TB-Profiler result

Run: SRR25827789
Summary

Run ID: SRR25827789

Sample name:

Date: 16-03-2024 08:31:29

Number of reads: 22410499

Percentage reads mapped: 98.24

Strain: lineage4.1.2.1;lineage2.2.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.22)
Isoniazid R katG p.Ser315Thr (0.20)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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 0.09
lineage4 Euro-American LAM;T;S;X;H None 0.78
lineage4.1 Euro-American T;X;H None 0.76
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.12
lineage4.1.2 Euro-American T;H None 0.78
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.09
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.79
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 0.22 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.2 isoniazid
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 491591 p.Lys270Met missense_variant 0.72
fgd1 491742 c.960T>C synonymous_variant 0.23
mshA 575679 p.Asn111Ser missense_variant 0.8
rpoB 760115 c.309C>T synonymous_variant 0.74
rpoC 763031 c.-339T>C upstream_gene_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 0.77
rpoC 766466 p.Glu1033Lys missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.24
PPE35 2167926 p.Leu896Ser missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.75
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 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.77
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.19
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
embB 4246563 p.Leu17Trp missense_variant 0.2
embB 4246567 c.54G>T synonymous_variant 0.16
embB 4247028 p.Leu172Arg missense_variant 0.19
embB 4247039 p.Phe176Val missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.2
gid 4408368 c.-166A>G upstream_gene_variant 0.77