TB-Profiler result

Run: ERR4817628
Summary

Run ID: ERR4817628

Sample name:

Date: 2024-04-14T23:53:11.669102

Number of reads: 5491408

Percentage reads mapped: 91.2

Median coverage: 98.0

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) RD219 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
dnaA 371 p.Pro124Leu missense_variant 1.0 isoniazid Not assoc w R
dnaA 1044 p.Met348Ile missense_variant 1.0 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8897 c.1596T>C synonymous_variant 0.1 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8915 c.1614A>G synonymous_variant 0.1 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0565c 656261 p.Arg404Trp missense_variant 1.0 ethionamide
rpoB 760376 p.Asp190Glu missense_variant 0.11 rifampicin Uncertain significance
rpoB 760380 p.Thr192Pro missense_variant 0.12 rifampicin
rpoB 760400 c.594G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760407 p.Ser201Ala missense_variant 0.15 rifampicin
rpoB 760430 c.624T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760436 c.630C>G synonymous_variant 0.16 rifampicin
rpoB 760460 c.654G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760475 c.669A>G synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoB 760508 c.702G>C synonymous_variant 0.13 rifampicin
rpoB 760511 c.705G>C synonymous_variant 0.13 rifampicin
rpoB 760514 c.708C>G synonymous_variant 0.13 rifampicin
rpoB 760532 c.726T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760533 p.Val243Leu missense_variant 0.13 rifampicin
rpoB 760541 c.735G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760547 c.741G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760553 c.747C>G synonymous_variant 0.15 rifampicin
rpoB 760565 c.759A>C synonymous_variant 0.12 rifampicin
rpoB 760568 c.762G>C synonymous_variant 0.13 rifampicin
rpoB 760571 c.765G>C synonymous_variant 0.12 rifampicin
rpoB 761174 c.1368T>C synonymous_variant 0.11 rifampicin
rpoB 761180 c.1374A>G synonymous_variant 0.11 rifampicin
rpoB 761189 c.1383T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761192 c.1386C>G synonymous_variant 0.11 rifampicin
rpoB 761198 c.1392G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761213 c.1407G>C synonymous_variant 0.12 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763558 c.189C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763699 c.330G>C synonymous_variant 0.13 rifampicin
rpoC 763702 c.333C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763708 c.339G>C synonymous_variant 0.14 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763732 c.363C>G synonymous_variant 0.15 rifampicin
rpoC 763735 c.366G>C synonymous_variant 0.16 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.16 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.16 rifampicin
rpoC 764308 c.939G>C synonymous_variant 0.1 rifampicin
rpoC 764320 c.951C>G synonymous_variant 0.11 rifampicin
rpoC 764353 c.984G>C synonymous_variant 0.12 rifampicin
rpoC 764387 c.1018T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764404 c.1035C>T synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.11 rifampicin
rpoC 764548 c.1179G>A synonymous_variant 0.11 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.12 rifampicin
rpoC 764695 c.1326T>C synonymous_variant 0.11 rifampicin
rpoC 764701 c.1332C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>C synonymous_variant 0.13 rifampicin
rpoC 764755 c.1386C>T synonymous_variant 0.13 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764780 c.1411_1413delAGCinsTCG synonymous_variant 0.15 rifampicin
rpoC 764797 c.1428G>C synonymous_variant 0.15 rifampicin
rpoC 764803 c.1434C>G synonymous_variant 0.17 rifampicin
rpoC 764812 c.1443C>G synonymous_variant 0.16 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
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 0.99 streptomycin Not assoc w R
rpsL 781802 c.243G>C synonymous_variant 0.11 streptomycin
rpsL 781805 c.246G>C synonymous_variant 0.11 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.12 streptomycin
rpsL 781814 c.255C>T synonymous_variant 0.11 streptomycin
rpsL 781817 c.258G>T synonymous_variant 0.11 streptomycin
rpsL 781829 c.270G>C synonymous_variant 0.13 streptomycin
rpsL 781832 c.273T>G synonymous_variant 0.14 streptomycin
rpsL 781838 c.279G>T synonymous_variant 0.13 streptomycin
rpsL 781841 c.282C>T synonymous_variant 0.11 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.13 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471918 n.73A>T non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471932 n.87A>G non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471938 n.93T>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.77 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.37 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.39 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.41 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.48 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476529 n.2872A>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rpsA 1833894 p.Ala118Glu missense_variant 0.11 pyrazinamide
rpsA 1833952 c.411C>T synonymous_variant 0.11 pyrazinamide
rpsA 1834340 p.Met267Leu missense_variant 0.1 pyrazinamide Uncertain significance
rpsA 1834348 c.807T>C synonymous_variant 0.11 pyrazinamide Not assoc w R - Interim
rpsA 1834423 c.882G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834451 c.910_912delTTGinsCC frameshift_variant&missense_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834456 c.915T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.15 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834501 c.960G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834504 c.963G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.1 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155098 c.1014C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
Rv1979c 2222717 p.Ala150Pro missense_variant 1.0 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
alr 3840764 c.657G>C synonymous_variant 1.0 cycloserine
clpC1 4038808 c.1896_1897insC frameshift_variant 0.14 pyrazinamide
clpC1 4038811 c.1893delT frameshift_variant 0.13 pyrazinamide
clpC1 4038860 c.1845G>T synonymous_variant 0.14 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4038896 c.1809C>G synonymous_variant 0.13 pyrazinamide
clpC1 4039004 c.1701C>G synonymous_variant 0.11 pyrazinamide
clpC1 4039016 c.1689C>G synonymous_variant 0.13 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.11 pyrazinamide
clpC1 4039091 c.1614G>C synonymous_variant 0.11 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039748 c.957G>C synonymous_variant 0.11 pyrazinamide
clpC1 4039751 c.954A>G synonymous_variant 0.12 pyrazinamide
clpC1 4039757 c.948A>G synonymous_variant 0.12 pyrazinamide
clpC1 4039766 c.939T>C synonymous_variant 0.12 pyrazinamide
clpC1 4039769 c.936C>G synonymous_variant 0.12 pyrazinamide
clpC1 4039778 c.927A>G synonymous_variant 0.11 pyrazinamide
clpC1 4039781 c.924G>C synonymous_variant 0.12 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246697 p.Gly62Arg missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338416 p.Gln36* stop_gained 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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
gid 4407535 p.Thr223Arg missense_variant 1.0 streptomycin