TB-Profiler result

Run: ERR230003
Summary

Run ID: ERR230003

Sample name:

Date: 31-03-2023 17:55:07

Number of reads: 3820402

Percentage reads mapped: 99.75

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 0.98
lineage4.1.2 Euro-American T;H None 0.97
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.98
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 761140 p.His445Leu missense_variant 0.98 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 0.98 ethambutol
ethA 4326292 c.1181delA frameshift_variant 1.0 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 490617 c.-166T>G upstream_gene_variant 0.97
fgd1 491591 p.Lys270Met missense_variant 0.98
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 0.97
rpoC 763513 c.144C>T synonymous_variant 0.96
rpoC 765150 p.Gly594Glu missense_variant 0.97
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.99
thyA 3073806 c.666C>G synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449025 c.522T>C synonymous_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613286 c.-170C>G upstream_gene_variant 0.99
embC 4242425 p.Arg855Gly missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.97
aftB 4268256 p.Gly194Ala missense_variant 0.96
ethR 4327941 p.Ser131Arg missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407967 p.Leu79Trp missense_variant 0.99