TB-Profiler result

Run: ERR12268474
Summary

Run ID: ERR12268474

Sample name:

Date: 2024-10-04T22:34:59.585479

Number of reads: 2476120

Percentage reads mapped: 99.71

Median coverage: 64.0

Strain: lineage4.1.2.1;lineage4.3.4.1

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 0.33
lineage4.1 Euro-American None 0.68
lineage4.1.2 Euro-American None 0.67
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.68
lineage4.3.4.1 Euro-American (LAM) RD174 0.31
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.34
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 6688 c.-614C>G upstream_gene_variant 0.65 levofloxacin
moxifloxacin
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 8334 p.Met345Val missense_variant 0.28 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13483 p.Ala26Thr missense_variant 0.33 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.68 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.79 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.64 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.65 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.31 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.7 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 781276 c.-284A>C upstream_gene_variant 0.66 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1303554 c.624G>A synonymous_variant 0.71 pretomanid
delamanid
clofazimine
sigE 1364434 p.Arg8Trp missense_variant 0.24 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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 2222854 p.Ile104Thr missense_variant 0.29 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.71 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.38 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339215 p.Gln33Pro missense_variant 0.59 pretomanid
delamanid
clofazimine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.3 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.43 pyrazinamide Not assoc w R
clpC1 4039991 c.714G>A synonymous_variant 0.34 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.64 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 0.56 ethambutol Not assoc w R
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
gid 4408029 c.174C>G synonymous_variant 0.64 streptomycin Not assoc w R - Interim
gid 4408156 p.Leu16Arg missense_variant 0.47 streptomycin Not assoc w R