TB-Profiler result

Run: ERR1034911
Summary

Run ID: ERR1034911

Sample name:

Date: 2024-04-14T09:22:01.954121

Number of reads: 6581217

Percentage reads mapped: 99.01

Median coverage: 143.0

Strain: lineage4.3.3;lineage4.3.4.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.49
lineage4.3.4 Euro-American (LAM) RD174 0.51
lineage4.3.4.2 Euro-American (LAM) RD174 0.52
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Glu Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Asp435Val Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Ile194Thr Uncertain significance Mutation from literature
katG p.Ser315Thr Assoc w R High-level resistance
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol embB p.Met423Thr Uncertain significance Mutation from literature
pyrazinamide pncA c.389_390insA Assoc w R
p.Val125Gly Assoc w R
streptomycin gid p.Ala80Pro Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ile194Thr Uncertain significance Mutation from literature
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 761100 p.Gln432Glu missense_variant 0.57 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761110 p.Asp435Val missense_variant 0.56 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.49 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.45 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
inhA 1674782 p.Ile194Thr missense_variant 0.56 isoniazid Uncertain significance Mutation from literature
ethionamide Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.52 isoniazid Assoc w R High-level resistance
pncA 2288852 c.389_390insA frameshift_variant 0.42 pyrazinamide Assoc w R
pncA 2288868 p.Val125Gly missense_variant 0.56 pyrazinamide Assoc w R
ahpC 2726145 c.-48G>A upstream_gene_variant 0.44 isoniazid Uncertain significance Mutation from literature
embB 4247781 p.Met423Thr missense_variant 0.48 ethambutol Uncertain significance Mutation from literature
gid 4407965 p.Ala80Pro missense_variant 0.54 streptomycin 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 6140 p.Val301Leu missense_variant 0.53 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 8040 p.Gly247Ser missense_variant 0.51 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 490655 c.-128T>C upstream_gene_variant 0.47 clofazimine
pretomanid
delamanid
mshA 576160 c.813C>T synonymous_variant 0.5 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rpoC 764817 p.Val483Gly missense_variant 0.18 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
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 800990 p.Lys61Thr missense_variant 0.37 linezolid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.12 capreomycin
linezolid Uncertain significance
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.1 capreomycin
linezolid
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.1 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289743 c.-502A>G upstream_gene_variant 0.17 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.48 isoniazid
thyX 3067954 c.-9G>A upstream_gene_variant 0.5 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.45 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 0.52 cycloserine
rpoA 3877586 p.Leu308Phe missense_variant 0.47 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.44 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGC frameshift_variant&missense_variant 0.51 ethambutol
ethR 4328127 c.579G>C synonymous_variant 0.53 ethionamide Not assoc w R - Interim
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 4408027 p.Leu59Arg missense_variant 0.52 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R