TB-Profiler result

Run: SRR25827551
Summary

Run ID: SRR25827551

Sample name:

Date: 2024-10-04T03:01:18.730881

Number of reads: 8607400

Percentage reads mapped: 99.04

Median coverage: 281.0

Strain: lineage3.1.2;lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.51
lineage3.1.2 East-African-Indian RD750 0.29
lineage4 Euro-American None 0.44
lineage4.8 Euro-American (mainly T) RD219 0.46
lineage3.1 East-African-Indian RD750 0.31
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
rpoC p.Leu527Val Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin gid c.102delG Assoc w R
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 761155 p.Ser450Leu missense_variant 0.22 rifampicin Assoc w R
rpoC 764948 p.Leu527Val missense_variant 0.2 rifampicin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.51 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.2 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.38 streptomycin Assoc w R
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 7585 p.Ser95Thr missense_variant 0.51 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13905 c.-347G>T upstream_gene_variant 0.24 isoniazid
fgd1 491742 c.960T>C synonymous_variant 0.55 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620241 c.351C>G synonymous_variant 0.37 kanamycin
capreomycin
amikacin
Rv0565c 657081 c.390G>A synonymous_variant 0.54 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.6 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.49 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.54 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.57 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 1253952 p.Ala195Pro missense_variant 0.15 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.48 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.58 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.53 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.52 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.57 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.35 pyrazinamide 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
Rv1979c 2223491 c.-327C>A upstream_gene_variant 0.4 bedaquiline Uncertain significance
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.55 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.51 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.55 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.49 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.49 cycloserine
ald 3087862 p.Gly348Glu missense_variant 0.23 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.5 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.46 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.53 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.58 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245131 c.1899G>A synonymous_variant 0.16 ethambutol Not assoc w R - Interim
whiB6 4338194 p.Arg110Trp missense_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 0.53 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.55 streptomycin Not assoc w R
gid 4407742 p.Arg154Pro missense_variant 0.21 streptomycin Uncertain significance
gid 4408273 c.-72delG upstream_gene_variant 0.51 streptomycin