TB-Profiler result

Run: de98fca4-eca4-4366-a5a2-1eedf1f34c80
Summary

Run ID: de98fca4-eca4-4366-a5a2-1eedf1f34c80

Sample name:

Date: 19-05-2024 22:43:00

Number of reads: 546964

Percentage reads mapped: 99.05

Median coverage: 0

Strain:

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
isoniazid
ethambutol embB p.His312Arg Uncertain significance
p.Ala356Val Uncertain significance
p.Tyr384Asn Uncertain significance
p.Asn399Asp Uncertain significance
pyrazinamide
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin rrs n.462C>T Uncertain significance
n.517C>T Assoc w R
amikacin
kanamycin eis c.-10G>C Uncertain significance
c.-10G>C Uncertain significance
capreomycin
clofazimine
ethionamide
para-aminosalicylic_acid
cycloserine
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
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin Assoc w R
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.52 streptomycin Assoc w R
eis 2715342 c.-10G>C upstream_gene_variant 1.0 kanamycin Uncertain significance
kanamycin Uncertain significance
embB 4247448 p.His312Arg missense_variant 0.12 ethambutol Uncertain significance
embB 4247580 p.Ala356Val missense_variant 0.14 ethambutol Uncertain significance
embB 4247663 p.Tyr384Asn missense_variant 0.21 ethambutol Uncertain significance
embB 4247708 p.Asn399Asp missense_variant 0.18 ethambutol Uncertain significance
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 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.49 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.24 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472314 n.469A>G non_coding_transcript_exon_variant 0.22 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472315 n.470T>C non_coding_transcript_exon_variant 0.21 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.34 linezolid
kanamycin
capreomycin
amikacin Uncertain significance
aminoglycosides
streptomycin
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.77 linezolid
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.77 linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.71 linezolid Uncertain significance
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.62 linezolid
rrl 1476032 n.2375C>T non_coding_transcript_exon_variant 0.62 linezolid
rrl 1476040 n.2383C>T non_coding_transcript_exon_variant 0.79 linezolid
rrl 1476046 n.2389G>A non_coding_transcript_exon_variant 0.78 linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.78 linezolid
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.76 linezolid
rrl 1476088 n.2431A>T non_coding_transcript_exon_variant 0.58 linezolid
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.76 linezolid
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.76 linezolid
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.74 linezolid
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.73 linezolid
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.73 linezolid
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.74 linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.74 linezolid
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.74 linezolid
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.79 linezolid
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.78 linezolid
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.78 linezolid
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.8 linezolid
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.8 linezolid Uncertain significance
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.79 linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.82 linezolid
rrl 1476608 n.2951C>T non_coding_transcript_exon_variant 0.83 linezolid
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.8 linezolid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
embB 4247386 c.873T>C synonymous_variant 0.11 ethambutol
embB 4247389 c.876C>G synonymous_variant 0.11 ethambutol
embB 4247392 p.Ile293Met missense_variant 0.1 ethambutol
embB 4247398 c.885G>C synonymous_variant 0.11 ethambutol
embB 4247401 c.888T>C synonymous_variant 0.11 ethambutol
