TB-Profiler result

Run: SRR13861233
Summary

Run ID: SRR13861233

Sample name:

Date: 2024-10-04T18:09:55.623373

Number of reads: 353734

Percentage reads mapped: 5.9

Median coverage: 11.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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
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 442 p.Pro148Ala missense_variant 1.0 isoniazid
gyrB 6667 p.Gln476His missense_variant 1.0 levofloxacin
moxifloxacin
rpoB 760214 p.Asn136Lys missense_variant 1.0 rifampicin
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrs 1471943 n.98T>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472075 n.230A>C non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.57 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.57 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.59 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.58 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.59 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.62 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.64 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.64 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.56 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473066 n.1221A>T non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.89 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.68 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid
inhA 1673813 c.-389G>T upstream_gene_variant 1.0 isoniazid
ethionamide
inhA 1674784 p.Arg195Gly missense_variant 1.0 isoniazid
ethionamide
bacA 2064693 p.Trp12Cys missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2169624 p.Gly330Asp missense_variant 1.0 pyrazinamide
Rv2681 2997779 c.1041C>G synonymous_variant 1.0 capreomycin
lpqB 3624763 p.Val50Leu missense_variant 1.0 rifampicin
bedaquiline
lpqB 3625054 c.-144C>G upstream_gene_variant 1.0 rifampicin
bedaquiline
alr 3841581 c.-161T>A upstream_gene_variant 1.0 cycloserine
embB 4246553 p.Arg14Trp missense_variant 1.0 ethambutol
embB 4248920 p.Val803Met missense_variant 1.0 ethambutol Uncertain significance
embB 4249551 p.Arg1013Leu missense_variant 1.0 ethambutol