TB-Profiler result

Run: ERR9119650
Summary

Run ID: ERR9119650

Sample name:

Date: 2024-10-03T22:22:30.102269

Number of reads: 6694598

Percentage reads mapped: 99.6

Median coverage: 202.0

Strain: lineage4.2.1;lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 0.37
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.63
lineage4.2.1 Euro-American (TUR) None 0.4
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
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
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 5524 c.285C>A synonymous_variant 0.6 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.36 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13363 c.195delC frameshift_variant 0.64 isoniazid Uncertain significance
Rv0010c 13442 p.Leu39Phe missense_variant 0.63 isoniazid Uncertain significance
fgd1 491247 c.465C>T synonymous_variant 0.38 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
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
rplC 800204 c.-605T>C upstream_gene_variant 0.35 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.64 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.37 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 0.27 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 0.36 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.62 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.37 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.62 capreomycin
ald 3086742 c.-78A>C upstream_gene_variant 0.36 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.36 cycloserine
Rv3083 3448428 c.-76A>C upstream_gene_variant 0.5 ethionamide
lpqB 3623222 c.1689A>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.46 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878051 p.Arg153Trp missense_variant 0.68 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249354 c.2841G>C synonymous_variant 0.63 ethambutol Not assoc w R - Interim
embB 4249594 c.3081G>A synonymous_variant 0.4 ethambutol Not assoc w R - Interim
ethA 4328376 c.-903G>C upstream_gene_variant 0.38 ethionamide
whiB6 4338561 c.-40T>C upstream_gene_variant 0.59 kanamycin
capreomycin
amikacin
whiB6 4338590 c.-69A>T upstream_gene_variant 0.62 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 0.46 kanamycin
capreomycin
amikacin