TB-Profiler result

Run: ERR245790
Summary

Run ID: ERR245790

Sample name:

Date: 2024-04-16T12:10:30.013057

Number of reads: 463754

Percentage reads mapped: 3.16

Median coverage: 7.0

Strain: lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.32
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.4
lineage4.3.4 Euro-American (LAM) RD174 0.38
lineage4.3.4.2 Euro-American (LAM) RD174 0.99
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
gyrB 6140 p.Val301Leu missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.91 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.95 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.95 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.94 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.86 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.97 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.97 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.96 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.96 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.57 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472584 n.739A>G non_coding_transcript_exon_variant 0.44 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 0.86 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.86 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.83 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.85 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.85 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.84 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.98 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.66 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472912 n.1067C>T non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472917 n.1072G>A non_coding_transcript_exon_variant 0.91 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1165delC non_coding_transcript_exon_variant 0.52 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.81 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.79 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.77 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473054 n.1209C>G non_coding_transcript_exon_variant 0.79 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.77 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.77 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473081 n.1236C>G non_coding_transcript_exon_variant 0.6 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.94 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.95 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.95 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.96 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.95 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.96 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.95 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.91 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.91 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.91 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.91 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.95 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.96 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.96 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.95 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.96 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.96 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.86 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R