TB-Profiler result

Run: SRR25827705
Summary

Run ID: SRR25827705

Sample name:

Date: 02-02-2024 15:41:44

Number of reads: 8509302

Percentage reads mapped: 99.09

Strain: lineage4.3.3;lineage2.2.1.1

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 (0.91)
Isoniazid R katG p.Ser315Thr (0.99)
Ethambutol R embB p.Met306Val (0.76)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.79)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA p.Tyr84Asp (0.16)
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 0.83
lineage4 Euro-American LAM;T;S;X;H None 0.13
lineage4.3 Euro-American (LAM) mainly-LAM None 0.08
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.83
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.82
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.12
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.09
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 0.91 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.79 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
embB 4247429 p.Met306Val missense_variant 0.76 ethambutol
ethA 4327224 p.Tyr84Asp missense_variant 0.16 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 7581 p.Asp94Cys missense_variant 0.58
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.82
mshA 575907 p.Ala187Val missense_variant 0.75
ccsA 620553 c.663T>C synonymous_variant 0.55
ccsA 620625 p.Ile245Met missense_variant 0.77
rpoC 763031 c.-339T>C upstream_gene_variant 0.84
rpoC 764817 p.Val483Ala missense_variant 0.63
rpoC 764995 c.1626C>G synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 776182 p.Asp767Asn missense_variant 0.77
mmpS5 779615 c.-710C>G upstream_gene_variant 0.79
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.79
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rpsA 1834177 c.636A>C synonymous_variant 0.8
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.84
PPE35 2167926 p.Leu896Ser missense_variant 0.89
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
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 0.8
alr 3841518 c.-98C>A upstream_gene_variant 0.55
alr 3841519 c.-99T>A upstream_gene_variant 0.55
embC 4240413 p.Leu184Arg missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.79
embB 4249757 p.Thr1082Ala missense_variant 0.55
aftB 4267647 p.Asp397Gly missense_variant 0.8
ethA 4327472 c.2T>C start_lost 0.22
whiB6 4338233 p.Ser97Pro missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.85
gid 4407927 p.Glu92Asp missense_variant 0.82
gid 4408156 p.Leu16Arg missense_variant 0.12