TB-Profiler result

Run: ERR4815695
Summary

Run ID: ERR4815695

Sample name:

Date: 2024-10-04T01:53:57.972838

Number of reads: 1807710

Percentage reads mapped: 99.16

Median coverage: 38.0

Strain: lineage1.2.1.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.2 Indo-Oceanic RD239 0.2
lineage4.3 Euro-American (LAM) None 0.78
lineage4 Euro-American None 0.81
lineage1 Indo-Oceanic RD239 0.17
lineage1.2.1.2.1 Indo-Oceanic RD239 0.17
lineage1.2.1 Indo-Oceanic RD239 0.17
lineage4.3.3 Euro-American (LAM) RD115 0.76
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 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 8040 p.Gly247Ser missense_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.22 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.32 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 13589 c.-31G>A upstream_gene_variant 0.76 isoniazid Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 763531 c.162G>C synonymous_variant 0.34 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.79 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
rplC 800357 c.-452C>A upstream_gene_variant 0.21 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406312 c.1029T>C synonymous_variant 0.24 streptomycin Not assoc w R
pyrazinamide Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.68 pyrazinamide Not assoc w R - Interim
tsnR 1853663 p.Gly20Ser missense_variant 0.88 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 2167926 p.Leu896Ser missense_variant 0.19 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.14 bedaquiline Not assoc w R - Interim
clofazimine 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
kasA 2518919 p.Gly269Ser missense_variant 0.84 isoniazid
Rv2477c 2782724 p.Ala440Val missense_variant 0.82 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783243 p.Thr267Ile missense_variant 0.73 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2680 2996056 c.-49G>C upstream_gene_variant 0.15 capreomycin
Rv2680 2996107 p.Leu1? start_lost 0.33 capreomycin Uncertain significance
Rv2752c 3065371 p.Arg274Thr missense_variant 0.75 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyA 3073868 p.Thr202Ala missense_variant 0.78 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568488 c.191delG frameshift_variant 0.27 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640557 c.15T>C synonymous_variant 0.16 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 0.82 pyrazinamide Not assoc w R
clpC1 4039004 c.1701C>T synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.26 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.21 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247578 c.1065G>A synonymous_variant 0.3 ethambutol Not assoc w R
embB 4248064 c.1551G>C synonymous_variant 0.81 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.26 ethambutol Not assoc w R
whiB6 4338361 p.Arg54Gln missense_variant 0.19 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin 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 4338603 c.-82C>T upstream_gene_variant 0.17 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 4407588 c.615A>G synonymous_variant 0.28 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.3 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.78 streptomycin Not assoc w R