embB 4247404 c.891G>C synonymous_variant 0.1 ethambutol
embB 4247407 c.894G>C synonymous_variant 0.11 ethambutol
embB 4247434 c.921C>G synonymous_variant 0.14 ethambutol
embB 4247437 c.924A>C synonymous_variant 0.15 ethambutol
embB 4247491 c.978G>T synonymous_variant 0.1 ethambutol
embB 4247494 c.981G>A synonymous_variant 0.1 ethambutol
embB 4247497 c.984T>C synonymous_variant 0.14 ethambutol
embB 4247500 c.987C>G synonymous_variant 0.14 ethambutol
embB 4247539 c.1026T>C synonymous_variant 0.17 ethambutol
embB 4247545 c.1032C>T synonymous_variant 0.12 ethambutol
embB 4247554 c.1041T>C synonymous_variant 0.14 ethambutol
embB 4247555 p.Leu348Ile missense_variant 0.14 ethambutol
embB 4247566 c.1053C>G synonymous_variant 0.13 ethambutol
embB 4247567 c.1054C>T synonymous_variant 0.1 ethambutol
embB 4247572 c.1059A>G synonymous_variant 0.13 ethambutol
embB 4247587 c.1074G>A synonymous_variant 0.1 ethambutol
embB 4247588 c.1075_1077delCTAinsTTG synonymous_variant 0.1 ethambutol
embB 4247591 p.Val360Ile missense_variant 0.13 ethambutol
embB 4247596 c.1083C>T synonymous_variant 0.1 ethambutol
embB 4247611 c.1098G>C synonymous_variant 0.2 ethambutol
embB 4247620 c.1107G>A synonymous_variant 0.2 ethambutol
embB 4247629 c.1116C>A synonymous_variant 0.21 ethambutol
embB 4247635 c.1122G>C synonymous_variant 0.18 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.21 ethambutol Uncertain significance
embB 4247683 c.1170C>G synonymous_variant 0.21 ethambutol
embB 4247684 c.1171T>C synonymous_variant 0.21 ethambutol
embB 4247689 c.1176G>C synonymous_variant 0.22 ethambutol
embB 4247716 c.1203C>A synonymous_variant 0.18 ethambutol
embB 4247725 c.1212G>C synonymous_variant 0.23 ethambutol
embB 4247743 c.1230C>G synonymous_variant 0.19 ethambutol
embB 4247746 c.1233C>A synonymous_variant 0.23 ethambutol
embB 4247779 c.1266C>G synonymous_variant 0.19 ethambutol
embB 4247785 c.1272G>A synonymous_variant 0.14 ethambutol
embB 4247794 c.1281G>C synonymous_variant 0.12 ethambutol
embB 4247797 c.1284C>G synonymous_variant 0.16 ethambutol
embB 4247800 c.1287A>G synonymous_variant 0.15 ethambutol
embB 4247815 c.1302C>G synonymous_variant 0.1 ethambutol
embB 4247816 p.Val435Ile missense_variant 0.14 ethambutol
embB 4247819 p.Val436Ile missense_variant 0.14 ethambutol
embB 4247827 c.1314C>G synonymous_variant 0.16 ethambutol
embB 4247830 c.1317A>G synonymous_variant 0.11 ethambutol
embB 4247836 c.1323A>C synonymous_variant 0.16 ethambutol
embB 4247839 c.1326G>C synonymous_variant 0.12 ethambutol
embB 4247848 c.1335G>A synonymous_variant 0.19 ethambutol
embB 4247851 c.1338C>G synonymous_variant 0.2 ethambutol
embB 4247854 c.1341C>G synonymous_variant 0.16 ethambutol
embB 4247881 c.1368G>C synonymous_variant 0.15 ethambutol
embB 4247887 c.1374C>T synonymous_variant 0.14 ethambutol
embB 4247899 p.Met462Ile missense_variant 0.16 ethambutol
embB 4247908 c.1395C>T synonymous_variant 0.14 ethambutol
embB 4247909 c.1396T>C synonymous_variant 0.14 ethambutol
embB 4247913 c.1401_1402insAAG conservative_inframe_insertion 0.11 ethambutol
embB 4247926 c.1413C>G synonymous_variant 0.12 ethambutol
embB 4247939 c.1426T>C synonymous_variant 0.12 ethambutol
embB 4247944 c.1431G>C synonymous_variant 0.12 ethambutol
embB 4247945 c.1432T>C synonymous_variant 0.15 ethambutol
embB 4247948 p.Val479Leu missense_variant 0.15 ethambutol
embB 4247983 c.1470G>C synonymous_variant 0.14 ethambutol
embB 4247995 c.1482C>T synonymous_variant 0.12 ethambutol
embB 4248013 c.1500A>G synonymous_variant 0.11 ethambutol
embB 4248037 c.1524T>C synonymous_variant 0.1 ethambutol
embB 4248041 p.Ala510Ser missense_variant 0.11 ethambutol
embB 4248046 c.1533A>G synonymous_variant 0.11 ethambutol
embB 4248055 c.1542G>C synonymous_variant 0.12 ethambutol
embB 4248058 c.1545C>T synonymous_variant 0.11 ethambutol
embB 4248064 c.1551G>C synonymous_variant 0.12 ethambutol
ethA 4326676 p.Ser266Arg missense_variant 0.58 ethionamide Uncertain significance
ethA 4326914 p.Ala187Val missense_variant 1.0 ethionamide Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Uncertain significance