TB-Profiler result

Run: ERR4830826
Summary

Run ID: ERR4830826

Sample name:

Date: 2024-10-04T21:54:11.976315

Number of reads: 2360963

Percentage reads mapped: 99.69

Median coverage: 72.5

Strain: lineage4.2.2.2;lineage4.8

Spoligotype:

Drug-resistance: HR-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 0.13
lineage4.2 Euro-American None 0.12
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.82
lineage4.2.2.2 Euro-American (Ural) None 0.13
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA p.Phe58Leu Assoc w R
streptomycin gid p.Gly69Asp Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Met1? 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
katG 2155168 p.Ser315Thr missense_variant 0.13 isoniazid Assoc w R High-level resistance
pncA 2289068 p.Phe58Leu missense_variant 0.17 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.15 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.14 ethambutol Assoc w R
ethA 4327472 p.Met1? start_lost 0.21 ethionamide Assoc w R
gid 4407997 p.Gly69Asp missense_variant 0.12 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
dnaA 499 p.Ser167Arg missense_variant 0.19 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8688 p.Ala463Ser missense_variant 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13705 c.-147G>A upstream_gene_variant 0.84 isoniazid Uncertain significance
mshA 576077 c.730C>T synonymous_variant 0.15 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
rpoB 760975 p.Met390Thr missense_variant 0.85 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254598 c.-65dupA upstream_gene_variant 0.87 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.85 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1475090 n.1433A>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.13 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 0.15 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 0.17 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.77 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726146 c.-47_-46insT upstream_gene_variant 0.23 isoniazid Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.87 capreomycin
thyA 3074100 p.Asp124Glu missense_variant 0.89 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.17 cycloserine
ald 3086767 c.-53A>C upstream_gene_variant 0.81 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.22 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267715 c.1122G>A synonymous_variant 0.92 ethambutol Not assoc w R - Interim
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 0.14 kanamycin
capreomycin
amikacin