TB-Profiler result

Run: SRR13861458
Summary

Run ID: SRR13861458

Sample name:

Date: 2024-04-15T14:54:25.131758

Number of reads: 482608

Percentage reads mapped: 8.05

Median coverage: 15.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: MDR-TB

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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 rpoB p.Gly442Glu Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
c.1327_1329delTTGinsAC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid katG p.Gln352* Assoc w R High-level resistance
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
rpoB 761131 p.Gly442Glu missense_variant 0.38 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761133 c.1327_1329delTTGinsAC frameshift_variant&missense_variant 0.38 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
katG 2155058 p.Gln352* stop_gained 1.0 isoniazid Assoc w R High-level resistance
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
Rv0010c 13575 c.-17G>T upstream_gene_variant 1.0 isoniazid
mshA 574999 c.-349G>C upstream_gene_variant 1.0 ethionamide
isoniazid
Rv0565c 657082 p.Val130Glu missense_variant 1.0 ethionamide
rpoB 760182 p.Pro126Ala missense_variant 1.0 rifampicin
rpoB 761126 c.1320G>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 761129 c.1323G>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpsL 781138 c.-422C>G upstream_gene_variant 1.0 streptomycin
rrs 1472286 n.441C>T non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rrs 1472762 n.917C>A non_coding_transcript_exon_variant 0.93 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472840 n.997delG non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.56 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.59 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.58 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.59 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.59 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.57 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 0.59 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.59 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.59 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.59 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.44 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.85 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 0.84 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 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.86 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 0.85 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.84 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 0.8 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.53 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834279 c.738C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
tsnR 1853488 c.-118A>C upstream_gene_variant 1.0 linezolid
tlyA 1917527 c.-413G>A upstream_gene_variant 1.0 capreomycin
ndh 2102692 c.350_351insA frameshift_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2155551 c.561G>T synonymous_variant 1.0 isoniazid
eis 2715425 c.-93G>C upstream_gene_variant 1.0 amikacin
kanamycin
Rv2680 2996102 c.-3C>G upstream_gene_variant 1.0 capreomycin
alr 3840436 p.Leu329Val missense_variant 1.0 cycloserine
clpC1 4038224 c.2481G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038878 c.1826_1827insG frameshift_variant 1.0 pyrazinamide
panD 4044932 c.-651G>A upstream_gene_variant 1.0 pyrazinamide
aftB 4268216 p.Trp207Cys missense_variant 1.0 ethambutol
aftB 4268782 p.Trp19Arg missense_variant 1.0 ethambutol
aftB 4269678 c.-842C>T upstream_gene_variant 1.0 ethambutol
ubiA 4269868 c.-35G>C upstream_gene_variant 1.0 ethambutol Uncertain significance
ethR 4327906 p.Val120Leu missense_variant 1.0 ethionamide
whiB6 4338910 c.-389G>C upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin