TB-Profiler result

Run: ERR2513859
Summary

Run ID: ERR2513859

Sample name:

Date: 2024-04-14T07:10:15.492244

Number of reads: 4182330

Percentage reads mapped: 99.57

Median coverage: 94.0

Strain: lineage4.1.1.3.1;lineage4.8.2

Spoligotype:

Drug-resistance: Pre-XDR-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 0.88
lineage4.1.1.3 Euro-American (X-type) RD193 0.89
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.1
lineage4.1.1 Euro-American (X-type) None 0.88
lineage4.1.1.3.1 Euro-American (X-type) RD193 0.87
lineage4.8.2 Euro-American (mainly T) RD219 0.08
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ile491Phe Assoc w R
isoniazid
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.86 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761277 p.Ile491Phe missense_variant 0.79 rifampicin Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.85 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.9 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 0.87 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8135 c.834C>T synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.89 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.12 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.89 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
rplC 800219 c.-590T>C upstream_gene_variant 0.89 linezolid
fbiC 1303601 p.Glu224Gly missense_variant 0.82 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.39 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.85 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.19 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
Rv1979c 2223372 c.-208C>G upstream_gene_variant 0.84 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223445 c.-281C>A upstream_gene_variant 0.17 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.12 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.89 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.81 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625836 p.Met260Val missense_variant 0.16 bedaquiline
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.91 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.86 ethambutol Not assoc w R
ubiA 4269540 c.294C>T synonymous_variant 0.9 ethambutol Not assoc w R
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 0.89 capreomycin
amikacin
kanamycin