TB-Profiler result

Run: SRR9028492
Summary

Run ID: SRR9028492

Sample name:

Date: 04-04-2023 22:04:42

Number of reads: 2461230

Percentage reads mapped: 99.74

Strain: lineage4.9

Drug-resistance: 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
lineage4.9 Euro-American (H37Rv-like) T1 None 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.Ser450Leu missense_variant 1.0 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.18 clofazimine, bedaquiline
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289081 p.Pro54Leu missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.98 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
mshA 576400 c.1053C>T synonymous_variant 1.0
mshA 576482 p.Val379Leu missense_variant 0.14
rpoB 761461 p.Arg552Leu 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
ald 3087013 p.Trp65* stop_gained 0.3
ald 3087367 p.Ala183Val missense_variant 1.0
ald 3087390 c.575_576dupCG frameshift_variant 0.26
fbiD 3339734 p.Ala206Gly missense_variant 0.22
rpoA 3877536 c.972C>T synonymous_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.43
ubiA 4269124 p.Ala237Val missense_variant 1.0
ethA 4326943 p.Asn177Lys missense_variant 1.0
whiB6 4338307 p.Ala72Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
ethR 4326936 c.-612_*250del transcript_ablation 1.0