TB-Profiler result

Run: SRR13870400
Summary

Run ID: SRR13870400

Sample name:

Date: 03-04-2023 09:40:33

Number of reads: 1126046

Percentage reads mapped: 99.82

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 7582 p.Asp94Gly missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289072 p.His57Leu missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>G 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 9304 p.Gly668Asp missense_variant 1.0
mshA 576556 c.1209T>C synonymous_variant 0.12
mshA 576751 p.Lys468Asn missense_variant 0.14
rpoC 764934 p.Ile522Thr missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155017 c.1095G>A synonymous_variant 1.0
PPE35 2170076 c.536delC frameshift_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726350 p.Trp53Leu missense_variant 0.12
folC 2747453 p.Arg49Gln missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074645 c.-174T>G upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448591 c.90_91dupGA frameshift_variant 0.66
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326693 p.Arg261Trp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>C upstream_gene_variant 1.0
gid 4408054 p.Leu50Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0