TB-Profiler result

Run: SRR28393367
Summary

Run ID: SRR28393367

Sample name:

Date: 2024-05-22T17:40:49.404209

Number of reads: 9346819

Percentage reads mapped: 99.59

Median coverage: 273.0

Strain: lineage4.1.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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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 0.25
lineage4.1 Euro-American None 0.76
lineage4.1.2 Euro-American None 0.74
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.77
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.22
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Pro54Leu Assoc w R
p.His51Arg Assoc w R
streptomycin gid c.115delC Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Gln254* Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289081 p.Pro54Leu missense_variant 0.54 pyrazinamide Assoc w R
pncA 2289090 p.His51Arg missense_variant 0.24 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.75 ethambutol Assoc w R
ethA 4326714 p.Gln254* stop_gained 0.79 ethionamide Assoc w R
gid 4408087 c.115delC frameshift_variant 0.78 streptomycin Assoc w R
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 0.19 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 491591 p.Lys270Met missense_variant 0.78 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 574862 c.-486T>C upstream_gene_variant 0.25 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.77 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.76 ethionamide Uncertain significance
Rv0565c 657730 c.-260A>C upstream_gene_variant 0.24 ethionamide
rpoB 760115 c.309C>T synonymous_variant 0.8 rifampicin Not assoc w R
rpoB 761880 p.Ala692Thr missense_variant 0.25 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.25 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.79 rifampicin Not assoc w R
rpoC 765639 p.Glu757Ala missense_variant 0.2 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.71 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801047 p.Tyr80Cys missense_variant 0.21 linezolid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.24 pyrazinamide Not assoc w R - Interim
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
katG 2154459 c.1653C>T synonymous_variant 0.23 isoniazid Not assoc w R - Interim
PPE35 2170515 p.Gly33Ala missense_variant 0.76 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2288758 p.Gly162Arg missense_variant 0.22 pyrazinamide Uncertain significance
kasA 2518076 c.-39C>T upstream_gene_variant 0.75 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.24 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.14 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.18 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.16 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.25 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626093 p.Gly174Ala missense_variant 0.77 bedaquiline Uncertain significance
rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.23 pyrazinamide Not assoc w R
panD 4044824 c.-543C>G upstream_gene_variant 0.24 pyrazinamide
glpK 4139183 c.572delG frameshift_variant 0.66 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.73 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 0.75 ethambutol Not assoc w R
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 1.0 capreomycin
amikacin
kanamycin
gid 4407720 c.483C>G synonymous_variant 0.2 streptomycin Not assoc w R - Interim
gid 4408003 p.Asp67Gly missense_variant 0.23 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.24 streptomycin Not assoc w R