TB-Profiler result

Run: SRR13861601
Summary

Run ID: SRR13861601

Sample name:

Date: 2025-09-15T16:17:57.510993

Number of reads: 1657754

Percentage reads mapped: 33.19

Median coverage: 55.0

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 100.0
lineage4.9 Euro-American (H37Rv-like) None 100.0
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 Uncertain significance
moxifloxacin Uncertain significance
nusG 734793 c.540C>G synonymous_variant 1.0 rifampicin Uncertain significance
mmpR5 779201 p.Ala71Val missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 800119 c.-690G>C upstream_gene_variant 1.0 linezolid Uncertain significance
rplC 800522 c.-287C>A upstream_gene_variant 1.0 linezolid Uncertain significance
Rv1129c 1253232 p.Asp435His missense_variant 0.98 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1253562 p.Gln325Lys missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254726 c.-192C>T upstream_gene_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
fbiC 1305062 p.Gly711Glu missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
sigE 1364621 p.Ala70Val missense_variant 1.0 pyrazinamide Uncertain significance
rrs 1472361 n.516C>G non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.17 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.17 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.16 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
streptomycin Uncertain significance
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.2 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1475981 n.2324G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834620 p.Leu360Ser missense_variant 1.0 pyrazinamide Uncertain significance
tlyA 1918366 p.Ala143Pro missense_variant 1.0 capreomycin Uncertain significance
bacA 2064408 c.321C>T synonymous_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
ndh 2101701 c.1341delG frameshift_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
ndh 2103327 c.-285C>A upstream_gene_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
PPE35 2170109 c.504C>T synonymous_variant 0.98 pyrazinamide Not assoc w R - Interim
kasA 2518676 p.Gly188Cys missense_variant 1.0 isoniazid Uncertain significance
eis 2714749 p.Val195Ala missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
eis 2715045 c.288G>A synonymous_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2752c 3067080 c.-889G>C upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
lpqB 3624325 p.Thr196Pro missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625849 p.His255Gln missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
clpC1 4039055 p.Ile550Met missense_variant 1.0 pyrazinamide Uncertain significance
embC 4242797 p.Asp979His missense_variant 1.0 ethambutol Uncertain significance
embB 4247936 p.Thr475Ala missense_variant 1.0 ethambutol Uncertain significance