TB-Profiler result

Run: SRR22536492
Summary

Run ID: SRR22536492

Sample name:

Date: 04-04-2023 04:19:45

Number of reads: 2090616

Percentage reads mapped: 99.85

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 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289096 p.Asp49Ala missense_variant 1.0 pyrazinamide
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 7567 p.Asp89Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471658 n.-188T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475405 n.1748A>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156100 c.12A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714388 c.945C>T synonymous_variant 1.0
Rv2752c 3065645 p.Thr183Ala missense_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3878630 c.-123G>C upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408055 c.148C>T synonymous_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0
gid 4407862 c.147_340del frameshift_variant 1.0