TB-Profiler result

Run: SRR13423561
Summary

Run ID: SRR13423561

Sample name:

Date: 03-04-2023 08:52:04

Number of reads: 2561406

Percentage reads mapped: 99.23

Strain: lineage4.2

Drug-resistance: MDR-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
lineage4.2 Euro-American H;T;LAM None 0.99
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 761095 p.Leu430Pro missense_variant 0.94 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761756 c.1950C>T synonymous_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
rrs 1473114 n.1269C>T non_coding_transcript_exon_variant 0.12
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.25
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.25
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.29
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.33
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.25
rrl 1474584 n.927C>A non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066276 c.-85G>A upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
Rv3236c 3612469 c.648A>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244803 p.Leu524Ser missense_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0