TB-Profiler result

Run: ERR4815677
Summary

Run ID: ERR4815677

Sample name:

Date: 20-10-2023 07:53:50

Number of reads: 5456653

Percentage reads mapped: 94.31

Strain: lineage4.8

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rrs n.888G>A (0.26)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.26 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
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.17
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.17
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.18
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.28
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.26
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.28
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.28
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.3
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.31
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.17
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.17
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.2
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103084 c.-43_-42insCGTAGTAGCTAAC upstream_gene_variant 0.81
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448322 c.-182G>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C upstream_gene_variant 0.99
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0