TB-Profiler result

Run: ERR1213930
Summary

Run ID: ERR1213930

Sample name:

Date: 2024-04-15T23:33:00.665200

Number of reads: 4865630

Percentage reads mapped: 92.47

Median coverage: 52.0

Strain: lineage4.3.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.2 Euro-American (LAM) None 0.99
lineage4 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 rrs n.462C>T Uncertain significance Mutation from literature
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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance Mutation from literature
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 8619 c.1318T>C synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8627 c.1326C>G synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 8636 c.1335A>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
nusG 734475 c.222T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_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
mmpL5 776230 c.2251T>C synonymous_variant 0.14 clofazimine
bedaquiline
mmpL5 776234 c.2247A>G synonymous_variant 0.12 clofazimine
bedaquiline
mmpL5 777455 c.1026G>C synonymous_variant 0.14 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.33 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.55 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445delCinsTT non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.6 capreomycin
linezolid Uncertain significance
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476746 n.3089T>A non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476755 n.3098G>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476759 n.3102T>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
fabG1 1674037 p.Gln200Glu missense_variant 0.17 ethionamide
isoniazid
inhA 1674051 c.-151A>G upstream_gene_variant 0.15 ethionamide
isoniazid
inhA 1674054 c.-148T>C upstream_gene_variant 0.13 ethionamide
isoniazid
inhA 1674060 c.-142A>G upstream_gene_variant 0.16 ethionamide
isoniazid
inhA 1674063 c.-139G>C upstream_gene_variant 0.16 ethionamide
isoniazid
fabG1 1674079 p.Pro214Ala missense_variant 0.19 ethionamide
isoniazid
inhA 1674570 c.369G>C synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674589 p.Met130Leu missense_variant 0.18 ethionamide
isoniazid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.97 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.97 pyrazinamide Not assoc w R
clpC1 4039064 c.1641C>A synonymous_variant 0.21 pyrazinamide
clpC1 4039079 c.1626C>G synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
clpC1 4039928 c.775_777delAGCinsTCG synonymous_variant 0.13 pyrazinamide
clpC1 4039937 c.768G>C synonymous_variant 0.12 pyrazinamide
clpC1 4039946 c.759A>C synonymous_variant 0.13 pyrazinamide
clpC1 4040063 c.642G>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
embC 4240853 c.991C>T synonymous_variant 0.13 ethambutol Not assoc w R - Interim
embC 4242498 p.Arg879Lys missense_variant 0.94 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4269372 c.-536G>A upstream_gene_variant 0.14 ethambutol
ubiA 4269380 p.Val152Ile missense_variant 0.13 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 0.13 ethambutol Not assoc w R
aftB 4269390 c.-554G>C upstream_gene_variant 0.12 ethambutol
aftB 4269402 c.-566T>C upstream_gene_variant 0.14 ethambutol
ubiA 4269411 c.423T>C synonymous_variant 0.13 ethambutol Not assoc w R - Interim
aftB 4269414 c.-578T>C upstream_gene_variant 0.13 ethambutol
aftB 4269420 c.-584T>C upstream_gene_variant 0.12 ethambutol
ubiA 4269424 p.Ala137Gly missense_variant 0.13 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
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R