TB-Profiler result

Run: SRR3082099
Summary

Run ID: SRR3082099

Sample name:

Date: 04-04-2023 04:53:36

Number of reads: 2709391

Percentage reads mapped: 99.6

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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289090 p.His51Pro missense_variant 1.0 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247429 p.Met306Leu 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
gyrB 6534 p.Ala432Asp missense_variant 0.87
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 759940 p.Pro45Arg missense_variant 1.0
rpoB 760823 c.1017G>T synonymous_variant 0.1
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155418 p.Pro232Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726146 c.-47_-46insT upstream_gene_variant 1.0
thyA 3073690 p.Val261Gly missense_variant 1.0
ald 3087095 c.276C>T synonymous_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326822 p.Arg218Gly missense_variant 0.1
ethA 4327413 p.Trp21Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C upstream_gene_variant 1.0
gid 4407917 p.Arg96Cys missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0