TB-Profiler result

Run: SRR13861603
Summary

Run ID: SRR13861603

Sample name:

Date: 2024-04-15T10:14:53.752928

Number of reads: 609717

Percentage reads mapped: 12.21

Median coverage: 19.0

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
gyrA 8827 p.Asp509Gly missense_variant 1.0 levofloxacin
moxifloxacin
nusG 734793 c.540C>G synonymous_variant 1.0 rifampicin
mmpR5 779201 p.Ala71Val missense_variant 1.0 clofazimine
bedaquiline
rplC 800119 c.-690G>C upstream_gene_variant 1.0 linezolid
rplC 800522 c.-287C>A upstream_gene_variant 1.0 linezolid
Rv1129c 1253232 p.Asp435His missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1253562 p.Gln325Lys missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1254726 c.-192C>T upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1305062 p.Gly711Glu missense_variant 1.0 clofazimine
pretomanid
delamanid
sigE 1364621 p.Ala70Val missense_variant 1.0 pyrazinamide
rrs 1472361 n.516C>G non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.37 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.4 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 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1475981 n.2324G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.8 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 0.81 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 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.86 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 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.83 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 0.84 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 0.82 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.83 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.55 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834620 p.Leu360Ser missense_variant 1.0 pyrazinamide
tlyA 1918366 p.Ala143Pro missense_variant 1.0 capreomycin
bacA 2064408 c.321C>T synonymous_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
ndh 2101701 c.1341delG frameshift_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
ndh 2103327 c.-285C>A upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
PPE35 2170109 c.504C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
kasA 2518676 p.Gly188Cys missense_variant 1.0 isoniazid
eis 2714749 p.Val195Ala missense_variant 1.0 amikacin
kanamycin
eis 2715045 c.288G>A synonymous_variant 1.0 amikacin
kanamycin
Rv2752c 3067080 c.-889G>C upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
clpC1 4039055 p.Ile550Met missense_variant 1.0 pyrazinamide
embC 4242797 p.Asp979His missense_variant 1.0 ethambutol
embB 4247936 p.Thr475Ala missense_variant 1.0 ethambutol