TB-Profiler result

Run: ERR4821578
Summary

Run ID: ERR4821578

Sample name:

Date: 2024-10-04T00:02:24.765597

Number of reads: 1555803

Percentage reads mapped: 87.27

Median coverage: 33.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.99
lineage4.1.2 Euro-American None 0.99
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American None 1.0
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13605 c.-47G>T upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.91 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.97 isoniazid Not assoc w R
ethionamide Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.86 rifampicin Not assoc w R
rpoB 760674 c.868T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761189 c.1383T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T 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
rplC 801405 c.597T>C synonymous_variant 0.18 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834546 c.1005T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834618 c.1077G>C synonymous_variant 0.23 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 1.0 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.2 capreomycin Uncertain significance
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 3877764 c.744C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoA 3877791 c.717C>G synonymous_variant 0.27 rifampicin
rpoA 3877818 c.690A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoA 3878806 c.-299C>G upstream_gene_variant 0.23 rifampicin
rpoA 3878809 c.-302T>C upstream_gene_variant 0.23 rifampicin
rpoA 3878824 c.-317G>C upstream_gene_variant 0.17 rifampicin
rpoA 3878836 c.-331_-329delAAGinsTCC upstream_gene_variant 0.17 rifampicin
rpoA 3878853 c.-346G>A upstream_gene_variant 0.21 rifampicin
clpC1 4038530 p.Glu725Asp missense_variant 0.19 pyrazinamide
clpC1 4038596 c.2109A>G synonymous_variant 0.32 pyrazinamide
clpC1 4038671 c.2034T>C synonymous_variant 0.28 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.18 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.28 pyrazinamide Not assoc w R - Interim
clpC1 4040033 c.672G>C synonymous_variant 0.28 pyrazinamide
clpC1 4040036 c.669C>G synonymous_variant 0.27 pyrazinamide
clpC1 4040105 c.600C>G synonymous_variant 0.21 pyrazinamide
glpK 4139183 c.572dupG frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 1.0 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 0.9 ethambutol Not assoc w R
embA 4245010 p.Ala593Val missense_variant 1.0 ethambutol Uncertain significance
embA 4245083 c.1851A>C synonymous_variant 0.2 ethambutol
embA 4245089 c.1857G>C synonymous_variant 0.2 ethambutol
embA 4245092 c.1860C>G synonymous_variant 0.2 ethambutol
embA 4245101 c.1869G>C synonymous_variant 0.19 ethambutol
embB 4247909 c.1396T>C synonymous_variant 0.19 ethambutol
embB 4248097 c.1584C>G 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
gid 4407635 p.Thr190Ala missense_variant 1.0 streptomycin Uncertain significance