TB-Profiler result

Run: SRR25206941

Summary

Run ID: SRR25206941

Sample name:

Date: 28-01-2024 02:15:58

Number of reads: 9961683

Percentage reads mapped: 99.66

Strain: lineage4.5

Drug-resistance: RR-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 (1.00)
Isoniazid
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Val180Phe (1.00)
Streptomycin R gid c.102delG (1.00)
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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.5 Euro-American H;T RD122 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 1.0 rifampicin
pncA 2288704 p.Val180Phe missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoB 761568 p.Ile588Val missense_variant 1.0
rpoC 764924 p.Gly519Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 1.0
rrl 1475998 n.2341C>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726141 c.-52C>A upstream_gene_variant 0.47
ribD 2986827 c.-12_-11delGCinsAA upstream_gene_variant 1.0
Rv2752c 3065179 p.Ser338Trp missense_variant 0.36
Rv2752c 3065188 p.Val335Gly missense_variant 0.52
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612447 p.Gly224Ser missense_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 0.99
clpC1 4038318 p.Pro796Leu missense_variant 0.99
embC 4241741 p.Val627Ile missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243198 c.-34delC upstream_gene_variant 0.41
embA 4245972 p.Ile914Val missense_variant 1.0
ethA 4326509 p.Ala322Val missense_variant 1.0
whiB6 4338440 c.81dupT frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0