TB-Profiler result

Run: SRR18665445
Summary

Run ID: SRR18665445

Sample name:

Date: 03-04-2023 19:57:58

Number of reads: 724775

Percentage reads mapped: 99.81

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 761161 p.Leu452Pro missense_variant 0.94 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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 7296 c.-6G>T upstream_gene_variant 0.43
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576482 p.Val379Leu missense_variant 0.25
rpoB 761105 c.1299C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781391 c.-169A>G upstream_gene_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
fabG1 1673380 c.-60C>G upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726589 p.Arg133Cys missense_variant 0.12
Rv2752c 3065512 p.Arg227Gln missense_variant 0.18
thyA 3073701 c.771C>T synonymous_variant 0.11
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3877835 p.Leu225Phe missense_variant 0.11
rpoA 3878637 c.-130G>C upstream_gene_variant 0.33
clpC1 4038602 c.2103G>T synonymous_variant 0.12
embC 4241873 c.2012delT frameshift_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.6
embB 4249418 p.Pro969Ser missense_variant 1.0
whiB6 4338550 c.-29A>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0