TB-Profiler result

Run: SRR13861713
Summary

Run ID: SRR13861713

Sample name:

Date: 2024-04-15T02:58:52.959619

Number of reads: 281823

Percentage reads mapped: 14.1

Median coverage: 9.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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 pncA p.Thr153Asn Mutation from literature
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
pncA 2288784 p.Thr153Asn missense_variant 1.0 pyrazinamide 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
dnaA 750 c.750C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
Rv0565c 657479 c.-9A>G upstream_gene_variant 0.93 ethionamide
rpoC 762989 c.-381G>C upstream_gene_variant 0.55 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 767026 c.3657G>C synonymous_variant 1.0 rifampicin
fbiC 1304225 p.Gly432Asp missense_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1305046 p.Ser706Pro missense_variant 1.0 clofazimine
pretomanid
delamanid
embR 1416546 p.Thr268Ser missense_variant 1.0 ethambutol
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474652 n.995T>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.68 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4 capreomycin Not assoc w R
linezolid Uncertain significance
bacA 2063152 p.Arg526Leu missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
katG 2156722 c.-611G>A upstream_gene_variant 1.0 isoniazid
Rv3236c 3612913 p.Leu68Phe missense_variant 1.0 pyrazinamide
lpqB 3624794 c.117G>C synonymous_variant 1.0 bedaquiline
rifampicin
ethA 4327893 c.-420C>A upstream_gene_variant 1.0 ethionamide
gid 4408070 p.Trp45Arg missense_variant 1.0 streptomycin Uncertain significance