TB-Profiler result

Run: ERR3276106
Summary

Run ID: ERR3276106

Sample name:

Date: 2024-03-27T03:16:58.740083

Number of reads: 2520156

Percentage reads mapped: 99.98

Median coverage: 46.0

Strain: lineage4.4.1.1

Spoligotype:

Drug-resistance: Sensitive

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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 1.0
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 1.0
lineage4.4 Euro-American None 1.0
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7844 c.543C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin 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 1305166 p.His746Tyr missense_variant 1.0 clofazimine
pretomanid
delamanid
embR 1417256 p.Gly31Ala missense_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.1 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 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 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 1.0 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
Rv2477c 2782409 p.Ala545Val missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin Uncertain significance
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448554 c.51C>A synonymous_variant 1.0 ethionamide
Rv3083 3448608 c.105G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626124 p.Ala164Ser missense_variant 1.0 bedaquiline
rifampicin
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246904 p.Val131Met missense_variant 1.0 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 1.0 capreomycin
amikacin
kanamycin