TB-Profiler result

Run: SRR1049656
Summary

Run ID: SRR1049656

Sample name:

Date: 02-04-2023 18:13:54

Number of reads: 4469661

Percentage reads mapped: 99.16

Strain: lineage4

Drug-resistance: RR-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
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
rpoB 761155 p.Ser450Leu missense_variant 0.57 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.35 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.61 streptomycin
eis 2715342 c.-10G>A upstream_gene_variant 0.55 kanamycin
ethA 4326718 c.754_755dupGC frameshift_variant 0.6 ethionamide, ethionamide
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
gyrB 6432 p.Ala398Val missense_variant 0.6
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 764916 p.Leu516Pro missense_variant 0.56
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778107 p.Ser125Cys missense_variant 0.42
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.97
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328378 c.-905G>C upstream_gene_variant 0.37
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0