TB-Profiler result

Run: SRR1173705
Summary

Run ID: SRR1173705

Sample name:

Date: 2024-10-03T18:34:47.035263

Number of reads: 50419

Percentage reads mapped: 1.41

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 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 rrs n.888G>A 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 1472733 n.888G>A non_coding_transcript_exon_variant 0.21 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
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.7 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.73 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.87 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.85 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.95 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.85 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472553 n.708C>T non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
capreomycin
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472574 n.729T>C non_coding_transcript_exon_variant 0.67 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472584 n.739A>G non_coding_transcript_exon_variant 0.67 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 0.68 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.57 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.5 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.48 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.48 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.52 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.99 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.78 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.95 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.97 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.98 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.99 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.98 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.75 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.75 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.99 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.98 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.96 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid