TB-Profiler result

Run: SRR20139560

Summary

Run ID: SRR20139560

Sample name:

Date: 03-04-2023 21:50:07

Number of reads: 2915952

Percentage reads mapped: 99.7

Strain: lineage4.8

Drug-resistance: MDR-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
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
rpsL 781821 p.Lys88Gln missense_variant 0.77 streptomycin
katG 2154611 c.1500delG frameshift_variant 1.0 isoniazid
pncA 2288836 p.Asp136Asn missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
ethA 4326585 c.888delG frameshift_variant 0.14 ethionamide
ethA 4326731 c.742dupG frameshift_variant 0.14 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
gyrA 7362 p.Glu21Gln 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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1834606 c.1065C>T synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726121 c.-72C>T upstream_gene_variant 1.0
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326446 p.Gly343Glu missense_variant 0.11
ethA 4327418 p.Ala19Glu missense_variant 0.34
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408103 p.Gly34Arg missense_variant 0.13
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0