TB-Profiler result

Run: ERR4815555
Summary

Run ID: ERR4815555

Sample name:

Date: 2024-10-04T14:48:15.730175

Number of reads: 4017108

Percentage reads mapped: 89.95

Median coverage: 91.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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
lineage4.1.2 Euro-American None 0.99
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.99
lineage4 Euro-American None 0.98
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
dnaA 414 c.414G>A synonymous_variant 1.0 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 8588 c.1287G>A synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.91 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.96 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.92 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.97 rifampicin Not assoc w R
rpoC 763456 c.87A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.14 rifampicin
rpoC 763853 p.Val162Ile missense_variant 0.13 rifampicin
rpoC 764236 c.867G>A synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>C synonymous_variant 0.13 rifampicin
rpoC 764651 p.Ser428Thr missense_variant 0.13 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.16 rifampicin Not assoc w R
rpoC 764815 c.1446A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 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
fbiC 1304808 c.1878C>G synonymous_variant 0.18 pretomanid
delamanid
clofazimine
fbiC 1304811 c.1881C>G synonymous_variant 0.19 pretomanid
delamanid
clofazimine
fbiC 1304817 c.1887T>C synonymous_variant 0.24 pretomanid
delamanid
clofazimine
fbiC 1304829 c.1899T>C synonymous_variant 0.31 pretomanid
delamanid
clofazimine
fbiC 1304832 c.1902C>T synonymous_variant 0.3 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304856 c.1926C>G synonymous_variant 0.61 pretomanid
delamanid
clofazimine
fbiC 1304862 c.1932G>A synonymous_variant 0.28 pretomanid
delamanid
clofazimine
fbiC 1304869 c.1939C>T synonymous_variant 0.23 pretomanid
delamanid
clofazimine
fbiC 1304875 p.Ile649Val missense_variant 0.2 pretomanid
delamanid
clofazimine
fbiC 1304883 p.Glu651Asp missense_variant 0.17 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476707 n.3050C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
inhA 1674888 c.687C>G synonymous_variant 0.14 isoniazid
ethionamide
inhA 1674903 c.702T>C synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674904 p.Ala235Pro missense_variant 0.15 isoniazid
ethionamide
rpsA 1833971 c.430C>T synonymous_variant 0.14 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.13 pyrazinamide
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
kasA 2518076 c.-39C>T upstream_gene_variant 0.99 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.24 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.17 capreomycin
thyX 3067850 c.96A>C synonymous_variant 0.12 para-aminosalicylic_acid
thyA 3074205 p.Glu89Asp missense_variant 0.13 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878716 c.-209C>G upstream_gene_variant 0.13 rifampicin
clpC1 4038749 c.1956C>G synonymous_variant 0.14 pyrazinamide
clpC1 4038755 c.1950G>T synonymous_variant 0.14 pyrazinamide
clpC1 4038770 c.1935C>T synonymous_variant 0.14 pyrazinamide
embC 4239298 c.-565C>T upstream_gene_variant 0.98 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 0.95 ethambutol Not assoc w R
embA 4245137 c.1905T>C synonymous_variant 0.14 ethambutol
embA 4245146 c.1914G>A synonymous_variant 0.14 ethambutol
embA 4245149 c.1917C>G synonymous_variant 0.16 ethambutol
embA 4245153 p.Ile641Val missense_variant 0.17 ethambutol
embA 4245182 c.1950T>C synonymous_variant 0.2 ethambutol
embA 4245189 c.1957C>T synonymous_variant 0.18 ethambutol
embA 4245198 p.Leu656Ile missense_variant 0.16 ethambutol
embA 4245207 c.1975T>C synonymous_variant 0.14 ethambutol
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