TB-Profiler result

Run: ERR6358742
Summary

Run ID: ERR6358742

Sample name:

Date: 2024-04-15T00:08:30.205530

Number of reads: 7002996

Percentage reads mapped: 99.62

Median coverage: 212.0

Strain: lineage4.2.2.2;lineage4.6.1.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.3
lineage4.6 Euro-American None 0.71
lineage4.2 Euro-American None 0.31
lineage4.6.1.2 Euro-American RD724 0.69
lineage4 Euro-American None 1.0
lineage4.6.1 Euro-American (Uganda) RD724 0.7
lineage4.2.2.2 Euro-American (Ural) None 0.31
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.His43Pro Assoc w R - Interim
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1215_1224delGTTGAATTAC 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 0.79 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.69 isoniazid Assoc w R High-level resistance
pncA 2289114 p.His43Pro missense_variant 0.69 pyrazinamide Assoc w R - Interim
embB 4247429 p.Met306Val missense_variant 0.7 ethambutol Assoc w R
ethA 4326249 c.1215_1224delGTTGAATTAC frameshift_variant 0.63 ethionamide 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 7539 p.Thr80Ala missense_variant 0.66 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8688 p.Ala463Ser missense_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
mshA 576077 c.730C>T synonymous_variant 0.31 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv0565c 657425 p.Gly16Ser missense_variant 0.36 ethionamide Uncertain significance
rpoB 761489 c.1683G>A synonymous_variant 0.32 rifampicin Not assoc w R
rpoC 764660 p.Val431Met missense_variant 0.68 rifampicin Uncertain significance
rpoC 764810 p.Pro481Thr missense_variant 0.72 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.27 linezolid
Rv1129c 1254638 c.-104C>T upstream_gene_variant 0.31 moxifloxacin
levofloxacin
rifampicin
isoniazid
embR 1416410 p.Leu313Arg missense_variant 0.7 ethambutol Uncertain significance
embR 1417485 c.-138T>G upstream_gene_variant 0.3 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
bacA 2063685 c.1044G>A synonymous_variant 0.37 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2170692 c.-80T>G upstream_gene_variant 0.67 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 2288800 p.Arg148Cys missense_variant 0.3 pyrazinamide
eis 2714308 p.Pro342Leu missense_variant 0.65 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2681 2996876 c.138A>C synonymous_variant 0.69 capreomycin Not assoc w R
Rv2752c 3065920 p.Pro91Leu missense_variant 0.67 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.33 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.29 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.26 cycloserine
whiB7 3569029 c.-350A>G upstream_gene_variant 0.64 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.27 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4139670 p.Cys29Tyr missense_variant 0.72 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Not assoc w R
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245055 p.Thr608Asn missense_variant 0.74 ethambutol Uncertain significance
ubiA 4269124 p.Ala237Val missense_variant 0.69 ethambutol Uncertain significance
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 4408094 p.Gly37Arg missense_variant 0.68 streptomycin Uncertain significance