TB-Profiler result

Run: SRR6824586
Summary

Run ID: SRR6824586

Sample name:

Date: 20-10-2023 19:31:26

Number of reads: 12104294

Percentage reads mapped: 99.23

Strain: lineage2.2.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.46), rpoB p.Leu452Pro (0.56)
Isoniazid R ahpC c.-57C>T (0.55)
Ethambutol R embB p.Gly406Ala (0.58)
Pyrazinamide R pncA p.Val155Met (0.32), pncA p.Val7Gly (0.21), pncA c.-11A>G (0.46)
Streptomycin R rpsL p.Lys43Arg (0.24), rpsL p.Lys88Met (0.33), rrs n.514A>C (0.43)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.1341delC (0.30), ethA c.1341delC (0.30)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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
rpoB 761155 p.Ser450Leu missense_variant 0.46 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.56 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.24 streptomycin
rpsL 781822 p.Lys88Met missense_variant 0.33 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.43 streptomycin
pncA 2288779 p.Val155Met missense_variant 0.32 pyrazinamide
pncA 2289222 p.Val7Gly missense_variant 0.21 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.46 pyrazinamide
ahpC 2726136 c.-57C>T upstream_gene_variant 0.55 isoniazid
embB 4247730 p.Gly406Ala missense_variant 0.58 ethambutol
ethA 4326132 c.1341delC frameshift_variant 0.3 ethionamide, ethionamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472864 n.1019C>T non_coding_transcript_exon_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154550 p.Leu521Pro missense_variant 0.56
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155418 p.Pro232Ser missense_variant 0.44
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3877960 p.Val183Gly missense_variant 0.42
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338280 p.Ile81Asn missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0