TB-Profiler result

Run: ERR10112361
Summary

Run ID: ERR10112361

Sample name:

Date: 2024-04-16T01:41:50.767654

Number of reads: 1979540

Percentage reads mapped: 99.71

Median coverage: 60.0

Strain: lineage4.3.2.1;lineage4.3.4.2;lineage4.4.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.49
lineage4.3.2 Euro-American (LAM) None 0.33
lineage4.3.2.1 Euro-American (LAM) RD761 0.37
lineage4.4.1 Euro-American (S-type) None 0.41
lineage4 Euro-American None 0.96
lineage4.4.1.1 Euro-American None 0.36
lineage4.3.4.2 Euro-American (LAM) RD174 0.06
lineage4.4 Euro-American None 0.41
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
gyrB 5520 p.Pro94Leu missense_variant 0.39 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6885 p.Phe549Cys missense_variant 0.43 levofloxacin
moxifloxacin
gyrB 7222 c.1983C>T synonymous_variant 0.36 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9138 p.Gln613Glu missense_variant 0.37 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
fgd1 491028 c.246C>T synonymous_variant 0.48 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
mshA 574697 c.-651C>T upstream_gene_variant 0.22 ethionamide Uncertain significance
isoniazid Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.4 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.12 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777416 c.1065G>T synonymous_variant 0.55 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1417839 c.-492C>A upstream_gene_variant 0.42 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.19 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
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
ndh 2102990 p.Val18Ala missense_variant 0.42 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
katG 2154454 p.Glu553Gly missense_variant 0.38 isoniazid
PPE35 2168479 p.Thr712Pro missense_variant 0.43 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.42 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714846 p.Val163Ile missense_variant 0.15 amikacin Not assoc w R
kanamycin Not assoc w R
folC 2746340 p.Ala420Val missense_variant 0.12 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.45 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.96 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.46 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.36 streptomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.31 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.96 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.13 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.42 pyrazinamide Not assoc w R
clpC1 4040252 c.453C>T synonymous_variant 0.29 pyrazinamide
embC 4238963 c.-900C>T upstream_gene_variant 0.43 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.11 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.16 ethambutol Not assoc w R
whiB6 4338466 p.Val19Ala missense_variant 0.11 capreomycin
amikacin
kanamycin
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 0.94 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.45 streptomycin Not assoc w R