TB-Profiler result

Run: ERR2653194
Summary

Run ID: ERR2653194

Sample name:

Date: 31-03-2023 22:38:59

Number of reads: 4094936

Percentage reads mapped: 97.6

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 0.99
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 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.98 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol
ethA 4326452 p.Ala341Val missense_variant 0.98 ethionamide
gid 4408087 c.115delC frameshift_variant 0.98 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.99
rpoB 760115 c.309C>T synonymous_variant 0.99
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
fbiC 1303717 p.Ile263Val missense_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170035 p.Val193Ala missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.26
PPE35 2170053 p.Thr187Ser missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T 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
rpoA 3877939 p.Asp190Ala missense_variant 0.99
embC 4241103 p.Glu414Gly missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407751 p.Pro151Leu missense_variant 0.98