TB-Profiler result

Run: ERR405190
Summary

Run ID: ERR405190

Sample name:

Date: 2024-10-04T23:06:13.575907

Number of reads: 16620

Percentage reads mapped: 0.31

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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 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
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
rpoB 762872 p.Met1022Ile missense_variant 1.0 rifampicin Uncertain significance
rpoB 762878 p.Ile1024Met missense_variant 1.0 rifampicin
rpoB 762879 p.Met1025Leu missense_variant 1.0 rifampicin Uncertain significance
rpoB 762899 c.3093G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 1.0 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 1.0 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 1.0 rifampicin Uncertain significance
rpoC 762980 c.-390T>C upstream_gene_variant 1.0 rifampicin
rpoC 762983 c.-387C>T upstream_gene_variant 1.0 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 1.0 rifampicin
rrs 1471917 n.72G>A non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471918 n.74_78delAAGGT non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471934 n.89A>T non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471935 n.92_96delCTCGA non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471948 n.103A>G non_coding_transcript_exon_variant 0.93 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.94 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 1472181 n.336G>A non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 1.0 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 1.0 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.79 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Not assoc w R
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 1472781 n.936C>T non_coding_transcript_exon_variant 0.99 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 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.71 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.95 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.91 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
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 1473192 n.1347A>G non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473193 n.1348G>T non_coding_transcript_exon_variant 0.64 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473204 n.1359C>A non_coding_transcript_exon_variant 0.64 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474838 n.1181C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474875 n.1218G>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474876 n.1219T>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474893 n.1236G>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474899 n.1242T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474910 n.1253C>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475499 n.1842C>G 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>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475553 n.1896G>C non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475571 n.1914A>T non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475575 n.1918C>A non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1475577 n.1920C>G non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476266 n.2609G>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476279 n.2622G>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 1.0 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 1476336 n.2679C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476339 n.2682G>A non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476356 n.2699C>T non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.99 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.95 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.79 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.79 capreomycin
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.95 capreomycin Uncertain significance
linezolid