TB-Profiler result

Run: SRR1140675
Summary

Run ID: SRR1140675

Sample name:

Date: 02-04-2023 20:57:33

Number of reads: 2900124

Percentage reads mapped: 99.61

Strain: lineage4.8

Drug-resistance: RR-TB

Download CSV Download TXT Download PDF Download JSON
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 761155 p.Ser450Leu missense_variant 0.7 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.29 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.69 streptomycin
eis 2715342 c.-10G>A upstream_gene_variant 0.75 kanamycin
ethA 4326718 c.754_755dupGC frameshift_variant 0.54 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 0.54
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778107 p.Ser125Cys missense_variant 0.46
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 0.96
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
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328378 c.-905G>C upstream_gene_variant 0.38
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0