TB-Profiler result

Run: DRR130150
Summary

Run ID: DRR130150

Sample name:

Date: 2024-10-03T15:05:10.924393

Number of reads: 2383143

Percentage reads mapped: 99.37

Median coverage: 126.0

Strain: lineage4.2.2

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 1.0
lineage4.2 Euro-American None 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 rpoB p.Leu430Pro Assoc w R
p.Asp435Tyr Assoc w R
p.Ser441Ala Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid ahpC c.-52C>T Uncertain significance Mutation from literature
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
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin Assoc w R
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin Assoc w R
rpoB 761127 p.Ser441Ala missense_variant 1.0 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
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
gyrB 4993 c.-247G>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 7121 p.Pro628Ala missense_variant 0.99 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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
mshA 576077 c.730C>T synonymous_variant 1.0 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
mshA 576224 p.Val293Trp missense_variant 0.99 isoniazid Uncertain significance
ethionamide Uncertain significance
nusG 734613 p.Trp120Cys missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781346 c.-214G>T upstream_gene_variant 1.0 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 1.0 linezolid
Rv1129c 1254519 p.Val6Ile missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254624 c.-90G>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
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 0.99 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2155928 p.Phe62Leu missense_variant 1.0 isoniazid Uncertain significance
Rv1979c 2222537 p.Val210Phe missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3064646 p.Glu516* stop_gained 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.99 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyX 3067949 c.-4C>T upstream_gene_variant 0.99 para-aminosalicylic_acid
thyA 3074042 p.Pro144Ser missense_variant 1.0 para-aminosalicylic_acid
thyA 3074095 c.376delC frameshift_variant 1.0 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087488 c.669C>T synonymous_variant 1.0 cycloserine
whiB7 3568819 c.-140C>G upstream_gene_variant 1.0 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
clpC1 4040110 p.Arg199Gly missense_variant 1.0 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 4239334 c.-529T>C upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244400 p.Leu390Met missense_variant 1.0 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.98 ethambutol Not assoc w R - Interim
embB 4248027 p.Ala505Val missense_variant 1.0 ethambutol Uncertain significance
embB 4249533 p.Ala1007Val missense_variant 1.0 ethambutol Uncertain significance
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 4407988 p.Ala72Asp missense_variant 1.0 streptomycin Uncertain significance