TB-Profiler result

Run: ERR133823
Summary

Run ID: ERR133823

Sample name:

Date: 31-03-2023 13:36:35

Number of reads: 14243975

Percentage reads mapped: 99.44

Strain: lineage4.2.1

Drug-resistance: HR-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
lineage4.2 Euro-American H;T;LAM None 0.99
lineage4.2.1 Euro-American (TUR) H3;H4 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
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 0.99 kanamycin
embB 4249518 p.His1002Arg 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302753 c.-178A>T upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918430 p.Leu164Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.26
PPE35 2169866 c.747G>C synonymous_variant 0.26
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2222712 c.453C>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.23
embC 4242425 p.Arg855Gly missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326758 p.Arg239Leu missense_variant 1.0
ethA 4326879 p.Ala199Ser missense_variant 0.99
whiB6 4338540 c.-19T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0