TB-Profiler result

Run: SRR2100206
Summary

Run ID: SRR2100206

Sample name:

Date: 2024-10-04T13:34:29.688898

Number of reads: 6873695

Percentage reads mapped: 99.59

Median coverage: 158.0

Strain: lineage4.1.2

Spoligotype:

Drug-resistance: RR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.96
lineage4.1.2 Euro-American None 0.96
lineage4 Euro-American 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 rpoB p.Leu443Trp Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Thr444Pro Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
c.1335_1337delCAA Assoc w R - Interim
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
rpoB 761134 p.Leu443Trp missense_variant 0.88 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761136 p.Thr444Pro missense_variant 0.89 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761139 c.1335_1337delCAA disruptive_inframe_deletion 0.89 rifampicin Assoc w R - Interim
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.98 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.94 rifampicin Not assoc w R
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
embR 1417140 p.Ala70Ser missense_variant 0.93 ethambutol Not assoc w R
embR 1418018 c.-671C>T upstream_gene_variant 0.95 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673249 c.-953C>T upstream_gene_variant 0.91 isoniazid
ethionamide
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
folC 2747022 p.Val193Ile missense_variant 0.96 para-aminosalicylic_acid
Rv2680 2996155 c.51C>T synonymous_variant 0.82 capreomycin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.98 cycloserine
Rv3083 3448894 p.Tyr131Asp missense_variant 0.97 ethionamide Uncertain significance
Rv3083 3449642 p.Asn380Ser missense_variant 0.93 ethionamide Uncertain significance
whiB7 3568921 c.-242G>C upstream_gene_variant 0.95 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641164 p.Ile208Val missense_variant 0.94 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.96 ethambutol Not assoc w R
aftB 4268861 c.-25T>C upstream_gene_variant 0.91 ethambutol 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 1.0 kanamycin
capreomycin
amikacin