TB-Profiler result

Run: ERR459445
Summary

Run ID: ERR459445

Sample name:

Date: 01-04-2023 06:28:07

Number of reads: 1781713

Percentage reads mapped: 99.59

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gyrB 6579 p.Ser447Phe missense_variant 0.39 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrB 6738 p.Thr500Asn missense_variant 0.87 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2156093 c.18dupA frameshift_variant 1.0 isoniazid
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 576057 c.712dupG frameshift_variant 0.71
mshA 576372 p.Ala342Glu missense_variant 0.31
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
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.4
rrs 1473243 n.1398G>A non_coding_transcript_exon_variant 0.4
rrs 1473382 n.1537T>C splice_region_variant&non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170530 p.Ala28Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726568 p.Asn126Asp missense_variant 1.0
thyA 3074422 p.Pro17Leu missense_variant 1.0
embC 4239809 c.-54C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0