TB-Profiler result

Run: SRR7535054
Summary

Run ID: SRR7535054

Sample name:

Date: 2024-10-04T15:35:28.880122

Number of reads: 2586121

Percentage reads mapped: 23.13

Median coverage: 52.0

Strain: lineage4.6.1.1

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
lineage4.6 Euro-American None 0.99
lineage4 Euro-American None 1.0
lineage4.6.1.1 Euro-American RD724 0.78
lineage4.6.1 Euro-American (Uganda) RD724 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 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764905 c.1536C>T synonymous_variant 0.12 rifampicin
rpoC 764911 c.1542A>C synonymous_variant 0.12 rifampicin
rpoC 764914 p.Met515Ile missense_variant 0.11 rifampicin Uncertain significance
rpoC 764918 p.Val517Ile missense_variant 0.11 rifampicin
rpoC 764939 c.1570C>T synonymous_variant 0.13 rifampicin
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.76 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.76 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.74 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.74 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.76 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.74 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.74 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.66 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.52 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
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
Rv2681 2996876 c.138A>C synonymous_variant 1.0 capreomycin Not assoc w R
whiB7 3569029 c.-350A>G upstream_gene_variant 1.0 kanamycin Not assoc w R
amikacin Uncertain significance
streptomycin Uncertain significance
glpK 4139297 c.459G>A synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4139670 p.Cys29Tyr missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4328329 c.-856C>G upstream_gene_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin