TB-Profiler result

Run: SRR15315955
Summary

Run ID: SRR15315955

Sample name:

Date: 03-04-2023 13:00:30

Number of reads: 9109317

Percentage reads mapped: 99.48

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 7521 p.Ala74Ser missense_variant 0.18 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7563 p.Gly88Cys missense_variant 0.82 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288757 p.Gly162Asp missense_variant 0.19 pyrazinamide
pncA 2289015 p.Thr76Ile missense_variant 0.7 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.69 ethambutol
embB 4249583 p.Asp1024Asn missense_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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoC 764363 p.Gly332Ser 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
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
eis 2715536 c.-204C>T upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embC 4240031 p.Ala57Thr missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethR 4327795 p.Ala83Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407614 p.Arg197Cys missense_variant 0.99
gid 4407712 p.Gly164Val missense_variant 0.24
gid 4408126 p.Leu26Ser missense_variant 0.77