TB-Profiler result

Run: SRR6824337
Summary

Run ID: SRR6824337

Sample name:

Date: 04-04-2023 16:29:15

Number of reads: 18464360

Percentage reads mapped: 99.06

Strain: lineage4.5

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Tyr missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.99 streptomycin
katG 2155597 p.Ala172Val missense_variant 1.0 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 0.99
rpoB 759636 c.-171C>T upstream_gene_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777810 p.Arg224Gln missense_variant 1.0
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
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289082 p.Pro54Ser missense_variant 1.0
eis 2715536 c.-204C>T upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612102 p.Ile339Val missense_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243156 c.-77T>G upstream_gene_variant 1.0
embB 4247595 p.Cys361Tyr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C upstream_gene_variant 0.99
gid 4407587 p.Arg206Gly missense_variant 1.0