TB-Profiler result

Run: ERR1035312
Summary

Run ID: ERR1035312

Sample name:

Date: 2024-04-16T06:46:38.681956

Number of reads: 5848725

Percentage reads mapped: 98.7

Median coverage: 40.0

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Trp Assoc w R
isoniazid
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
pyrazinamide pncA p.Trp68Arg Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine ald c.436_437dupGC Mutation from literature
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 7570 p.Ala90Val missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Trp missense_variant 1.0 rifampicin Assoc w R
pncA 2289040 p.Trp68Arg missense_variant 1.0 pyrazinamide Assoc w R
ald 3087252 c.436_437dupGC frameshift_variant 0.96 cycloserine Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol 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
dnaA 1081 p.Ile361Val missense_variant 1.0 isoniazid Uncertain significance
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 8040 p.Gly247Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764582 c.1213C>T synonymous_variant 1.0 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765804 p.Thr812Ile missense_variant 0.33 rifampicin Uncertain significance
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.47 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.61 capreomycin
linezolid Uncertain significance
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1473981 n.324delGinsAT non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.36 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rpsA 1833678 p.Val46Ala missense_variant 1.0 pyrazinamide
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
bacA 2063078 c.1650dupG frameshift_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.97 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 1.0 isoniazid
Rv2752c 3066014 c.177dupG frameshift_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.97 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
glpK 4138443 p.Ile438Thr missense_variant 0.22 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242182 p.Ala774Ser missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245187 p.Thr652Lys missense_variant 1.0 ethambutol Uncertain significance
ubiA 4268987 p.Val283Leu 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
whiB6 4338862 c.-349_-342delAGACTTTC upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408105 p.Arg33Pro missense_variant 1.0 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R