TB-Profiler result

Run: ERR1034625
Summary

Run ID: ERR1034625

Sample name:

Date: 2024-04-16T11:52:30.975228

Number of reads: 9871408

Percentage reads mapped: 99.34

Median coverage: 227.0

Strain: lineage4.1.1.1;lineage4.1.2

Spoligotype:

Drug-resistance: Other

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 1.0
lineage4.1.1.1 Euro-American (X-type) RD183 0.38
lineage4.1.2 Euro-American None 0.6
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.38
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 ethR p.Phe110Leu Uncertain significance Mutation from literature
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
ethR 4327876 p.Phe110Leu missense_variant 0.62 ethionamide Uncertain significance Mutation from literature
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
dnaA 108 c.108C>T synonymous_variant 0.6 isoniazid Not assoc w R - Interim
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13844 c.-286T>G upstream_gene_variant 0.37 isoniazid
fgd1 491591 p.Lys270Met missense_variant 0.56 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.58 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800200 c.-609C>G upstream_gene_variant 0.6 linezolid
rplC 800219 c.-590T>C upstream_gene_variant 0.43 linezolid
rplC 800889 c.81C>A synonymous_variant 0.61 linezolid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476417 n.2760T>C non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
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
PPE35 2168303 c.2310G>T synonymous_variant 0.6 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.6 isoniazid
ahpC 2726210 c.18T>C synonymous_variant 0.38 isoniazid Not assoc w R - Interim
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.25 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3613023 p.Pro32Ser missense_variant 0.62 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641447 p.Thr302Met missense_variant 0.44 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
alr 3840263 c.1158C>T synonymous_variant 0.58 cycloserine
rpoA 3877553 p.Glu319Lys missense_variant 0.41 rifampicin Not assoc w R
embC 4240897 c.1035C>G synonymous_variant 0.46 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.38 ethambutol Not assoc w R
ethA 4327587 c.-114C>T upstream_gene_variant 0.42 ethionamide
whiB6 4338498 p.Glu8Asp missense_variant 0.35 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.99 capreomycin
amikacin
kanamycin