TB-Profiler result

Run: SRR13861338
Summary

Run ID: SRR13861338

Sample name:

Date: 2024-04-16T00:58:58.535242

Number of reads: 444147

Percentage reads mapped: 11.11

Median coverage: 14.0

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
dnaA 715 p.Thr239Pro missense_variant 1.0 isoniazid
fgd1 490955 p.Met58Arg missense_variant 1.0 clofazimine
pretomanid
delamanid
hadA 731861 c.-69G>C upstream_gene_variant 1.0 isoniazid
rpsL 781155 c.-405G>A upstream_gene_variant 1.0 streptomycin
Rv1258c 1406845 p.Ala166Pro missense_variant 1.0 streptomycin
isoniazid
pyrazinamide
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.48 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.45 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.42 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.42 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.44 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 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.82 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.44 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674607 p.Pro136Ser missense_variant 1.0 ethionamide
isoniazid
inhA 1674778 p.Pro193Ala missense_variant 1.0 ethionamide
isoniazid
bacA 2064115 p.Ala205Asp missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
PPE35 2169081 p.Leu511Ser missense_variant 1.0 pyrazinamide
PPE35 2169202 p.Ser471Pro missense_variant 1.0 pyrazinamide
Rv1979c 2222091 c.1074G>T synonymous_variant 1.0 clofazimine
bedaquiline
Rv1979c 2223306 c.-142T>A upstream_gene_variant 1.0 clofazimine
bedaquiline
pncA 2289228 p.Ile5Asn missense_variant 1.0 pyrazinamide
eis 2714755 p.Pro193Gln missense_variant 1.0 amikacin
kanamycin
ahpC 2726324 c.132A>G synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ahpC 2726362 p.Phe57Ser missense_variant 1.0 isoniazid
pepQ 2859580 p.Leu280Arg missense_variant 1.0 clofazimine
bedaquiline
Rv2681 2997338 c.600G>C synonymous_variant 1.0 capreomycin
thyX 3067940 c.6C>G synonymous_variant 1.0 para-aminosalicylic_acid
mtrB 3626051 p.Ser188Trp missense_variant 1.0 bedaquiline
rifampicin
ddn 3986889 p.Phe16Val missense_variant 1.0 delamanid
pretomanid
embC 4242041 p.Met727Leu missense_variant 1.0 ethambutol
embA 4244723 p.Gln497His missense_variant 1.0 ethambutol Uncertain significance
aftB 4267979 c.858G>C synonymous_variant 1.0 ethambutol