TB-Profiler result

Run: SRR1013597
Summary

Run ID: SRR1013597

Sample name:

Date: 2024-10-04T23:26:26.260734

Number of reads: 269594

Percentage reads mapped: 6.15

Median coverage: 6.0

Strain: lineage2.2.2;lineage4

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.22
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.21
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
lineage4 Euro-American None 0.75
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
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
rpoC 762896 c.-474G>C upstream_gene_variant 0.9 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.86 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.86 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.86 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.86 rifampicin
rpoB 762929 c.3123G>T synonymous_variant 0.86 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.8 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.75 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.63 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.61 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764338 p.Glu323Asp missense_variant 0.57 rifampicin
rpoC 764344 c.975C>T synonymous_variant 0.6 rifampicin
rpoC 764348 p.Met327Leu missense_variant 0.6 rifampicin
rpoC 764355 p.Gln329Pro missense_variant 0.64 rifampicin
rpoC 764377 c.1008C>G synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.56 rifampicin
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 764398 c.1029G>C synonymous_variant 0.64 rifampicin
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 764410 c.1041G>T synonymous_variant 0.56 rifampicin
rpoC 764428 c.1059G>T synonymous_variant 0.46 rifampicin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.56 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 0.61 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.68 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.77 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.76 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.75 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.71 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.71 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.65 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.65 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.78 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 0.78 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 0.78 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.88 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 0.78 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.65 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.55 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.6 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.62 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 0.65 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 0.65 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.65 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1475894 n.2237C>A non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.63 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.75 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 0.67 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R