TB-Profiler result

Run: SRR28393588
Summary

Run ID: SRR28393588

Sample name:

Date: 2024-05-22T18:56:58.258768

Number of reads: 5232674

Percentage reads mapped: 99.61

Median coverage: 147.0

Strain: lineage4.1.2.1;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
lineage4.1 Euro-American None 0.68
lineage4.1.2 Euro-American None 0.7
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.7
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.29
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA p.Thr135Pro Assoc w R
streptomycin rpsL p.Lys88Thr Uncertain significance Mutation from literature
gid c.351delG 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781822 p.Lys88Thr missense_variant 0.62 streptomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.34 isoniazid Assoc w R High-level resistance
pncA 2288839 p.Thr135Pro missense_variant 0.35 pyrazinamide Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.29 ethambutol Assoc w R
gid 4407851 c.351delG frameshift_variant 0.43 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
gyrA 7585 p.Ser95Thr missense_variant 0.72 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.67 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.69 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.7 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.62 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.65 rifampicin Not assoc w R
rpoB 760555 p.Glu250Gly missense_variant 0.74 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 0.7 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
fbiC 1302920 c.-11G>A upstream_gene_variant 0.66 clofazimine Uncertain significance
pretomanid
delamanid 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 0.24 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.69 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063078 c.1650dupG frameshift_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.56 isoniazid
folC 2746277 p.Asp441Gly missense_variant 0.75 para-aminosalicylic_acid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.17 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.16 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.7 cycloserine
ald 3087095 c.276C>T synonymous_variant 0.3 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.76 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.37 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.72 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.69 ethambutol Not assoc w R
ubiA 4269015 p.Glu273Asp missense_variant 0.24 ethambutol Uncertain significance
ethA 4326908 p.Thr189Lys missense_variant 0.33 ethionamide Uncertain significance
ethA 4327761 c.-288C>T upstream_gene_variant 0.68 ethionamide
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 0.72 capreomycin
amikacin
kanamycin