TB-Profiler result

Run: SRR19303813
Summary

Run ID: SRR19303813

Sample name:

Date: 2025-09-15T16:57:47.069288

Number of reads: 1991908

Percentage reads mapped: 28.93

Median coverage: 55.0

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) RD219 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 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13705 c.-147G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
rpoB 760975 p.Met390Thr missense_variant 1.0 rifampicin Uncertain significance
rpoC 764611 c.1242G>C synonymous_variant 0.27 rifampicin Uncertain significance
rpoC 764632 c.1263T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764644 c.1275G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764656 c.1287C>G synonymous_variant 0.25 rifampicin Uncertain significance
rpoC 764662 c.1293G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764668 c.1299C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764671 c.1302G>C synonymous_variant 0.24 rifampicin Uncertain significance
rpoC 764672 p.Gln435Glu missense_variant 0.24 rifampicin Uncertain significance
rpoC 764677 c.1308C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764686 c.1317C>T synonymous_variant 0.23 rifampicin Uncertain significance
rpoC 764695 c.1326T>C synonymous_variant 0.25 rifampicin Uncertain significance
rpoC 764701 c.1332C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764705 p.Leu446Lys missense_variant 0.23 rifampicin Uncertain significance
rpoC 764716 c.1347G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254598 c.-65dupA upstream_gene_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.5 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 0.45 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin Uncertain significance
ald 3086767 c.-53A>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3448507 c.5_*1407del frameshift_variant&stop_lost&splice_region_variant 0.97 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244990 c.1758G>C synonymous_variant 1.0 ethambutol Not assoc w R - Interim
aftB 4267715 c.1122G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R