18 rifampicin
rpoC 763504 c.135C>G synonymous_variant 0.14 rifampicin
rpoC 763507 c.138G>C synonymous_variant 0.14 rifampicin
rpoC 763573 c.204G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763621 c.252C>T synonymous_variant 0.15 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.2 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
rpsL 781502 c.-58G>T upstream_gene_variant 1.0 streptomycin Uncertain significance
rpsL 781793 c.234G>C synonymous_variant 0.18 streptomycin
rpsL 781796 p.Met79Ile missense_variant 0.17 streptomycin
rpsL 781802 c.243G>C synonymous_variant 0.15 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.14 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.14 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473062 n.1217T>G non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473201 n.1356A>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.15 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474232 n.575C>G non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474239 n.582G>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474688 n.1031G>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474777 n.1120T>G non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1474896 n.1239A>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475508 n.1851A>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475883 n.2226A>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.24 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2169902 p.Leu237Phe missense_variant 0.25 pyrazinamide
PPE35 2169910 p.Asn235Tyr missense_variant 0.26 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3065873 p.Phe107Val missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
clpC1 4039865 c.840T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039875 p.Asn277Arg missense_variant 0.16 pyrazinamide
clpC1 4039889 c.816G>C synonymous_variant 0.15 pyrazinamide
clpC1 4040063 c.642G>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4040066 c.639G>C synonymous_variant 0.17 pyrazinamide
clpC1 4040644 c.61A>C synonymous_variant 0.21 pyrazinamide
clpC1 4040648 c.57G>A synonymous_variant 0.2 pyrazinamide
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 4338766 c.-246delT upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin