TB-Profiler result

Run: SRR1048987
Summary

Run ID: SRR1048987

Sample name:

Date: 2024-03-27T04:01:14.841010

Number of reads: 227031

Percentage reads mapped: 7.35

Median coverage: 5.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 0.44
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG c.421_423delTTGinsCC Assoc w R High-level resistance
p.Ser140Asn Uncertain significance Mutation from literature
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
katG 2155689 c.421_423delTTGinsCC frameshift_variant&missense_variant 0.8 isoniazid Assoc w R High-level resistance
katG 2155693 p.Ser140Asn missense_variant 0.76 isoniazid 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
rpoB 762917 c.3111C>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.5 rifampicin
rpoB 762929 c.3123G>T synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 762939 c.3133_3135delATGinsCC frameshift_variant&missense_variant 0.5 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.5 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.5 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.48 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.39 rifampicin
rpoB 762995 c.3189G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764338 p.Glu323Asp missense_variant 0.55 rifampicin
rpoC 764344 c.975C>T synonymous_variant 0.58 rifampicin
rpoC 764348 p.Met327Leu missense_variant 0.58 rifampicin
rpoC 764355 p.Gln329Pro missense_variant 0.54 rifampicin
rpoC 764377 c.1008C>G synonymous_variant 0.64 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.64 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.64 rifampicin
rpoC 764387 c.1018_1020delTTGinsCC frameshift_variant&missense_variant 0.64 rifampicin
rpoC 764398 c.1029G>C synonymous_variant 0.64 rifampicin
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.64 rifampicin
rpoC 764410 c.1041G>T synonymous_variant 0.58 rifampicin
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.7 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.79 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 0.72 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.71 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.65 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
katG 2155655 p.Lys153Gln missense_variant 0.69 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 0.71 isoniazid
katG 2155668 c.444G>C synonymous_variant 0.73 isoniazid
katG 2155704 c.408C>T synonymous_variant 0.75 isoniazid
katG 2155716 c.396T>C synonymous_variant 0.8 isoniazid
katG 2155722 c.390G>C synonymous_variant 0.78 isoniazid
katG 2155728 c.384G>C synonymous_variant 0.76 isoniazid
katG 2155735 p.Met126Gln missense_variant 0.68 isoniazid
katG 2155737 c.375C>T synonymous_variant 0.68 isoniazid
katG 2155741 p.Gly124Ala missense_variant 0.68 isoniazid Uncertain significance
katG 2155743 c.369G>T synonymous_variant 0.68 isoniazid
katG 2155765 p.His116Thr missense_variant 0.73 isoniazid