TB-Profiler result

Run: ERR11044603
Summary

Run ID: ERR11044603

Sample name:

Date: 2024-04-15T03:43:00.587839

Number of reads: 4266066

Percentage reads mapped: 99.73

Median coverage: 135.0

Strain: lineage4.4.1.1;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
lineage4.4.1 Euro-American (S-type) None 0.75
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.27
lineage4.4.1.1 Euro-American None 0.75
lineage4.4 Euro-American None 0.74
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
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
katG 2155168 p.Ser315Thr missense_variant 0.74 isoniazid Assoc w R High-level resistance
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 7585 p.Ser95Thr missense_variant 0.77 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.74 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 574783 c.-565C>G upstream_gene_variant 0.28 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.2 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.31 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
Rv1129c 1253330 p.Gly402Glu missense_variant 0.24 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.7 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 0.75 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.27 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.71 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.27 capreomycin
Rv2752c 3065887 p.Val102Ala missense_variant 0.25 ethambutol Uncertain significance
moxifloxacin
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.77 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 0.77 pyrazinamide Not assoc w R
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.29 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.63 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625324 c.1290C>T synonymous_variant 0.32 bedaquiline
rifampicin Not assoc w R - Interim
clpC1 4039729 p.Asp326Asn missense_variant 0.28 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.76 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243190 c.-43G>C upstream_gene_variant 0.72 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 0.76 capreomycin
amikacin
kanamycin