TB-Profiler result

Run: ERR2184246
Summary

Run ID: ERR2184246

Sample name:

Date: 31-03-2023 15:59:39

Number of reads: 2436819

Percentage reads mapped: 99.64

Strain: lineage4.3.3;lineage4.1.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.63
lineage4.1 Euro-American T;X;H None 0.35
lineage4.1.2 Euro-American T;H None 0.34
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.63
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.41
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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.59 isoniazid, ethionamide
pncA 2289090 p.His51Arg missense_variant 0.66 pyrazinamide
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 8040 p.Gly247Ser missense_variant 0.65
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.35
mshA 575679 p.Asn111Ser missense_variant 0.46
rpoB 760115 c.309C>T synonymous_variant 0.38
rpoC 764995 c.1626C>G synonymous_variant 0.57
rpoC 765150 p.Gly594Glu missense_variant 0.36
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775854 p.Gly876Asp missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834683 p.Ala381Val missense_variant 0.62
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.31
kasA 2518919 p.Gly269Ser missense_variant 0.6
thyA 3073868 p.Thr202Ala missense_variant 0.7
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.67
embC 4242182 p.Ala774Ser missense_variant 0.73
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.4
ethA 4328212 c.-740delC upstream_gene_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407591 c.612C>T synonymous_variant 0.46
gid 4408006 p.Val66Ala missense_variant 0.38
gid 4408156 p.Leu16Arg missense_variant 0.68