TB-Profiler result

Run: SRR7504773
Summary

Run ID: SRR7504773

Sample name:

Date: 2024-10-03T19:00:13.645386

Number of reads: 101264843

Percentage reads mapped: 92.43

Median coverage: 338.0

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
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.42 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.65 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.67 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.69 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.89 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 0.9 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.87 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 0.86 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 0.74 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.61 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472953 n.1108_1109insA non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.62 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.61 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.58 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473080 n.1235C>A non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473084 n.1239T>A non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473094 n.1249T>A non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.58 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.63 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.61 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 0.69 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 0.78 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473336 n.1491T>A non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474236 n.579G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475672 n.2015C>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475688 n.2031G>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.43 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.88 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>A non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.87 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.81 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.41 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.18 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476601 n.2944G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
whiB7 3569039 c.-360T>C upstream_gene_variant 0.26 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
embA 4244481 p.Leu417Phe missense_variant 0.13 ethambutol