TB-Profiler result

Run: ERR4020182
Summary

Run ID: ERR4020182

Sample name:

Date: 2024-04-15T13:53:29.873290

Number of reads: 3610510

Percentage reads mapped: 99.73

Median coverage: 106.0

Strain: lineage4.3.4.2.1;lineage4.4.1.1

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 0.2
lineage4.4.1 Euro-American (S-type) None 0.79
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.77
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.19
lineage4.3.4 Euro-American (LAM) RD174 0.2
lineage4.3.4.2 Euro-American (LAM) RD174 0.21
lineage4.4 Euro-American None 0.78
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Met434Ile Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Ser450Trp Assoc w R
p.Ile491Phe Assoc w R
rpoC p.Ile491Thr Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.His51Asp Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
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 761108 p.Met434Ile missense_variant 0.78 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761155 p.Ser450Trp missense_variant 0.24 rifampicin Assoc w R
rpoB 761277 p.Ile491Phe missense_variant 0.72 rifampicin Assoc w R
rpoC 764841 p.Ile491Thr missense_variant 0.16 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.84 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289091 p.His51Asp missense_variant 0.84 pyrazinamide 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
gyrB 6140 p.Val301Leu missense_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 9138 p.Gln613Glu missense_variant 0.83 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
rpoB 761406 p.Val534Met missense_variant 0.88 rifampicin Uncertain significance
rpoB 761558 c.1752C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.14 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777416 c.1065G>T synonymous_variant 0.79 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1258c 1406353 p.Pro330Thr missense_variant 0.28 streptomycin
isoniazid
pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673380 c.-60C>G upstream_gene_variant 0.1 ethionamide
isoniazid
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
ndh 2102990 p.Val18Ala missense_variant 0.81 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 0.75 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.76 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518496 c.382C>T synonymous_variant 0.8 isoniazid
Rv2752c 3065023 p.Pro390Leu missense_variant 0.84 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.2 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448522 p.Val7Phe missense_variant 0.78 ethionamide Uncertain significance
Rv3083 3448608 c.105G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.8 streptomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
Rv3236c 3612009 p.Ala370Thr missense_variant 0.2 pyrazinamide Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.73 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.18 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.28 pyrazinamide Not assoc w R
glpK 4138401 c.1354delG frameshift_variant 0.81 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.82 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGA frameshift_variant&missense_variant 0.21 ethambutol
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 4408156 p.Leu16Arg missense_variant 0.27 streptomycin Not assoc w R