TB-Profiler result

Run: ERR551537
Summary

Run ID: ERR551537

Sample name:

Date: 20-10-2023 18:32:29

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.3.4.2;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 0.88
lineage4.1.2 Euro-American T;H None 0.87
lineage4.3.4 Euro-American (LAM) LAM RD174 0.1
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.91
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.07
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 0.91 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.81 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.86 isoniazid
pncA 2288839 p.Thr135Pro missense_variant 0.9 pyrazinamide
ahpC 2726136 c.-57C>T upstream_gene_variant 0.87 isoniazid
ethA 4326613 c.860delA frameshift_variant 0.87 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
gyrB 6140 p.Val301Leu missense_variant 0.12
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 491591 p.Lys270Met missense_variant 0.94
mshA 575679 p.Asn111Ser missense_variant 0.9
rpoB 760115 c.309C>T synonymous_variant 0.89
rpoC 764995 c.1626C>G synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 0.89
rpoC 766488 p.Pro1040Arg 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840719 c.702A>G synonymous_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 0.89