TB-Profiler result

Run: SRR1048869
Summary

Run ID: SRR1048869

Sample name:

Date: 2024-04-15T12:17:27.783779

Number of reads: 400108

Percentage reads mapped: 11.19

Median coverage: 8.0

Strain: lineage2.2.1;lineage2.2.2

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 0.45
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.08
lineage2.2 East-Asian (Beijing) RD105;RD207 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 katG c.421_423delTTGinsCC Assoc w R High-level resistance
p.Ser140Asn Uncertain significance Mutation from literature
p.Gln127Pro Uncertain significance Mutation from literature
ethambutol embB p.Met306Leu Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1004_1014delCTGACATCATC Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.69 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
katG 2155689 c.421_423delTTGinsCC frameshift_variant&missense_variant 0.62 isoniazid Assoc w R High-level resistance
katG 2155693 p.Ser140Asn missense_variant 0.67 isoniazid Uncertain significance Mutation from literature
katG 2155732 p.Gln127Pro missense_variant 0.41 isoniazid Uncertain significance Mutation from literature
pncA 2289252 c.-11A>G upstream_gene_variant 0.8 pyrazinamide Assoc w R
embB 4247429 p.Met306Leu missense_variant 0.58 ethambutol Assoc w R
ethA 4326459 c.1004_1014delCTGACATCATC frameshift_variant 0.64 ethionamide Assoc w R
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 762893 c.-477C>T upstream_gene_variant 0.6 rifampicin
rpoC 762896 c.-474G>C upstream_gene_variant 0.67 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.76 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.76 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.73 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.73 rifampicin
rpoB 762929 c.3123G>T synonymous_variant 0.7 rifampicin Not assoc w R - Interim
rpoB 762939 c.3133_3135delATGinsCC frameshift_variant&missense_variant 0.67 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.67 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.64 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.68 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.56 rifampicin
rpoC 764338 p.Glu323Asp missense_variant 0.47 rifampicin
rpoC 764344 c.975C>T synonymous_variant 0.53 rifampicin
rpoC 764348 p.Met327Leu missense_variant 0.53 rifampicin
rpoC 764355 p.Gln329Pro missense_variant 0.6 rifampicin
rpoC 764377 c.1008C>G synonymous_variant 0.59 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.57 rifampicin
rpoC 764387 c.1018_1020delTTGinsCC frameshift_variant&missense_variant 0.59 rifampicin
rpoC 764398 c.1029G>C synonymous_variant 0.59 rifampicin
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.57 rifampicin
rpoC 764410 c.1041G>T synonymous_variant 0.54 rifampicin
rpoC 764428 c.1059G>T synonymous_variant 0.38 rifampicin
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.63 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.72 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.69 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.56 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.61 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.53 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.53 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.56 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.7 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.7 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
katG 2155600 p.Cys171Val missense_variant 0.67 isoniazid
katG 2155613 p.Phe167Leu missense_variant 0.64 isoniazid
katG 2155614 c.498T>C synonymous_variant 0.6 isoniazid
katG 2155617 p.Ile165Met missense_variant 0.6 isoniazid
katG 2155626 c.486G>C synonymous_variant 0.65 isoniazid
katG 2155637 p.Leu159Ile missense_variant 0.58 isoniazid
katG 2155641 p.Lys157Arg missense_variant 0.61 isoniazid
katG 2155650 c.462G>A synonymous_variant 0.61 isoniazid Not assoc w R - Interim
katG 2155655 p.Lys153Gln missense_variant 0.61 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 0.61 isoniazid
katG 2155668 c.444G>C synonymous_variant 0.61 isoniazid
katG 2155704 c.408C>T synonymous_variant 0.67 isoniazid
katG 2155716 c.396T>C synonymous_variant 0.62 isoniazid
katG 2155722 c.390G>C synonymous_variant 0.5 isoniazid
katG 2155728 c.384G>C synonymous_variant 0.41 isoniazid
katG 2155735 p.Met126Gln missense_variant 0.41 isoniazid
katG 2155737 c.375C>T synonymous_variant 0.44 isoniazid
katG 2155741 p.Gly124Ala missense_variant 0.47 isoniazid Uncertain significance
katG 2155743 c.369G>T synonymous_variant 0.44 isoniazid
katG 2155765 p.His116Thr missense_variant 0.44 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.8 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877960 p.Val183Gly missense_variant 0.7 rifampicin Uncertain significance