TB-Profiler result

Run: ERR11082673
Summary

Run ID: ERR11082673

Sample name:

Date: 2024-10-04T13:54:27.840071

Number of reads: 4705245

Percentage reads mapped: 99.69

Median coverage: 153.0

Strain: lineage4.8

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 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 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.Asp435Val Assoc w R
p.Ser450Gln Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid katG p.Ser315Arg Assoc w R High-level resistance
ethambutol embB p.Gly406Ala Assoc w R
p.His1002Arg Uncertain significance Mutation from literature
pyrazinamide pncA p.Val139Gly Assoc w R
c.-11A>G Assoc w R
streptomycin gid c.351delG Assoc w R
c.48delT Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA p.Leu74Pro Uncertain significance Mutation from literature
c.564delG Assoc w R
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 761110 p.Asp435Val missense_variant 0.79 rifampicin Assoc w R
rpoB 761154 p.Ser450Gln missense_variant 0.18 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
tlyA 1918160 p.Leu74Pro missense_variant 0.12 capreomycin Uncertain significance Mutation from literature
tlyA 1918499 c.564delG frameshift_variant 0.75 capreomycin Assoc w R
katG 2155167 p.Ser315Arg missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288826 p.Val139Gly missense_variant 0.59 pyrazinamide Assoc w R
pncA 2289252 c.-11A>G upstream_gene_variant 0.32 pyrazinamide Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.18 ethambutol Assoc w R
embB 4249518 p.His1002Arg missense_variant 0.83 ethambutol Uncertain significance Mutation from literature
gid 4407851 c.351delG frameshift_variant 0.13 streptomycin Assoc w R
gid 4408154 c.48delT frameshift_variant 0.13 streptomycin 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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
fbiC 1303747 p.Thr273Ala missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471862 n.17T>G non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
thyX 3067226 p.Glu240Asp missense_variant 1.0 para-aminosalicylic_acid
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246151 c.2919A>G synonymous_variant 1.0 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
gid 4407794 p.Arg137Trp missense_variant 0.12 streptomycin Uncertain significance