TB-Profiler result

Run: ERR4813049
Summary

Run ID: ERR4813049

Sample name:

Date: 01-04-2023 12:30:12

Number of reads: 5119515

Percentage reads mapped: 99.54

Strain: lineage4.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 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
tlyA 1918247 c.309delT frameshift_variant 0.12 capreomycin
katG 2155168 p.Ser315Asn missense_variant 0.99 isoniazid
ethA 4326718 c.754_755dupGC frameshift_variant 0.97 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8164 p.Ala288Val missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303991 p.Trp354Leu missense_variant 0.17
fbiC 1304254 p.Ala442Ser missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471797 n.-49G>A upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rpsA 1834333 c.792C>T synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642339 p.Asp269Asn missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249354 c.2841G>T synonymous_variant 1.0
ethA 4327599 c.-126G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407925 p.Pro93Gln missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0